Murray Wiki - User contributions [en]

Yosemite Trip - 2015

2014-11-03T18:13:24Z

Edelossa: /* Currently booked housing */

__NOTOC__
(partially plagiarized from Yosemite Trip 2007) 
We are organizing a winter Murray Group trip to Yosemite this year. This will be a fun and casual trip for all group members, there will be no special skills or special gear required.

Snowshoes, skis (downhill and cross country), and snowboards are available for rent at Yosemite for those in the group desiring to take part in such activities.

= Details =

=== Trip Date ===
We've selected the trip date based on people's availability and Richard's schedule:
* 13-15 March, 2015

If you are interested in joining the group trip, email Zachary Sun. We will have housing openings up to two weeks' before departure.

=== Trip Itinerary ===
* Friday - Meet your carpool from early morning to early afternoon and drive to Yosemite. Check into cabins.
* Saturday - Hang out at Yosemite. There are a couple of possible day activities depending on the snow state, including hiking, cross-country skiing, downhill skiing at Badger Pass, "research" if you're so inclined, or just hanging around camp :) Equipment can be rented at Yosemite.
* Sunday - Open activities (including day hikes or sleeping in) in the morning, return to Pasadena in the afternoon/evening.

=== Information about Yosemite ===
* [http://www.yosemitepark.com/Accommodations_CurryVillage.aspx Lodging in Curry Village]
* [http://www.nps.gov/yose/ Yosemite National Park]
* [http://www.yosemitepark.com/BadgerPass_RentalPricing.aspx Gear Rental]

= Participants =
* Richard Murray, +1 - ___ departure
* Zachary Sun - ___ departure (can drive, room for 4)
* Ioannis Fillippidis
* Marcella Gomez, +1
* Samira Farahani
* Enoch Yeung, +1.5
* Yong Wu
* Vipul Singhal
* Sean Sanchez + 1
* Clare Hayes
* Yutaka Hori
* Emzo de los Santos
* Shaobin Guo

= Housing =

1) The majority of people will probably choose to live in Camp Curry. These are either tents or cabins.

*Unheated tent. If you dare to brave the cold! It will cost the night's low temperature (average 30's)./night + 11% tax. Can sleep 4 comfortably (1 double bed, 3 single beds). *These have cots and sheets, this is not camping but rather low-cost glamping*
*Heated tent. Will cost the night's low + $20. (max $60/night + 11% tax). Can sleep 3 comfortably (1 double bed, 2 single beds). *These have cots and sheets, this is not camping but rather low-cost glamping*
*Cabin w/o private bathroom. $153/night + 11% tax. 2 double beds.
*Cabin w/ private bathroom. $204/night + 11% tax. 2 double beds.

<gallery>
nonheatedtent.jpg | Non-heated canvas tent. Live here at your own risk of freezing!
heatedtent.jpg | Heated canvas tent.
cabin.jpg | Curry Village cabins, heated.
</gallery>
(Images c.www.yosemitepark.com)

2) There is also housing at Yosemite Lodge and the Ahwahnee. These are pricier options though starting at $200/night, and you'll be a drive or shuttle away from Camp. See http://www.yosemitepark.com/the-ahwahnee.aspx or http://www.yosemitepark.com/yosemite-lodge.aspx.

= Currently booked housing =
*Curry Village Heated Tent: 3 beds, Held by Zachary Sun for last minute stays and modifications, Conf 399SB123372
*Curry Village Heated Tent: 3 beds, Held by Zachary Sun for last minute stays and modifications, Conf 399SB123374
*Curry Village Heated Tent: 3 beds, Held by Zachary Sun for last minute stays and modifications, Conf 399SB123375
*Curry Village Heated Tent: 3 beds, Zachary Sun / Shaobin Guo / Yutaka Hori, Conf 399SB123409
*Curry Village Heated Tent: 3 beds, Conf #: 399SB123664

= Meals =
This is old, will update with new information:
<pre>
John will coordinate the group breakfasts, lunches, and snacks to help save on the trip cost. We will plan to bring two breakfasts and two lunchs. For dinners there is a local cafe where we can apparently get pizza and other food items. The following items are suggested for breakfast, lunch, and snacks. Please let John know if you want anything added to this list

*Breakfasts: bagels, cream cheese, butter, orange juice, oatmeal (variety of flavors)
*Lunches: sandwiches (wheat bread, pita, salami/cold cuts, cheese, lettuce, tomatos, mustard, peanut butter, jelly), lemonade, apples, bananas, carrots (peeled)
*Snacks: Granola bars, trail mix, apples, bananas, cookies, lemonade, dark chocolate! (and some milk chocolate too...), oh and Skittles for Richard.

There is supposed to be an eating area at Curry Village with a toaster and microwave, so we will hopefully be able to warm the bagels...
</pre>

= Packing List =

'''Head and Hands'''
* Winter hat
* Gloves or mittens
* Scarf (optional)

'''Upper Body Layers'''
* 2 t-shirts
* Mid-weight long sleeve shirt (long underwear is best, cotton is okay)
* Sweater or sweatshirt
* Fleece jacket or wool sweater
* Winter coat and/or a rain coat or shell if it fits over the fleece jacket

'''Lower Body'''
* Underwear as needed
* Jeans are okay for skiing if you're not planning to fall down a lot, fine for wearing at night
* If you're not an expert skiier I'd recommend snow pants or fleece pants/jeans with synthetic athletic-style pants over them
* Synthetic long underwear bottoms (if you have them)

'''Feet'''
* 1 pair hiking boots or sturdy sneakers (if you want to snowshoe you should bring boots)
* Socks

'''Travel Gear'''
* Small backpack for day hiking/skiing

'''Sleeping'''
* The tents come with cots, but to supplment you can either bring blankets or a sleeping bag. (This is not necessarily necessary in the heated tents and cabins, but very much so in the unheated tents)! You can rent both from the [http://www.caltechy.org/services/rentals/outrent/ Caltech Y] for a small fee.

'''Micellaneous'''
* 2 quart-sized water bottles
* 1 small flashlight or headlamp
* 1 toilet kit: toothbrush, toothpaste, shampoo, soap
* Towel for showering (though they should have 1 in case you forget)
* Sunscreen, lip balm, tissues
* Sunglasses
* Any medications you need
* Camera (optional)
* Board games to play at night (Pictionary, Cranium, etc.)
* BYOB
* Money for ski rentals, dinner, food on the drive up

= Pictures =
These pictures are from the 2003 Murray Group winter trip to Yosemite.
[[Image:Yosemite03-1.jpg|frame|none|Richard, Lars, and Domitilla]]
[[Image:Yosemite03-2.jpg|frame|none|Half Dome]]

Tom Ellis, September 2013

2013-09-09T23:10:03Z

Edelossa: /* Schedule: 12 Sep (Thu) */

Tom Ellis from Imperial College will be visiting on 12 Sep (Thu). If you would like to meet with him, please sign up for a slot below.

=== Schedule: 12 Sep (Thu) ===

{{agenda begin}}
{{agenda item|10:00 am|Richard and Dan S-G, 109 Steele Lab}}
{{agenda item|11:00 am|Continued discussion with Dan S-G [and others?]}}
{{agenda item|11:45 am|Grab lunch (Chandler or Annenberg)}}
{{agenda item|12:15 pm|Lunch seminar: 243 Annenberg}}
{{agenda item|1:15 pm|Zach Sun (meet in 243 ANB)}}
{{agenda item|2:00 pm|John Doyle, 210 ANB}}
{{agenda item|2:45 pm|Open}}
{{agenda item|3:30 pm|Emzo}}
{{agenda item|4:15 pm|Joe M (Steele 110?)}}
{{agenda item|5:00 pm|Wrap up meeting with Richard}}
{{agenda item|5:30 pm|Done for the day}}
{{agenda end}}

=== Seminar ===

<center>
Characterising, modelling and rewiring the effect synthetic genetic circuits have on the capacity of their host chassis
 
Tom Ellis, Imperial College, London 
12 Sep (Thu), 12-1:15, 243 ANB
</center>

Characterisation and understanding of genetic components is a key part of both synthetic biology and systems biology. Quantitative knowledge of how DNA parts encode function allows parts to be predictably constructed into synthetic gene circuits. Less understood is how the expression of a synthetic gene circuit can have a detrimental effect on its host cell (the chassis) and how these effects can feedback to the behaviour of the circuit. We investigate how synthetic circuits use cellular resources (e.g. DNA polymerase, RNA polymerase, ribosomes, tRNA, etc.) to replicate and express and we quantify these effects and model gene expression in a way that accounts for this. This is done by considering this shared 'resource pool' as an interface between the host cell and the synthetic circuit. Through genetic engineering and synthetic biology, we have created a system that monitors the availability of shared resources in E. coli, thus enabling the quantification of the burden a synthetic circuit places on the cell's resources. We then measure the burden of a combinatorial library of different designs to examine how different genetic components influence the magnitude of burden. This is accompanied by a mathematical model. Through this method we work towards a system that will enable the prediction of how to optimise the design of a synthetic circuit with regards to its output and the levels of burden it places on a cell.

