Murray Wiki - User contributions [en]

Chelsea Hu, Apr 2018

2018-04-06T06:06:05Z

Vsinghal: /* Tuesday */

Chelsea Hu, a PhD student working with Julius Lucks at Northwestern, is going to be visiting on 9-10 Apr. Sign up below for a time to meet with her.

=== Monday ===
* ~9:15 am: Richard, 107 Steele
* 10 am: Biocircuits group meeting
* 12 pm: Lunch with current postdocs
* 1:30 pm: Andy
* 2:15 pm: Joe
* 3:00 pm: Sam
* 3:45 pm: Open
* 4:30 pm: Open

=== Tuesday ===
* 9:30 am: Pradeep Ramesh <pramesh@caltech.edu>
* 10:15 am: Vipul
* 11:00 am: Open
* 12:00 pm: IST lunch bunch or lunch on your own
* Leave afternoon open for now
* 4:00 pm: Hold for BBE seminar
* 5:00 pm: Niles Pierce, 165 Broad
* 5:30 pm: Richard, 107 Steele

Mary Dunlop, Oct 2017

2017-10-18T21:49:39Z

Vsinghal: /* Friday */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Anandh - 24/7/365

| width=33% |

==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Ania - 1pm - 4pm
* Vipul - available 1-5p
* Name - availability
| width=33% |

==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available 1-5p
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Ania
* 10:15 am: Vipul/Anandh (system ID etc)
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

Mary Dunlop, Oct 2017

2017-10-18T21:44:55Z

Vsinghal: /* Topic #3: TX-TL (modeling and experiments) */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Anandh - 24/7/365

| width=33% |

==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Ania - 1pm - 4pm
* Vipul - available 1-5p
* Name - availability
| width=33% |

==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available 1-5p
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Ania
* 10:15 am: Vipul
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

Mary Dunlop, Oct 2017

2017-10-18T21:44:42Z

Vsinghal: /* Topic #2: feedback control of biological systems */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Anandh - 24/7/365

| width=33% |

==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Ania - 1pm - 4pm
* Vipul - available 1-5p
* Name - availability
| width=33% |

==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available all day
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Ania
* 10:15 am: Vipul
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

Mary Dunlop, Oct 2017

2017-10-18T21:43:53Z

Vsinghal: /* Topic #2: feedback control of biological systems */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Anandh - 24/7/365

| width=33% |

==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Ania - 1pm - 4pm
* Vipul - all day
* Name - availability
| width=33% |

==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available all day
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Ania
* 10:15 am: Vipul
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

Mary Dunlop, Oct 2017

2017-10-18T21:42:50Z

Vsinghal: /* Friday */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Anandh - 24/7/365

| width=33% |

==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Ania - 1pm - 4pm

| width=33% |

==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available all day
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Ania
* 10:15 am: Vipul
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

Mary Dunlop, Oct 2017

2017-10-18T21:37:46Z

Vsinghal: /* Topic #3: TX-TL (modeling and experiments) */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Name - availability

| width=33% |
==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Name - availability

| width=33% |
==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available all day
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Open
* 10:15 am: Open
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

May 2017 meeting schedule

2017-05-14T23:45:23Z

Vsinghal: /* 21 May (Sun) */

Richard will be in town several different times in May. Please sign up for a time to meet below. Please note that these are likely the last "sabbatical" meetings until Richard returns to Pasadena in early July. __NOTOC__

{| border=1 width=100%
|- valign=top
| width=33% |
| width=33% |
==== 15 May (Mon) ====
* 9:30 am: William
* 10:15 am: Miki
* 11:00 am: Faculty meeting
* 11:30 am: Andy
* 12:15 pm: Lunch
* 1:30 pm: Sam
* 2:15 pm: Reed
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Ania
* 5:30 pm: Anandh
* 6:15 pm: Done for the day

| width=33% |

==== 16 May (Tue)====
* 9:30 am: Yong
* 10:15 am: Tung
* 11:00 am: Faculty meeting
* 12:00 pm: Lunch
* 1:30 pm: Depart

|- valign=top
| width=33% |

====21 May (Sun) ====
* 1:45 pm: Sofie
* 2:30 pm: Ioannis
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Rory
* 5:00 pm: Tony
* 5:45 pm: Vipul
* 6:30 pm: Done for the day