SURF 2013

2013-06-03T14:21:23Z

Edelossa: /* Students */

This page is intended for students working on SURF projects in the Summer of 2013. Mainly for me to keep track of everything that is going on. __NOTOC__

== Students ==
{| width=100% border=1
|-
| Student
| Mini-group
| Co-mentor(s)
| Project
|-
| Bern, James || NCS || Eric || Robot Motion Planning with Complex Tasks
|-
| Falt, Mattias || NCS || Marcella || The role of delays in biological systems
|-
| Grigonyte, Aurelija || Biocricuits || Emzo || Characterizing gene expression for different extracts
|-
| Li, Monica || Biocircuits || Anu || Investigating physical methods of protecting linear DNA fragments in cell free expression systems
|-
| Mickelin, Oscar || NCS || Necmiye || Synthesis of correct-by-construction control protocols for air management systems of aircraft
|-
| Ng, Andrew || Biocircuits || Enoch || Understanding and Quantifying the Effect of Compositional Context on Biocircuit Performance
|-
| Quijano, Juan || Biocircuits || Jongmin || Synthetic logic circuits using RNA aptamers
|-
| Sharma, Rohit || Biocircuits || Zach || Synthetic biological circuit design implementing protein degradation in-vitro
|-
| Zheng, Chris || NCS || Scott || Experiments with dynamic obstacles and correct-by-construction controllers
|-
| Zhou, Tiffany || Biocircuits || Dan || The costs and benefits of various designs of biochemical 'decision engines'
|}

=== Meetings on 18-24 June ===
{| border=1 width=100%
|- valign=top
| width=20% |
===== Tue (18 Jun) =====
* SURF orientation
| width=20% |
===== Wed (19 Jun) =====
* 10:00 - Meeting with co-mentors, 114 Steele Lab
** Lab orientation/cleanup
* 12:00 - SURF seminar
* 1:30 - Caltech safety briefing (mandatory)
* 2:30-5:00 - TX-TL course (biocircuits)
| width=20% |
===== Thu (20 Jun) =====
* 10:00-5:00 - TX-TL course (biocircuits)
| width=20% |
===== Fri (21 Jun) =====
* 10:00-5:00 - TX-TL course (biocircuits)
| width=20% |
===== Mon (24 Jun) =====
* 10:00-12:00 - SURF group meeting with Richard and co-mentors, 114 Steele
** 1 chart overviews (5 min each)
|}

== Original project descriptions ==

This section is intended for students interested in working on SURF projects in the Summer of 2013. It contains a list of project areas where I will be supervising projects this year along with information about how to apply for a SURF project in my group.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student or part of one of our CDS exchange programs (Lund, KTH), I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 12 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2013.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 18 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2013|The costs and benefits of various designs of biochemical 'decision engines'}}
| [[Molecular Programming Project|MPP]]
| Dan Siegal-Gaskins
|
|-
| {{SURF entry|2013|Robot Motion Planning with Complex Tasks}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| Eric Wolff
|
|-
| {{SURF entry|2013|Experiments with dynamic obstacles and correct-by-construction controllers}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| [http://scottman.net Scott C. Livingston]
|
|-
| {{SURF entry|2013|Synthetic logic circuits using RNA aptamers}}
| [[Molecular Programming Project|MPP]]
| Jongmin Kim
|
|-
| {{SURF entry|2013|Role of Delays in Biological Processes}}
| [[Molecular Programming Project|MPP]]
| Marcella Gomez
|
|-
| {{SURF entry|2013|Designing phosphorylation sensitive protein domains for use in synthetic circuits}}
| [[Molecular Programming Project|MPP]]
| Emzo de los Santos
|
|-
| {{SURF entry|2013|Synthetic biological circuit design implementing protein degradation in-vitro}}
| [[Molecular Programming Project|MPP]]
| [http://www.its.caltech.edu/~zsun Zach Sun]
|
|-
|{{SURF entry|2013|Understanding the Effect of Compositional Context on Biocircuit Performance}}
| [[Molecular Programming Project|MPP]]
| [http://www.cds.caltech.edu/~eyeung Enoch Yeung]
|
|-
|{{SURF entry|2013|Investigating physical methods of protecting linear DNA fragments in cell-free expression systems}}
| [[Molecular Programming Project|MPP]]
| Anu Thubagere
|
|-
| {{SURF entry|2013|The connection between biological structure and function in dynamic environments}}
|
| Chris Kempes
|
|}

March 2013 meeting schedule

2013-03-03T03:10:44Z

Edelossa: /* 12 Mar (Tue) */

The list below has times that I am available to meet between 4 March and 13 March. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). Please only sign up for one time slot. __NOTOC__

{| width=100% border=1
|- valign=top
| width=30% |
==== 6 Mar (Wed) ====
{{agenda begin}}
{{agenda item|8:45-9:45|Ophelia}}
{{agenda item||}}
{{agenda item|1:15-2:00|Stephanie}}
{{agenda item||}}
{{agenda item|5:00-5:45|Open}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |
==== 7 Mar (Thu) ====
{{agenda begin}}
{{agenda item|2:00-3:30|DARPA breadboards}}
{{agenda item|4:00-4:15|UG advisee}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:45|Open}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Anandh}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |

==== 8 Mar (Fri) ====
{{agenda begin}}
{{agenda item|8:45-9:30|Open}}
{{agenda item||}}
{{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}
{{agenda item||}}
{{agenda item|12:00-1:15|NCS group meeting}}
{{agenda item|1:15-2:00|Open (might get shortened)}}
{{agenda item||}}
{{agenda item|5:00-5:45|Eric}}
{{agenda item|5:45-6:30|Open}}
{{agenda end}}

|- valign=top
|

==== 10 Mar (Sun) ====
{{agenda begin}}
{{agenda item|2:30-2:45|UG advisee}}
{{agenda item|2:45-3:00|UG advisee}}
{{agenda item|3:00-4:00|Open}}
{{agenda item|4:00-5:00|Open}}
{{agenda item|5:00-6:00|Open}}
{{agenda item|6:00-6:15|UG advisee}}
{{agenda item|6:15-6:30|UG advisee}}
{{agenda end}}
|
==== 11 Mar (Mon) ====
{{agenda begin}}
{{agenda item|3:30-4:15|Open}}
{{agenda item|4:15-5:00|Shaobin}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|

==== 12 Mar (Tue) ====
{{agenda begin}}
{{agenda item|11:00-11:45|Emzo}}
{{agenda item||}}
{{agenda item|1:00-3:00|Biocircuits meeting}}
{{agenda item||}}
{{agenda item|3:30-4:15|Nathan Belliveau}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|}

BE 150/Bi 250b project ideas, Winter 2013

2013-02-01T06:10:06Z

Edelossa:

{{warning|This page is still being written. Do not start thinking about these projects until this banner is removed.}}
{| style="float: right"
|-
| align=right | [[BE 150/Bi 250b Winter 2013|Course home]]
|-
| __TOC__
|}

This page contains a list of course project ideas for BE 150/Bi 250b, Winter 2013.

'''Instructions:'''
{{BE 150 project instructions, Winter 2013}}

=== Digit patterning ===

* [http://www.sciencemag.org/content/338/6113/1476 Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism] by Sheth and Marco, et al, Science Dec 2012

Idea: build a reaction diffusion model to replicate the results in the paper, showing how multiple digit patterns can be generated in mice. Show how to tune the number of digits on the hand by progressively removing copies of a hox gene. Discuss this as evidence for a turing type patterning process (with modeling).

Note: This is a pretty difficult project. You should probably only select it if you already know about reaction diffusion models (we will cover this in Weeks 7-8)

=== Scaling of embryonic patterning ===

* [http://www.nature.com/nature/journal/v493/n7430/full/nature11804.html Scaling of embryonic patterning based on phase-gradient encoding] by Lauschke and Tsiairis et al, Nature, Jan 2013.

Idea: this paper shows an ''ex vivo'' model of the presomitic mesoderm wave propagation system for simile patterning, ie they cut some of these cells out from the mouse embryo and show that they can still make segments similar to in vivo. They then use the system to show that there is scaling of number and size of segments with overall explant size. Reproduce the model used in the paper and explore the application of the principles that we covered in class to provide some insight into this behavior.

Note: this problem will require some iteration with the instructors to make the goals more concrete.

=== Robustness and tunability comparison for synthetic oscillators ===

* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], M. B. Elowitz and S. Leibler,. ''Nature'', 403(6767):335–338, 2000.
* [http://www.cell.com/retrieve/pii/S0092867403003465 Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli], M. R. Atkinson, M. A. Savageau, J. T. Myers, and A. J. Ninfa. ''Cell'', 113(5):597–607, 2003.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty. ''Nature'', 456( 7221):516–519, 2008.

Idea: put together models of different types of oscillators in ''E. coli'' using a consistent set parameters. Explore parameter sensitivity, noise attenuation and behavioral diversity in each and comment on the relevant robustness and tunability of each circuit. Answer, once and for all, the question of whether the repressilator is robust or fragile.

=== Robustness and loading effects in MAPK cascades ===

* [http://www.pnas.org/content/78/11/6840.abstract An amplified sensitivity arising from covalent modification in biological systems], Goldbeter and D.E.Koshland, ''Proceedings of the National Academy of Sciences'', 78(11): 6840–6844, 1981.
* [http://www.pnas.org/content/93/19/10078.abstract Ultra sensitivity in the mitogen-activated protein kinase cascade], C.Y. Huang and J.E.Ferrell. ''Proceedingsof the National Academy of Sciences'', 93(19):10078–10083,1996.

In class we showed that one of the advantages of a two component signaling system and multi-stage MAPK cascades is that you can get higher input/output gain. Another potential benefit of such constructs may be the robustness to downstream loads as well as insensitivity to noise and parameters. Construct models of a set of different signalling mechanisms and explore some of these tradeoffs.

=== Feedback loops operating at different time scales ===

* [http://www.nature.com/nature/journal/v488/n7411/full/nature11259.html Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells], P Wei, WW Wong*, JS Park, EE Corcoran, SG Peisajovich, JJ Onuffer, A Weiss, WA Lim. Nature 488, 384–388 (2012)

Explore feedback loops operating on different time scales and look at the effect of this on pulses with different frequencies. Possible extensions to the model can include: effect of multiple feedback loops, looking at the entire frequency response curve or doing sensitivity analysis on the different parameters.


=== Utilization of a conserved resource ===
* [http://www.nature.com/msb/journal/v7/n1/full/msb201194.html Queueing up for enzymatic processing: correlated signaling through coupled degradation], NA Cookson, WH Mather, T Danino, O Mondragon-Palomino, RJ Williams, LS Tsimring and J Hasty. Molecular Systems Biology 7:561
* [http://www.cds.caltech.edu/~murray/preprints/snm13-acc_s.pdf Biomolecular resource utilization in elementary cell-free gene circuits], D Siegal-Gaskins, V Noireaux, RM Murray ACC 2013 (submitted)

The papers above show correlations between seemingly independent outputs because of crosstalk due to limitations of a shared resource. Explore this in more detail or look at another limited shared resource.

Note: If you choose this project, you might find it useful to talk to Dan Siegal-Gaskins, a postdoc in Richard Murray's group, for possible extensions/modeling ideas.

=== Robustness in KaiABC oscillations due to a slow binding step ===
* [http://www.pnas.org/content/110/3/1124.full.pdf?with-ds=yes Robust and tunable circadian rhythms from differentially sensitive catalytic domains], C Phong, JS Markson, CM Wilhoite and MJ Rust. PNAS 110(3):1124-9 (2013)

The oscillations of the KaiABC cycle are known to be robust to the ATP/ADP ratio, even if ATP is a substrate for KaiC. Experimentally the researchers in the paper found found that this might be due to the ATPase activity of the CI domain (which is slow compared to everything else). They built a model to explore this which added slow binding steps to the existing model. Modify their model and use an alternate mechanism for delay ( such as explicit time delay in the differential equation), calculate sensitivities for the period for both models or potentially model a simpler, synthetic circuit that has this feature and also demonstrates invariance to substrate input.

=== Asymmetric positive feedback (VH) ===
* Paper: http://www.nature.com/msb/journal/v8/n1/full/msb201210.html
* Idea: Positive feedback is one of the central components of biological circuits. In this paper by Ratushny et al, they analyze the effects of having asymmetrical positive feedback loops, in which only one of the molecules in a heterodimer is self-upregulates. In the paper, they mention a number of biological systems with this circuit motif. Choose one of the examples which is not demonstrated in the paper with which to perform a thorough analysis. Model the system to include additional features other than the ASSURE system and compare that to a model in which there is symmetrical upregulation. How does this affect the behavior of your system? What implications does it have for the organism as a whole?

=== Propose you own project ===

Guidelines: propose a project that involves reading a set of papers in the literature and performing some modeling and analysis to propose a testable hypothesis about the behavior of the system you investigate. Your writeup should include a list of 1-3 papers along with a short (1-2 sentence summary of their main results), followed by a 1-2 paragraph description of the question you propose to explore. All proposals must be submitted by a 2 person team, ideally with one student in Bi 250b and one student in BE 150.

BE 150/Bi 250b project ideas, Winter 2013

2013-02-01T05:55:31Z

Edelossa: /* Feedback loops operating at different time scales (EDLS) */

{{warning|This page is still being written. Do not start thinking about these projects until this banner is removed.}}
{| style="float: right"
|-
| align=right | [[BE 150/Bi 250b Winter 2013|Course home]]
|-
| __TOC__
|}

This page contains a list of course project ideas for BE 150/Bi 250b, Winter 2013.

'''Instructions:'''
{{BE 150 project instructions, Winter 2013}}

=== Digit patterning ===

* [http://www.sciencemag.org/content/338/6113/1476 Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism] by Sheth and Marco, et al, Science Dec 2012

Idea: build a reaction diffusion model to replicate the results in the paper, showing how multiple digit patterns can be generated in mice. Show how to tune the number of digits on the hand by progressively removing copies of a hox gene. Discuss this as evidence for a turing type patterning process (with modeling).

Note: This is a pretty difficult project. You should probably only select it if you already know about reaction diffusion models (we will cover this in Weeks 7-8)

=== Scaling of embryonic patterning ===

* [http://www.nature.com/nature/journal/v493/n7430/full/nature11804.html Scaling of embryonic patterning based on phase-gradient encoding] by Lauschke and Tsiairis et al, Nature, Jan 2013.

Idea: this paper shows an ''ex vivo'' model of the presomitic mesoderm wave propagation system for simile patterning, ie they cut some of these cells out from the mouse embryo and show that they can still make segments similar to in vivo. They then use the system to show that there is scaling of number and size of segments with overall explant size. Reproduce the model used in the paper and explore the application of the principles that we covered in class to provide some insight into this behavior.

Note: this problem will require some iteration with the instructors to make the goals more concrete.

=== Robustness and tunability comparison for synthetic oscillators ===

* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], M. B. Elowitz and S. Leibler,. ''Nature'', 403(6767):335–338, 2000.
* [http://www.cell.com/retrieve/pii/S0092867403003465 Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli], M. R. Atkinson, M. A. Savageau, J. T. Myers, and A. J. Ninfa. ''Cell'', 113(5):597–607, 2003.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty. ''Nature'', 456( 7221):516–519, 2008.

Idea: put together models of different types of oscillators in ''E. coli'' using a consistent set parameters. Explore parameter sensitivity, noise attenuation and behavioral diversity in each and comment on the relevant robustness and tunability of each circuit. Answer, once and for all, the question of whether the repressilator is robust or fragile.

=== Robustness and loading effects in MAPK cascades ===

* [http://www.pnas.org/content/78/11/6840.abstract An amplified sensitivity arising from covalent modification in biological systems], Goldbeter and D.E.Koshland, ''Proceedings of the National Academy of Sciences'', 78(11): 6840–6844, 1981.
* [http://www.pnas.org/content/93/19/10078.abstract Ultra sensitivity in the mitogen-activated protein kinase cascade], C.Y. Huang and J.E.Ferrell. ''Proceedingsof the National Academy of Sciences'', 93(19):10078–10083,1996.

In class we showed that one of the advantages of a two component signaling system and multi-stage MAPK cascades is that you can get higher input/output gain. Another potential benefit of such constructs may be the robustness to downstream loads as well as insensitivity to noise and parameters. Construct models of a set of different signalling mechanisms and explore some of these tradeoffs.

=== Feedback loops operating at different time scales (EDLS) ===

* [http://www.nature.com/nature/journal/v488/n7411/full/nature11259.html Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells], P Wei, WW Wong*, JS Park, EE Corcoran, SG Peisajovich, JJ Onuffer, A Weiss, WA Lim. Nature 488, 384–388 (2012)

Explore feedback loops operating on different time scales and look at the effect of this on pulses with different frequencies. Possible extensions to the model can include: effect of multiple feedback loops, looking at the entire frequency response curve or doing sensitivity analysis on the different parameters.

* Zi, Z., Liebermeister, W. & Klipp, E. A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. PloS one 5, e9522 (2010).

=== Utilization of a conserved resource (EDLS) ===
* [http://www.nature.com/msb/journal/v7/n1/full/msb201194.html Queueing up for enzymatic processing: correlated signaling through coupled degradation], NA Cookson, WH Mather, T Danino, O Mondragon-Palomino, RJ Williams, LS Tsimring and J Hasty. Molecular Systems Biology 7:561
* [http://www.cds.caltech.edu/~murray/preprints/snm13-acc_s.pdf Biomolecular resource utilization in elementary cell-free gene circuits], D Siegal-Gaskins, V Noireaux, RM Murray ACC 2013 (submitted)

The papers above show correlations between seemingly independent outputs because of crosstalk due to limitations of a shared resource. Explore this in more detail or look at another limited shared resource.

Note: If you choose this project, you might find it useful to talk to Dan Siegal-Gaskins, a post-doc in the Murray Lab, for possible extensions/modeling ideas.

=== Asymmetric positive feedback (VH) ===
* Paper: http://www.nature.com/msb/journal/v8/n1/full/msb201210.html
* Idea: Positive feedback is one of the central components of biological circuits. In this paper by Ratushny et al, they analyze the effects of having asymmetrical positive feedback loops, in which only one of the molecules in a heterodimer is self-upregulates. In the paper, they mention a number of biological systems with this circuit motif. Choose one of the examples which is not demonstrated in the paper with which to perform a thorough analysis. Model the system to include additional features other than the ASSURE system and compare that to a model in which there is symmetrical upregulation. How does this affect the behavior of your system? What implications does it have for the organism as a whole?

=== Propose you own project ===

Guidelines: propose a project that involves reading a set of papers in the literature and performing some modeling and analysis to propose a testable hypothesis about the behavior of the system you investigate. Your writeup should include a list of 1-3 papers along with a short (1-2 sentence summary of their main results), followed by a 1-2 paragraph description of the question you propose to explore. All proposals must be submitted by a 2 person team, ideally with one student in Bi 250b and one student in BE 150.

BE 150/Bi 250b project ideas, Winter 2013

2013-02-01T05:55:17Z

Edelossa:

{{warning|This page is still being written. Do not start thinking about these projects until this banner is removed.}}
{| style="float: right"
|-
| align=right | [[BE 150/Bi 250b Winter 2013|Course home]]
|-
| __TOC__
|}

This page contains a list of course project ideas for BE 150/Bi 250b, Winter 2013.