| width=33% |

==== 22 May (Mon) ====
* 10:15 am: Mark
* 11:00 am: Cindy
* 11:45 am: Lunch
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Swati + Reed
* 2:45 pm: Off campus
* 4:15 pm: James
* 5:00 pm: Non-Caltech meetings
* 6:30 pm: Done for the day

| width=33% |

==== 23 May (Tue) ====
* 9:30 am: Faculty discussion
* 10:30 am: Hold (Susan)
* 11:30 am: Lunch
* 12:00 pm: Telecon
* 1:00 pm: Anu thesis defense
* 3:00 pm: Open (short slot)
* 3:30 pm: Depart

|- valign=top
| width=33% |

====28 May (Sun) ====
* 1:45 pm: Richard C
* 2:30 pm: George
* 3:15 pm: Andy
* 4:00 pm: Done for the day
| width=33% |

====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Sumanth
* 4:00 pm: Done for the day
| width=33% |

==== 30 May (Tue) ====
* 9:30 am: Shan
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Andrey
* 3:00 pm: Depart
|}

May 2017 meeting schedule

2017-05-14T23:45:13Z

Vsinghal: /* 15 May (Mon) */

Richard will be in town several different times in May. Please sign up for a time to meet below. Please note that these are likely the last "sabbatical" meetings until Richard returns to Pasadena in early July. __NOTOC__

{| border=1 width=100%
|- valign=top
| width=33% |
| width=33% |
==== 15 May (Mon) ====
* 9:30 am: William
* 10:15 am: Miki
* 11:00 am: Faculty meeting
* 11:30 am: Andy
* 12:15 pm: Lunch
* 1:30 pm: Sam
* 2:15 pm: Reed
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Ania
* 5:30 pm: Anandh
* 6:15 pm: Done for the day

| width=33% |

==== 16 May (Tue)====
* 9:30 am: Yong
* 10:15 am: Tung
* 11:00 am: Faculty meeting
* 12:00 pm: Lunch
* 1:30 pm: Depart

|- valign=top
| width=33% |

====21 May (Sun) ====
* 1:45 pm: Sofie
* 2:30 pm: Ioannis
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Rory
* 5:00 pm: Tony
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=33% |

==== 22 May (Mon) ====
* 10:15 am: Mark
* 11:00 am: Cindy
* 11:45 am: Lunch
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Swati + Reed
* 2:45 pm: Off campus
* 4:15 pm: James
* 5:00 pm: Non-Caltech meetings
* 6:30 pm: Done for the day

| width=33% |

==== 23 May (Tue) ====
* 9:30 am: Faculty discussion
* 10:30 am: Hold (Susan)
* 11:30 am: Lunch
* 12:00 pm: Telecon
* 1:00 pm: Anu thesis defense
* 3:00 pm: Open (short slot)
* 3:30 pm: Depart

|- valign=top
| width=33% |

====28 May (Sun) ====
* 1:45 pm: Richard C
* 2:30 pm: George
* 3:15 pm: Andy
* 4:00 pm: Done for the day
| width=33% |

====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Sumanth
* 4:00 pm: Done for the day
| width=33% |

==== 30 May (Tue) ====
* 9:30 am: Shan
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Andrey
* 3:00 pm: Depart
|}

May 2017 meeting schedule

2017-05-09T21:55:59Z

Vsinghal: /* 15 May (Mon) */

Richard will be in town several different times in May. Please sign up for a time to meet below. Please note that these are likely the last "sabbatical" meetings until Richard returns to Pasadena in early July. __NOTOC__

{| border=1 width=100%
|- valign=top
| width=33% |
| width=33% |
==== 15 May (Mon) ====
* 9:30 am: Open
* 10:15 am: Open
* 11:00 am: Faculty meeting
* 11:30 am: Andy
* 12:15 pm: Lunch
* 1:30 pm: Sam
* 2:15 pm: Reed
* 3:00 pm: Vipul
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Ania
* 5:30 pm: Anandh
* 6:15 pm: Done for the day

| width=33% |

==== 16 May (Tue)====
* 9:30 am: Yong
* 10:15 am: Tung
* 11:00 am: Faculty meeting
* 12:00 pm: Lunch
* 1:30 pm: Depart
* 12:00 pm: Lunch
* 1:30 pm: Depart

|- valign=top
| width=33% |

====21 May (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Ioannis
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=33% |