'''Instructions:'''
{{BE 150 project instructions, Winter 2013}}

=== Digit patterning ===

* [http://www.sciencemag.org/content/338/6113/1476 Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism] by Sheth and Marco, et al, Science Dec 2012

Idea: build a reaction diffusion model to replicate the results in the paper, showing how multiple digit patterns can be generated in mice. Show how to tune the number of digits on the hand by progressively removing copies of a hox gene. Discuss this as evidence for a turing type patterning process (with modeling).

Note: This is a pretty difficult project. You should probably only select it if you already know about reaction diffusion models (we will cover this in Weeks 7-8)

=== Scaling of embryonic patterning ===

* [http://www.nature.com/nature/journal/v493/n7430/full/nature11804.html Scaling of embryonic patterning based on phase-gradient encoding] by Lauschke and Tsiairis et al, Nature, Jan 2013.

Idea: this paper shows an ''ex vivo'' model of the presomitic mesoderm wave propagation system for simile patterning, ie they cut some of these cells out from the mouse embryo and show that they can still make segments similar to in vivo. They then use the system to show that there is scaling of number and size of segments with overall explant size. Reproduce the model used in the paper and explore the application of the principles that we covered in class to provide some insight into this behavior.

Note: this problem will require some iteration with the instructors to make the goals more concrete.

=== Robustness and tunability comparison for synthetic oscillators ===

* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], M. B. Elowitz and S. Leibler,. ''Nature'', 403(6767):335–338, 2000.
* [http://www.cell.com/retrieve/pii/S0092867403003465 Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli], M. R. Atkinson, M. A. Savageau, J. T. Myers, and A. J. Ninfa. ''Cell'', 113(5):597–607, 2003.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty. ''Nature'', 456( 7221):516–519, 2008.

Idea: put together models of different types of oscillators in ''E. coli'' using a consistent set parameters. Explore parameter sensitivity, noise attenuation and behavioral diversity in each and comment on the relevant robustness and tunability of each circuit. Answer, once and for all, the question of whether the repressilator is robust or fragile.

=== Robustness and loading effects in MAPK cascades ===

* [http://www.pnas.org/content/78/11/6840.abstract An amplified sensitivity arising from covalent modification in biological systems], Goldbeter and D.E.Koshland, ''Proceedings of the National Academy of Sciences'', 78(11): 6840–6844, 1981.
* [http://www.pnas.org/content/93/19/10078.abstract Ultra sensitivity in the mitogen-activated protein kinase cascade], C.Y. Huang and J.E.Ferrell. ''Proceedingsof the National Academy of Sciences'', 93(19):10078–10083,1996.

In class we showed that one of the advantages of a two component signaling system and multi-stage MAPK cascades is that you can get higher input/output gain. Another potential benefit of such constructs may be the robustness to downstream loads as well as insensitivity to noise and parameters. Construct models of a set of different signalling mechanisms and explore some of these tradeoffs.

=== Feedback loops operating at different time scales (EDLS) ===

* [http://www.nature.com/nature/journal/v488/n7411/full/nature11259.html Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells], P Wei, WW Wong*, JS Park, EE Corcoran, SG Peisajovich, JJ Onuffer, A Weiss, WA Lim. Nature 488, 384–388 (2012)

Explore feedback loops operating on different time scales and look at the effect of this on pulses with different frequencies. Possible extensions to the model can include: effect of multiple feedback loops, looking at the entire frequency response curve or doing sensitivity analysis on the different parameters.

** Zi, Z., Liebermeister, W. & Klipp, E. A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. PloS one 5, e9522 (2010).

=== Utilization of a conserved resource (EDLS) ===
* [http://www.nature.com/msb/journal/v7/n1/full/msb201194.html Queueing up for enzymatic processing: correlated signaling through coupled degradation], NA Cookson, WH Mather, T Danino, O Mondragon-Palomino, RJ Williams, LS Tsimring and J Hasty. Molecular Systems Biology 7:561
* [http://www.cds.caltech.edu/~murray/preprints/snm13-acc_s.pdf Biomolecular resource utilization in elementary cell-free gene circuits], D Siegal-Gaskins, V Noireaux, RM Murray ACC 2013 (submitted)

The papers above show correlations between seemingly independent outputs because of crosstalk due to limitations of a shared resource. Explore this in more detail or look at another limited shared resource.

Note: If you choose this project, you might find it useful to talk to Dan Siegal-Gaskins, a post-doc in the Murray Lab, for possible extensions/modeling ideas.

=== Asymmetric positive feedback (VH) ===
* Paper: http://www.nature.com/msb/journal/v8/n1/full/msb201210.html
* Idea: Positive feedback is one of the central components of biological circuits. In this paper by Ratushny et al, they analyze the effects of having asymmetrical positive feedback loops, in which only one of the molecules in a heterodimer is self-upregulates. In the paper, they mention a number of biological systems with this circuit motif. Choose one of the examples which is not demonstrated in the paper with which to perform a thorough analysis. Model the system to include additional features other than the ASSURE system and compare that to a model in which there is symmetrical upregulation. How does this affect the behavior of your system? What implications does it have for the organism as a whole?

=== Propose you own project ===

Guidelines: propose a project that involves reading a set of papers in the literature and performing some modeling and analysis to propose a testable hypothesis about the behavior of the system you investigate. Your writeup should include a list of 1-3 papers along with a short (1-2 sentence summary of their main results), followed by a 1-2 paragraph description of the question you propose to explore. All proposals must be submitted by a 2 person team, ideally with one student in Bi 250b and one student in BE 150.

SURF discussions, Jan 2013

2013-01-24T22:19:34Z

Edelossa: /* 30 Jan (Wed) */

Slots for talking with applicants and co-mentors about SURF projects. Please sign up for one of the slots below. All times are PST.

{| width=100% border=1
|- valign=top
|
==== 28 Jan (Mon) ====
* 9:00: Anu/ Monica
* 9:20: Andrew + Enoch
* 9:40: James + Eric
|

==== 30 Jan (Wed) ====
* 14:00: Open
* 14:20: Open
* 14:40: Emzo + Aurelija
|

==== 31 Jan (Thu) ====
* 10:30: Open
* 10:50: Open
* 11:10: Marcella + Mattias
|}

The agenda for the phone call is (roughly):

# Description of the basic idea behind the project (based on applicant's understanding)
# Discussion about approaches, things to read, variations to consider, etc
# Discussion of the format of the proposal
# Questions and discussion about the process

File:SimbiologyTutorial.pdf

2013-01-11T18:00:40Z

Edelossa:

BE 150/Bi 250b Winter 2013

2013-01-11T18:00:04Z

Edelossa: /* Lecture Schedule */

{| width=100%
|-
| colspan=3 align=center |
Systems Biology__NOTOC__
|- valign=top
|
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 200 BRD
|
'''Teaching Assistants'''
* Emzo de los Santos
* Victoria Hsiao
* Recitation: Fr 10-11, location TBD
| rowspan=2 width=20% align=right |
__TOC__
|-
| colspan=2 |
This is the course homepage for BE 150/Bi 250b for Winter 2013. This page contains all of the information about the material that will be covered in the class, as well as links to the homeworks and information about the course projects and grading.
|}

=== Lecture Schedule ===
There will be 2-3 one-hour lectures each week, as well as occasional one-hour tutorials, recitations or journal club.
{| width=100% border=1 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
'''1'''
| 7 Jan 9 Jan+ MBE/RMM
| Course overview, gene circuit dynamics
* Principles in systems biology
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
Recitation section:
* [[Media:MatlabTutorial.pdf|MATLAB]] and [[Media:SimbiologyTutorial.pdf|SimBiology]] Tutorial

|
Bi 250b:
* Alon, Ch 1: Introduction
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts (skim)
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques (skim)
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

| [http://www.cds.caltech.edu/~murray/courses/be150/wi13/hw1.pdf HW1]
|- valign=top
|

'''2'''
| 13 Jan 15 Jan MBE
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
Recitation (17 Jan): sample problems
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

| HW 2

|- valign=top
|

'''3'''
| <s>21 Jan</s> 23 Jan* 25 Jan RMM
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
No recitation
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
| HW 3

|- valign=top
|

'''4'''
| 28 Jan 30 Jan RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
Recitation (1 Feb): sensitivity analysis
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| HW 4

|-
|
| 1 Feb
| colspan=3 | Class project discussion and selection

|- valign=top
|

'''5'''
| 4 Feb 6 Feb MBE
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-stochastic_29Jan12.pdf|BFS, Ch 4}}: Stochastic behavior
* {{be150 pdf|wi12|caltech/bfs-class-random_29Jan12.pdf|BFS, App C}}: Probability and random processes (optional)
| rowspan=2 | HW 5

|- valign=top
|

'''6'''
| 11 Feb 13 Feb+ MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010

|-
|
| 20 Feb+* 
| colspan=3 | Class project discussion with TAs

|- valign=top
|

'''7'''
| 22 Feb* 25 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| rowspan=2 | HW 6

|- valign=top
|

'''8'''
| 27 Feb 1 Mar RMM
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90

|- valign=top
|

'''9'''
| 4 Mar 6 Mar 8 Mar 
| colspan=3 | Project presentations

|- valign=top
|

'''10'''
| 11 Mar 13 Mar
| colspan=3 | Project presentations
|}

 

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''[[http:www.cds.caltech.edu/~murray/amwiki/BFS|Biomolecular Feedback Systems]]'' (available online)
* Note: these notes are being written and will be updated during the course
* The public version is missing some copyrighted figures. These are available in the class version.
* Class version (Caltech access only, 5 Jan 2013): {{be150 pdf|wi13|caltech/bfs-class-frontmatter_05Jan13.pdf|TOC}}, {{be150 pdf|wi13|caltech/bfs-class-intro_05Jan13.pdf|Ch 1}}, {{be150 pdf|wi13|caltech/bfs-class-coreproc_05Jan13.pdf|Ch 2}}, {{be150 pdf|wi13|caltech/bfs-class-dynamics_05Jan13.pdf|Ch 3}}, {{be150 pdf hold|wi13|caltech/bfs-class-stochastic_29Jan13.pdf|Ch 4}}, {{be150 pdf hold|wi13|caltech/bfs-class-chemotaxis_29Jan13.pdf|Sec 5.2}}, {{be150 pdf hold|wi13|caltech/bfs-class-random_29Jan13.pdf|App C}}, {{be150 pdf|wi13|caltech/bfs-class-backmatter_05Jan13.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Course project ===
All students enrolled in the course will be expected to participate in a course project, which will be assigned after the fourth week of class. Course projects will generally consist of reviewing one or more papers on a topic that makes use principles and tools discussed in the course. Each project will be undertaking by two students (nominally one from BE 150, one from Bi 250). Topic suggestions will be posted here (eventually). Students can also propose their own topic of student by preparing a 1-2 page proposal and submitting this to the instructors no later than 1 Feb for consideration.

Course project timeline:
* 30 Jan (Wed): course projects posted on home page and announced in class
* 1 Feb (Fri): in class discussion of course project possibilities
* 4 Feb (Mon): course project preferences due
* 6 Feb (Wed): project assignments available
* 20 Feb (Wed): discussion of course projects with TAs and others
* 4-13 Mar: course project presentations. 15-20 minutes per project + 5-10 minutes questions.

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets (75%) and a course project (25%). The homework will be due in class approximately one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average. The class project will be assigned and the end of the 5th week of instruction and project presentations will be scheduled for the last two weeks of class.

=== Collaboration Policy ===
Collaboration on homework assignments and the course project is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing. Your course project presentation to properly acknowledge all source materials.

[[Category:Courses]]

File:SimBiologyTutorial.pdf

2013-01-11T17:57:38Z

Edelossa:

SURF 2013: Designing phosphorylation sensitive protein domains for use in synthetic circuits

2013-01-06T22:33:07Z

Edelossa: Created page with "'''2013 SURF project description''' * Mentor: Richard Murray * Co-mentor: Emzo de los Santos Synthetic biology aims take advantage of biological process to engi..."

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Emzo de los Santos

Synthetic biology aims take advantage of biological process to engineer systems and devices with novel and useful functions. Since it is still in its infancy, much work is necessary in order to build a framework to make it easier to design using biological parts. This project aims to contribute to this framework and expand the synthetic biology toolkit.

The project involves characterizing peptide domains that are designed to have thermostability differences in the phgosphorylated and non-phosphorylated states. By inserting these domains into different proteins, we believe that we can get a general method for stimulus-dependent modulation of protein activity. This work builds on previous work that has previously shown modulation in activity of enzymes through insertion of light-sensitive [1] and chemically-sensitive domains [2]. Phosphorylation events are widely used in natural systems to control the dynamics of gene networks. Circuits including proteins that using phosphorylation as a trigger for modulation of activity should be able to respond on a faster time scale than traditional synthetic circuits.

Biochemical characterization will be done both of the domains on their own and inserted into at least one enzyme. Mathematical modeling and characterization of circuits that use this mechanism can also be performed.

===References===
# Reynolds, Kimberly A, Richard N McLaughlin, and Rama Ranganathan. “Hot Spots for Allosteric Regulation on Protein Surfaces..” Cell 147.7 (2011): 1564–1575.
# Erster, O, M Eisenstein, and M Liscovitch. “Ligand Interaction Scan: a General Method for Engineering Ligand- Sensitive Protein Alleles.” Nature methods (2007)

Group Schedule, Fall 2012

2012-09-24T04:19:59Z

Edelossa: /* Week 10: 3-7 Dec */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings. Unless otherwise noted, here are the locations of the meetings:
:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 114 Steele Lab
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 110 Steele
|}

{| width=100% border=1
|- valign=top
| width=30% |
=== Week 1: 1-5 Oct ===
'''Biocircuits: 4 Oct (Thu), 10 am - 12 pm'''
* Gita Mahmoudabadi (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 4 Oct (Thu), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* Richard out of town Tue-Wed
* No group meeting this week

| width=30% |

=== Week 2: 8-12 Oct ===
'''NCS: 10 Oct (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 11 Oct (Thu), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

<hr>
* Richard out of town Mon, Tue am, Fri pm
* Aaron Ames visiting on Thu (seminar @ noon)
* No group meeting this week
| width=30% |

=== Week 3: 15-19 Oct ===
* Richard out of town all week
* Biocircuits lab cleanup: 16 Oct (Tue), 10 am - 12 pm

|- valign=top
| width=30% |
=== Week 4: 22-26 Oct ===
'''Biocircuits: 23 Oct (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 23 Oct (Tue), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* Ram Vasuvian visiting on Mon (seminar @ 11)
* DARPA Living Foundries west coast meeting on Thu (Richard out)
* No group meeting this week

| width=30% |
=== Week 5: 29 Oct - 2 Nov ===
'''NCS: 31 Oct (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 1 Nov (Thu), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

<hr>
* Richard out of town on Tue
* iGEM World Jamboree, Fri-Mon
* No group meeting this week
| width=30% |

=== Week 6: 5-9 Nov ===
'''Biocircuits: 6 Nov (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Emzo (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 7 Nov (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

|- valign=top
| width=30% |

=== Week 7: 12-16 Nov ===
'''Biocircuits: 15 Nov (Thu), 10 am - 12 pm'''
* Ophelia (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 15 Nov (Thu), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 8: 19-23 Nov ===
* Richard out of town all week
* Biocircuits lab cleanup: 20 Nov (Tue), 10 am - 12 pm
* Thanksgiving break, Thu-Fri
* No group meeting this week

| width=30% |
=== Week 9: 26-30 Nov ===
'''Biocircuits: 27 Nov (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 28 Nov (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* DARPA breadboards telecon, Thu @ 9:30 am
* SoCal Control Workshop, Fri (UC San Diego)
* No group meeting this week

|- valign=top
| width=30% |
=== Week 10: 3-7 Dec ===
'''Biocircuits: 4 Dec (Tue), 10 am - 12 pm'''
* Emzo (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 5 Dec (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 11: 10-14 Dec ===
* CDC week, no group meetings
* Biocircuits lab cleanup: 11 Dec (Tue), 10 am - 12 pm

| width=30% |
=== Week 12: 17-21 Dec ===
* Winter break, no group meetings
* Richard around Mon-Thu
|}

Group Schedule, Fall 2012

2012-09-24T04:19:48Z

Edelossa: /* Week 6: 5-9 Nov */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings. Unless otherwise noted, here are the locations of the meetings:
:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 114 Steele Lab
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 110 Steele
|}

{| width=100% border=1
|- valign=top
| width=30% |
=== Week 1: 1-5 Oct ===
'''Biocircuits: 4 Oct (Thu), 10 am - 12 pm'''
* Gita Mahmoudabadi (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 4 Oct (Thu), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* Richard out of town Tue-Wed
* No group meeting this week

| width=30% |

=== Week 2: 8-12 Oct ===
'''NCS: 10 Oct (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 11 Oct (Thu), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

<hr>
* Richard out of town Mon, Tue am, Fri pm
* Aaron Ames visiting on Thu (seminar @ noon)
* No group meeting this week
| width=30% |

=== Week 3: 15-19 Oct ===
* Richard out of town all week
* Biocircuits lab cleanup: 16 Oct (Tue), 10 am - 12 pm

|- valign=top
| width=30% |
=== Week 4: 22-26 Oct ===
'''Biocircuits: 23 Oct (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 23 Oct (Tue), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* Ram Vasuvian visiting on Mon (seminar @ 11)
* DARPA Living Foundries west coast meeting on Thu (Richard out)
* No group meeting this week

| width=30% |
=== Week 5: 29 Oct - 2 Nov ===
'''NCS: 31 Oct (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 1 Nov (Thu), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

<hr>
* Richard out of town on Tue
* iGEM World Jamboree, Fri-Mon
* No group meeting this week
| width=30% |

=== Week 6: 5-9 Nov ===
'''Biocircuits: 6 Nov (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Emzo (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 7 Nov (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

|- valign=top
| width=30% |

=== Week 7: 12-16 Nov ===
'''Biocircuits: 15 Nov (Thu), 10 am - 12 pm'''
* Ophelia (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 15 Nov (Thu), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 8: 19-23 Nov ===
* Richard out of town all week
* Biocircuits lab cleanup: 20 Nov (Tue), 10 am - 12 pm
* Thanksgiving break, Thu-Fri
* No group meeting this week

| width=30% |
=== Week 9: 26-30 Nov ===
'''Biocircuits: 27 Nov (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 28 Nov (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* DARPA breadboards telecon, Thu @ 9:30 am
* SoCal Control Workshop, Fri (UC San Diego)
* No group meeting this week

|- valign=top
| width=30% |
=== Week 10: 3-7 Dec ===
'''Biocircuits: 4 Dec (Tue), 10 am - 12 pm'''
* Research presentation (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 5 Dec (Wed), 4:30-6:00 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |
=== Week 11: 10-14 Dec ===
* CDC week, no group meetings
* Biocircuits lab cleanup: 11 Dec (Tue), 10 am - 12 pm

| width=30% |
=== Week 12: 17-21 Dec ===
* Winter break, no group meetings
* Richard around Mon-Thu
|}

Group Schedule, Summer 2012

2012-06-07T22:35:52Z

Edelossa: /* Week 15: 24-28 September */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 18-22 June ===

'''Biocircuits: 21 Jun (Thu), 10 am - 12 pm'''
* SURF introductions (40 min)
* Ophelia (20-30 min)
* Shaunak K (10-15 min)
* Lab updates

'''Group meeting: 21 Jun (Thu), 12-1'''
* Richard (research overview)

'''NCS/Robotics: 21 Jun (Thu), 4-6 pm'''
* SURF introductions (20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* Richard out of town Mon-Tue
* SURF students start on Tue
| width=30% |

=== Week 2: 25-29 June ===
* American Control Conference (Montreal)
* Richard out of town all week
| width=30% |

=== Week 3: 2-6 July ===
* Richard out of town all week
* Institute holiday on Wed
|- valign=top
|

=== Week 4: 9-13 July ===
'''Biocircuits: 10 Jul (Tue), 10 am - 12 pm'''
* Meeting may shift to Mon, 10a-12p
* Victoria (25-30 min)
* Anu (10-15 min)
* Research update (10-15 min)
* Instrument: Microscope/CellASIC
* Lab updates

'''Group meeting: 13 Jul (Fri), 12-1:15'''
* Tim Sullivan?

'''NCS/Robotics: 13 Jul (Fri), 1:15-3 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* Richard out of town Tue pm - Thu (Living Foundries PI meeting)
|

=== Week 5: 16-20 July ===
'''Biocircuits: 17 Jul (Tue), 10 am - 12 pm'''
* Anu (30-40 min)
* Zach (10-15 min)
* SURF: Vinay V (10-15 min)
* SURF update (10-15 min)
* Instrument: Computing
* Lab updates

'''NCS/Robotics: 18 Jul (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates

'''Group meeting: 19 Jul (Thu), 12-1:15'''
* Chin-Lin Guo (BE)
<hr>
* Shaunak K SURF presentation
|

=== Week 6: 23-27 July ===
'''Biocircuits: 24 Jul (Tue), 10 am - 12 pm'''
* Emzo (30-40 min)
* Enoch (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Instrument: FACSCalibur/Quanta
* Lab updates

'''Group meeting: 25 Jul (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 25 Jul (Wed), 4-6 pm'''
* Pavithra (15-20 min)
* Research update (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates
<hr>
* Richard out of town Thu-Fri
|- valign=top
|

=== Week 7: 30 July - 3 August ===
'''Biocircuits: 31 Jul (Tue), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Research presentation (30-40 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Lab updates

'''NCS/Robotics: 1 Aug (Wed), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* KISS workshop; Richard unavailable
|

=== Week 8: 6-10 August ===
'''Biocircuits: 7 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Victoria (10-15 min)
* Research update (10-15 min)
* Instrument: Victor X3/BioTek H1MF
* Lab updates

'''Group meeting: 8 Aug (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 8 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

|

=== Week 9: 13-17 August ===
* Richard out all week
|- valign=top
|

=== Week 10: 20-24 August ===
'''Biocircuits: 22 Aug (Wed), 10 am - 12 pm'''
* Research presentation [non-MPP] (30-40 min)
* Enoch [non-MPP] (10-15 min)
* Research update [non-MPP] (10-15 min)
* Instrument: freezers/cold room
* Lab updates

'''NCS/Robotics: 22 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 23 Aug (Thu), 12-1:15'''
* Lea Goentoro (Bi)
<hr>
* MPP retreat, Sun-Tue
|

=== Week 11: 27-31 August ===
'''Biocircuits: 28 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instruments: Nanodrop/electroporator
* Lab updates

'''NCS/Robotics: 29 Aug (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 30 Aug (Thu), 12-1:15'''
* Open
<hr>
* Richard out of town on Fri
|

=== Week 12: 3-7 September ===
'''Biocircuits: 4 Sep (Tue), 10 am - 12 pm'''
* Marcella (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: gel rigs/gel imager
* Lab updates

'''NCS/Robotics: 5 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 6 Sep (Thu), 12-1:15'''
* Open
<hr>
* Institute holiday on Mon
|- valign=top
|

=== Week 13: 10-14 September ===
'''Biocircuits: 11 Sep (Tue), 10 am - 12 pm'''
* Zach (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: PCR machines/centrifuges
* Lab updates

'''NCS/Robotics: 12 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 13 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Fri
|

=== Week 14: 17-21 September ===
* Richard out all week
|
=== Week 15: 24-28 September ===
'''Biocircuits: 25 Sep (Tue), 10 am - 12 pm'''
* Enoch (30-40 min)
* Emzo (10-15 min)
* Research update (10-15 min)
* Lab updates

'''NCS/Robotics: 26 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 26 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Mon
|}

Group Schedule, Summer 2012

2012-06-07T22:35:37Z

Edelossa: /* Week 6: 23-27 July */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 18-22 June ===

'''Biocircuits: 21 Jun (Thu), 10 am - 12 pm'''
* SURF introductions (40 min)
* Ophelia (20-30 min)
* Shaunak K (10-15 min)
* Lab updates

'''Group meeting: 21 Jun (Thu), 12-1'''
* Richard (research overview)

'''NCS/Robotics: 21 Jun (Thu), 4-6 pm'''
* SURF introductions (20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* Richard out of town Mon-Tue
* SURF students start on Tue
| width=30% |

=== Week 2: 25-29 June ===
* American Control Conference (Montreal)
* Richard out of town all week
| width=30% |

=== Week 3: 2-6 July ===
* Richard out of town all week
* Institute holiday on Wed
|- valign=top
|

=== Week 4: 9-13 July ===
'''Biocircuits: 10 Jul (Tue), 10 am - 12 pm'''
* Meeting may shift to Mon, 10a-12p
* Victoria (25-30 min)
* Anu (10-15 min)
* Research update (10-15 min)
* Instrument: Microscope/CellASIC
* Lab updates

'''Group meeting: 13 Jul (Fri), 12-1:15'''
* Tim Sullivan?

'''NCS/Robotics: 13 Jul (Fri), 1:15-3 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* Richard out of town Tue pm - Thu (Living Foundries PI meeting)
|

=== Week 5: 16-20 July ===
'''Biocircuits: 17 Jul (Tue), 10 am - 12 pm'''
* Anu (30-40 min)
* Zach (10-15 min)
* SURF: Vinay V (10-15 min)
* SURF update (10-15 min)
* Instrument: Computing
* Lab updates

'''NCS/Robotics: 18 Jul (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates

'''Group meeting: 19 Jul (Thu), 12-1:15'''
* Chin-Lin Guo (BE)
<hr>
* Shaunak K SURF presentation
|

=== Week 6: 23-27 July ===
'''Biocircuits: 24 Jul (Tue), 10 am - 12 pm'''
* Emzo (30-40 min)
* Enoch (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Instrument: FACSCalibur/Quanta
* Lab updates

'''Group meeting: 25 Jul (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 25 Jul (Wed), 4-6 pm'''
* Pavithra (15-20 min)
* Research update (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates
<hr>
* Richard out of town Thu-Fri
|- valign=top
|

=== Week 7: 30 July - 3 August ===
'''Biocircuits: 31 Jul (Tue), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Research presentation (30-40 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Lab updates

'''NCS/Robotics: 1 Aug (Wed), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* KISS workshop; Richard unavailable
|

=== Week 8: 6-10 August ===
'''Biocircuits: 7 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Victoria (10-15 min)
* Research update (10-15 min)
* Instrument: Victor X3/BioTek H1MF
* Lab updates

'''Group meeting: 8 Aug (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 8 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

|

=== Week 9: 13-17 August ===
* Richard out all week
|- valign=top
|

=== Week 10: 20-24 August ===
'''Biocircuits: 22 Aug (Wed), 10 am - 12 pm'''
* Research presentation [non-MPP] (30-40 min)
* Enoch [non-MPP] (10-15 min)
* Research update [non-MPP] (10-15 min)
* Instrument: freezers/cold room
* Lab updates

'''NCS/Robotics: 22 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 23 Aug (Thu), 12-1:15'''
* Lea Goentoro (Bi)
<hr>
* MPP retreat, Sun-Tue
|

=== Week 11: 27-31 August ===
'''Biocircuits: 28 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instruments: Nanodrop/electroporator
* Lab updates

'''NCS/Robotics: 29 Aug (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 30 Aug (Thu), 12-1:15'''
* Open
<hr>
* Richard out of town on Fri
|

=== Week 12: 3-7 September ===
'''Biocircuits: 4 Sep (Tue), 10 am - 12 pm'''
* Marcella (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: gel rigs/gel imager
* Lab updates

'''NCS/Robotics: 5 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 6 Sep (Thu), 12-1:15'''
* Open
<hr>
* Institute holiday on Mon
|- valign=top
|

=== Week 13: 10-14 September ===
'''Biocircuits: 11 Sep (Tue), 10 am - 12 pm'''
* Zach (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: PCR machines/centrifuges
* Lab updates

'''NCS/Robotics: 12 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 13 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Fri
|

=== Week 14: 17-21 September ===
* Richard out all week
|
=== Week 15: 24-28 September ===
'''Biocircuits: 25 Sep (Tue), 10 am - 12 pm'''
* Enoch (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates

'''NCS/Robotics: 26 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 26 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Mon
|}

Vivek Mutalik, April 2012

2012-05-02T04:38:11Z

Edelossa: /* Schedule */

Vivek Mutalik will be visiting Caltech on 3 May (Thu).

=== Schedule ===
{{agenda begin}}
{{agenda item|7:30a|(optional) Breakfast with Richard and Domitilla (Ath)}}
{{agenda item|9:30a|Michael Elowtiz, 167 Broad}}
{{agenda item|10:15|Walk to Steele Lab; seminar prep}}
{{agenda item|10:30|Seminar, Steele Lab library}}
{{agenda item|11:30|Meeting with Paul Rothemund}}
{{agenda item|12:15|Murray group meeting, Steele Lab library}}
{{agenda item|1:15|Shaunak Sen}}
{{agenda item|2:00|Emzo de los Santos}}
{{agenda item|2:45|Open}}
{{agenda item|3:15|Open}}
{{agenda item|4:00|Open}}
{{agenda item|4:45|Open}}
{{agenda item|5:30|Depart for airport}}
{{agenda end}}

=== Abstract ===
<center>
'''Reliably Reuseable Standard Biological Parts'''

Vivek K Mutalik,PhD 
California Institute for Quantitative Biosciences (QB3) 
and Berkeley National Lab, Berkeley

3 May (Thu), 10:30-11:30 
114 Steele
</center>

The process of engineering biology is limited because many natural genetic elements function differently when reused in novel combinations or across changing contexts. Foundational synthetic biology research aims to standardize biological parts in support of more reliable reuse or develop computational methods that optimize individual parts to work within specific contexts. However, the capabilities realized by current methods remain poor. For example, while it is now possible to re-synthesize natural bacterial genomes, best available methods for engineering novel prokaryotic gene expression systems still require experimental validation on a single gene basis.

In this talk, I will present my recent work at the BIOFAB, an initiative that is committed to the proposition that a collection of well-characterized and refined genetic parts will eventually allow us to achieve this goal.In addition to the development of library of promoters (constitutaive and inducible) and terminators, We have devised a method that allows for reliable functional coupling of prokaryotic transcription and translation control elements thereby enabling a reliable expression of genes regardless of local gene context. Our hope is that these well characterized components will aid genetic engineers to achieve their own design goals faster and in a more predictable way.The datasets for these libraries are freely accessible via our BIoFAB registry.

Group Schedule, Spring 2012

2012-03-21T14:43:30Z

Edelossa: /* Week 10: 4 Jun - 8 Jun */

Group Schedule, Spring 2012

2012-03-21T14:43:12Z

Edelossa: /* Week 6: 7 May - 11 May */

Group Schedule, Spring 2012

2012-03-21T14:42:52Z

Edelossa: /* Week 3: 16-20 Apr */

Group Schedule, Spring 2012

2012-03-21T06:02:50Z

Edelossa: /* Week 10: 4 Jun - 8 Jun */

Group Schedule, Spring 2012

2012-03-21T06:01:35Z

Edelossa: /* Week 3: 16-20 Apr */

BE 150/Bi 250b Winter 2012

2012-02-26T02:18:05Z

Edelossa: /* 8 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MW 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
|}

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
*[http://www.cds.caltech.edu/~murray/courses/be150/wi12/problem1.nb problem1.nb]
*[http://www.cds.caltech.edu/~murray/courses/be150/wi12/chemotaxis.m chemotaxis.m]
|- valign=top
|

===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-stochastic_29Jan12.pdf|BFS, Ch 4}}: Stochastic behavior
* {{be150 pdf|wi12|caltech/bfs-class-random_29Jan12.pdf|BFS, App C}}: Probability and random processes (optional)

|
[https://www.cds.caltech.edu/~murray/wiki/images/6/68/Hw5-be.pdf BEHW5] [https://www.cds.caltech.edu/~murray/wiki/images/a/a7/Hw5-bio.pdf BIOHW5]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/runner.m runner.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/hw5.sbproj hw5.sbproj]
|- valign=top
|

===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| [https://www.cds.caltech.edu/~murray/wiki/images/7/75/Hw6-be.pdf BEHW6] [https://www.cds.caltech.edu/~murray/wiki/images/f/fe/Hw6-bio.pdf BIOHW6]
|- valign=top
|

===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/df/Hw7-be.pdf BEHW7] [https://www.cds.caltech.edu/~murray/wiki/images/d/d5/Hw7-bio.pdf BioHW7]
|- valign=top
|

===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}
 

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}}, {{be150 pdf|wi12|caltech/bfs-class-stochastic_29Jan12.pdf|Ch 4}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-random_29Jan12.pdf|App C}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

[[Category:Courses]]

File:Hw7-bio.pdf

2012-02-26T02:17:02Z

Edelossa:

File:Hw7-be.pdf

2012-02-26T02:16:47Z

Edelossa:

Group Schedule, Winter 2012

2012-02-07T23:59:22Z

Edelossa: /* Week 7: 13-17 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Vanessa (10-15 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab organization, round II
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 12 Jan (Thu), 1-3 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Safety briefing @ 4:00 pm (30-40 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 3-5 pm'''
* Anu (10-15 min)
* Enoch (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
<hr>
UTRC visit on 17 Jan (Tue)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Group meeting: 23 Jan (Mon), 12-1:15'''
* Necmiye
'''Robotics: 24 Jan (Tue), 1-3 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Dan (10-15 min)
* Lab updates
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Elisa (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Ufuk
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Chris Kempes
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Anu (30-40 min)
* Marcella (10-15 min)
* Paul (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Pavithra (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

BE 150/Bi 250b Winter 2012

2012-01-31T02:21:09Z

Edelossa: /* 5 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MW 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
*[http://www.cds.caltech.edu/~murray/courses/be150/wi12/problem1.nb problem1.nb]
*[http://www.cds.caltech.edu/~murray/courses/be150/wi12/chemotaxis.m chemotaxis.m]
|- valign=top
|

===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

BE 150/Bi 250b Winter 2012

2012-01-31T02:20:17Z

Edelossa: /* 5 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MW 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
*[https://www.cds.caltech.edu/~murray/courses/be150/wi12/problem1.nb problem1.nb]
*[https://www.cds.caltech.edu/~murray/courses/be150/wi12/chemotaxis.m chemotaxis.m]
|- valign=top
|

===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

BE 150/Bi 250b Winter 2012

2012-01-31T02:19:54Z

Edelossa: /* 5 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MW 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
*[www.cds.caltech.edu/~murray/courses/be150/wi12/problem1.nb problem1.nb]
*[www.cds.caltech.edu/~murray/courses/be150/wi12/chemotaxis.m chemotaxis.m]
|- valign=top
|

===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

BE 150/Bi 250b Winter 2012

2012-01-31T02:19:19Z

Edelossa: /* 5 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MW 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
*[www.cds.caltech.edu:~murray/public_html/courses/be150/wi12/problem1.nb problem1.nb]
*[www.cds.caltech.edu:~murray/public_html/courses/be150/wi12/chemotaxis.m chemotaxis.m]
|- valign=top
|

===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

BE 150/Bi 250b Winter 2012

2012-01-31T02:17:59Z

Edelossa: /* 5 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MW 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
|- valign=top
|

===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

File:Bi250bHw4.pdf

2012-01-31T02:17:31Z

Edelossa:

File:Be150hw4.pdf

2012-01-31T02:17:10Z

Edelossa: uploaded a new version of "File:Be150hw4.pdf"

File:Be150hw4.pdf

2012-01-31T02:16:31Z

Edelossa:

BE 150/Bi 250b Winter 2012

2012-01-26T06:50:43Z

Edelossa: /* 4 */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 18 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be250c pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|Ch 3}},  {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Plant clocks/circadian rhythm
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m ddeoscillate.m]
|- valign=top
|

===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* BFS, Sec 5.4: Bacterial chemotaxis
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000.
| HW #4
|- valign=top
|
===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

File:Hw3.pdf

2012-01-26T06:48:47Z

Edelossa: uploaded a new version of "File:Hw3.pdf"

File:Hw3bio.pdf

2012-01-26T06:48:22Z

Edelossa: uploaded a new version of "File:Hw3bio.pdf"

File:Hw3bio.pdf

2012-01-26T06:46:59Z

Edelossa: uploaded a new version of "File:Hw3bio.pdf"

File:Hw3bio.pdf

2012-01-26T06:41:53Z

Edelossa:

File:Hw3.pdf

2012-01-26T06:41:31Z

Edelossa: uploaded a new version of "File:Hw3.pdf"

BE 150/Bi 250b Winter 2012

2012-01-18T23:21:55Z

Edelossa: /* Lecture Schedule */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 18 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 17 Jan 2012: created a [http://piazza.com/class#winter2012/be150bi250b Piazza] account for the class. Please use this for sending questions to the TAs.
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 18 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}}, {{be250c pdf|wi12|caltech/bfs-class-dynamics_08Jan12.pdf|Ch 3}},  {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* Alon, Ch 4: The feed-forward loop network motif
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems

Papers discussed in lecture:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross. ''Molecular Systems Biology'', 5:272, 2009.
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
* Optional: plant clocks/circadian rhythm
Background slides on modeling and stability
* [http://www.cds.caltech.edu/~murray/books/AM08/pdf/bfs09-L1_modeling_26Aug09.pdf Modeling of core processes]
* [http://www.cds.caltech.edu/~murray/courses/cds101/fa08/pdf/L2-1_stability_h.pdf Dynamics and stability in ODEs]
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
| HW #3
|- valign=top
|
===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* BFS, Sec 5.4: Bacterial chemotaxis
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000.
| HW #4
|- valign=top
|
===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

File:Hw1.pdf

2012-01-12T20:55:53Z

Edelossa: uploaded a new version of "File:Hw1.pdf"

BE 150/Bi 250b Winter 2012

2012-01-12T19:06:05Z

Edelossa: /* Lecture Schedule */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 0 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 8 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|Ch 2}}, {{be250c pdf|wi12|caltech/bfs-class-dynamics_08Jan12.pdf|Ch 3}},  {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers Discussed in Lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.


BE 150:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_08Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems
| HW #2
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
* Optional: plant clocks/circadian rhythm
Background slides on modeling and stability
* [http://www.cds.caltech.edu/~murray/books/AM08/pdf/bfs09-L1_modeling_26Aug09.pdf Modeling of core processes]
* [http://www.cds.caltech.edu/~murray/courses/cds101/fa08/pdf/L2-1_stability_h.pdf Dynamics and stability in ODEs]
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
| HW #3
|- valign=top
|
===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* BFS, Sec 5.4: Bacterial chemotaxis
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000.
| HW #4
|- valign=top
|
===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

BE 150/Bi 250b Winter 2012

2012-01-12T18:56:32Z

Edelossa: /* Lecture Schedule */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 0 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 8 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|Ch 2}}, {{be250c pdf|wi12|caltech/bfs-class-dynamics_08Jan12.pdf|Ch 3}},  {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers Discussed in Lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. ''Nature'', 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrel. ''Nature'', 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.


BE 150:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_08Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems
| HW #2
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
* Optional: plant clocks/circadian rhythm
Background slides on modeling and stability
* [http://www.cds.caltech.edu/~murray/books/AM08/pdf/bfs09-L1_modeling_26Aug09.pdf Modeling of core processes]
* [http://www.cds.caltech.edu/~murray/courses/cds101/fa08/pdf/L2-1_stability_h.pdf Dynamics and stability in ODEs]
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
| HW #3
|- valign=top
|
===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* BFS, Sec 5.4: Bacterial chemotaxis
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000.
| HW #4
|- valign=top
|
===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

BE 150/Bi 250b Winter 2012

2012-01-12T18:55:36Z

Edelossa: /* Lecture Schedule */

{| width=100%
|-
| colspan=2 align=center |
Systems Biology__NOTOC__
|- valign=top
| width=50% |
'''Instructors'''
* Michael Elowitz (Bi/BE/APh)
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 101 Kerckhoff
| width=50% |
'''Teaching Assistants'''
* Emzo de los Santos
* Vanessa Jonsson
|}

=== Course Description ===
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

===Announcements ===
* 0 Jan 2012: updated copy of BFS, Ch 2 has been posted
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
* 4 Jan 2012: course time and location have been updated
* 11 Dec 2011: updated syllabus (should be final now)
* 19 Nov 2011: added TAs; updated schedule
* 2 Oct 2011: web page creation

=== Textbook ===

The primary text for the BE 150 and Bi 250b is
{|
|- valign=top
| align=right |  [Alon] 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
|}
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
{|
|- valign=top
| align=right |  [BFS] 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
* Note: these notes are being written and will be updated during the course
* Class version (Caltech access only, 8 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|Ch 2}}, {{be250c pdf|wi12|caltech/bfs-class-dynamics_08Jan12.pdf|Ch 3}},  {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
|}

The following additional texts and notes may be useful for some students:
{|
|- valign=top
| align=right |  [FBS] 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.
|- valign=top
| align=right |  [Klipp] 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009.
|- valign=top
| align=right |  [Strogatz] 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.
|}

=== Grading ===
The ﬁnal grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

=== Collaboration Policy ===
Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reﬂect your understanding of the subject matter at the time of writing.

=== Lecture Schedule ===
There will be two 1-hour lectures each week, as well as a 1-hour recitation section.
{| width=100% border=1 cellspacing=0 cellpadding=5
|-
| '''Week'''
| '''Date'''
| width=40% | '''Topic'''
| width=40% | '''Reading'''
| '''Homework'''
|- valign=top
|- valign=top
|
===== 1 =====
| 4 Jan 6 Jan+ MBE/RMM
| Course overview
* Principles in systems biology
Recitation section:
* MATLAB tutorial (optional)
[https://www.cds.caltech.edu/~murray/wiki/images/6/64/MatlabTutorial.pdf Matlab Tutorial]
|
Bi 250b:
* Alon, Ch 1: Introduction

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.1: Modeling Techniques
|
|- valign=top
|
===== 2 =====
| 9 Jan 11 Jan+ MBE
| Gene circuit dynamics
* Core processes in cells
* Modeling transcription, translation and regulation using ODEs
* Negative auto-regulation
|
Bi 250b:
* Alon, Ch 2: Transcription networks : basic concepts
* Alon, Ch 3: Autoregulation : a network motif

BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers Discussed in Lecture:
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in Escherichia coli ], Gardner TS, Cantor CR, Collins JJ. "Nature", 403:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrel. "Nature", 426:460-465, 2003.
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosedMain.m lacIClosedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpen.m lacIOpen.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIClosed.m lacIClosed.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggleMain.m toggleMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/toggle.m toggle.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeedMain.m posFeedMain.m]
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/posFeed.m posFeed.m]
|- valign=top
|

===== 3 =====
| <s>16 Jan</s> 18 Jan* 20 Jan* RMM
| Circuit motifs
* Feedforward loops (FFLs)
* Phosphorylation cascades
* Two-component signaling systems
* Sequestration for ultrasensitivty
|
Bi 250b:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.


BE 150:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE. ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_08Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptoinal regulation
** Section 2.5: cellular subsystems
| HW #2
|- valign=top
|

===== 4 =====
| 23 Jan 25 Jan MBE
| Biological clocks: how to produce oscillations in cells
* Synthetic oscillators (repressilator, dual-feedback oscillator)
* Circadian clocks in cyanobacteria
* Optional: plant clocks/circadian rhythm
Background slides on modeling and stability
* [http://www.cds.caltech.edu/~murray/books/AM08/pdf/bfs09-L1_modeling_26Aug09.pdf Modeling of core processes]
* [http://www.cds.caltech.edu/~murray/courses/cds101/fa08/pdf/L2-1_stability_h.pdf Dynamics and stability in ODEs]
|
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516-519, 2008.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
| HW #3
|- valign=top
|
===== 5 =====
| 30 Jan 1 Feb RMM
| Robustness
* Chemotaxis and perfect adaptation
* Fold change detection
* Controls analysis of robustness
|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* BFS, Sec 5.4: Bacterial chemotaxis
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000.
| HW #4
|- valign=top
|
===== 6 =====
| 6 Feb* 8 Feb RMM
| Noise
* Random processes
* Intrinsic and extrinsic noise
* Stochastic modeling: master equation, SSA
|
* BFS, Ch 4 and App C
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain. ''Science'', 297(5584):1183-1186, 2002.
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie. ''Nature'', 440:358-362, 2006.
| HW #5
|- valign=top
|
===== 7 =====
| 13 Feb+ 15 Feb MBE
| Burstiness in gene expression and signalling
* Birth-death processes
|
* [http://www.nature.com/ng/journal/v36/n2/full/ng1293.html Dynamics of the p53-Mdm2 feedback loop in individual cells], Galit Lahav ''et al''. ''Nature Genetics'', 36:147-150, 2004.
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz. Nature 455:485-490, 2008.
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''. ''Nature'', 466(7303):267-271, 2010
| HW #6
|- valign=top
|
===== 8 =====
| <s>20 Feb</s> 22 Feb 24 Feb RMM
| Patterning
* Morphogenesis
* Robust morphagen gradient
* Proportionality and scaling
|
* Alon, Ch 8: Robust Patterning in Development
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai. ''PNAS'', 107(15):6924-6929, 2010.
| HW #7
|- valign=top
|
===== 9 =====
| 27 Feb 29 Feb*+ MBK
| Modeling of complex biological networks (Mary Kennedy)
|
* [http://www.ncbi.nlm.nih.gov/pubmed/20168991 A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II]. Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). PLoS Comput Biol 6, e1000675.
* [http://www.ncbi.nlm.nih.gov/pubmed/20151023 Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces]. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.-C.J., Baden, S.B., Sejnowski, T.J., and Stiles, J.R. (2008). SIAM Journal on Scientific Computing 30, 3126-3149.
* [http://www.ncbi.nlm.nih.gov/pubmed/12447978 Complexity of calcium signaling in synaptic spines]. Franks, K.M., and Sejnowski, T.J. (2002). Bioessays 24, 1130-1144.
| 
|- valign=top
|

===== 10 =====
| 5 Mar 7 Mar MBE
| Fine grain patterns
* Lateral inhibition
* Notch-delta
|
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8

|}

== Old Announcements ==

[[Category:Courses]]

Group Schedule, Winter 2012

2011-12-10T03:55:25Z

Edelossa: /* Week 8: 20-24 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Open (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Necmiye (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
'''Group meeting: 25 Jan (Wed), 12-1:15'''
* Necmiye
'''Robotics: 25 Jan (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Open (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Open
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2011-12-09T17:28:22Z

Edelossa: /* Week 4: 23-27 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Open (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Open (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Emzo (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 25 Jan (Wed), 12-1:15'''
* Necmiye
'''Robotics: 25 Jan (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Open (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Open
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Safety briefing (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Open (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Open
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Fall 2011

2011-09-26T04:56:58Z

Edelossa: /* Week 6: 31 Oct - 4 Nov */

Group Schedule, Fall 2011

2011-09-26T04:56:41Z

Edelossa: /* Week 9: 21-25 Nov */

Group Schedule, Fall 2011

2011-09-26T04:56:15Z

Edelossa: /* Week 2: 3-7 Oct */