==== 22 May (Mon) ====
* 10:15 am: Mark
* 11:00 am: Cindy
* 11:45 am: Lunch
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Swati + Reed
* 2:45 pm: Off campus
* 4:15 pm: James
* 5:00 pm: Non-Caltech meetings
* 6:30 pm: Done for the day

| width=33% |

==== 23 May (Tue) ====
* 9:30 am: Faculty discussion
* 10:30 am: Hold (Susan)
* 11:30 am: Lunch
* 12:00 pm: Telecon
* 1:00 pm: Anu thesis defense
* 3:00 pm: Terri (?)
* 3:30 pm: Depart

|- valign=top
| width=33% |

====28 May (Sun) ====
* 1:45 pm: Richard C
* 2:30 pm: George
* 3:15 pm: Andy
* 4:00 pm: Done for the day
| width=33% |

====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Sumanth
* 4:00 pm: Done for the day
| width=33% |

==== 30 May (Tue) ====
* 9:30 am: Shan
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Andrey
* 3:00 pm: Depart
|}

Apr 2017 meeting schedule

2017-04-12T15:06:50Z

Vsinghal: /* 20 Apr (Thu) */

Richard will be in town 19-21 Apr. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 19 Apr (Wed) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Admin meeting (SP, MC)
* 11:15 am: Open
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Candidacy exam
* 3:00 pm: CDS tea
* 3:45 pm: Open
* 4:30 pm: Admin meeting (LL)
* 5:00 pm: Open (tentative)
* 5:45 pm: Associates event

| width=25% |

==== 20 Apr (Thu) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Mark
* 11:15 am: Tony Fragoso
* 12:00 pm: Lunch
* 1:30 pm: EBRC telecon
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Vipul
* 4:45 pm: Break
* 5:00 pm: Open
* 5:45 pm: Open
* 6:00 pm: Open (if needed)
* 6:45 pm: Open (if needed)
* 7:30 pm: Done for the day

| width=25% |

==== 21 Apr (Fri) ====
* 9:15 am: Open
* 10:00 am: JPL CIF meeting
* 11:15 am: Open
* 12:00 pm: Lunch
* 12:45 pm: Open
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Break
* 3:15 pm: Open
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Done for the day

| width=25% |

==== 23 Apr (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Shan
* 6:30 pm: Done for the day
|}

Mar 2017 meeting schedule

2017-02-28T07:58:29Z

Vsinghal: /* 3 Mar (Fri) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Reed
* 11:45 am: Shaobin
* 12:30 pm: Lunch
* 1:00 pm: Hold: DARPA telecon
* 2:00 pm: Open
* 2:45 pm: Mark
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: William
* 6:30 pm: Done for the day

| width=25% |

==== 5 Mar (Sun) ====
* 1:45 pm: Anandh
* 2:30 pm: Andrey
* 3:15 pm: Sam
* 4:00 pm: Break
* 4:15 pm: Ioannis
* 5:00 pm: Open
* 5:45 pm: Sumanth Dathathri
* 6:30 pm: Done for the day

| width=25% |

==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Yong
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:30 pm: Hold: DARPA telecon
* 1:30 pm: Richard C
* 2:15 pm: Vipul
* 3:00 pm: Miki
* 3:45 pm: Break
* 4:00 pm: James
* 4:45 pm: Karena
* 5:30 pm: Ania
* 6:15 pm: Done for the day

| width=25% |

==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:15 am: Tung
* 11:00 am: Hold: DARPA telecon
* 12:00 pm: Lunch
* 12:45 pm: Hold
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

Mar 2017 meeting schedule

2017-02-28T07:58:18Z

Vsinghal: /* 6 Mar (Mon) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Reed
* 11:45 am: Shaobin
* 12:30 pm: Lunch
* 1:00 pm: Hold: DARPA telecon
* 2:00 pm: Vipul
* 2:45 pm: Mark
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: William
* 6:30 pm: Done for the day

| width=25% |

==== 5 Mar (Sun) ====
* 1:45 pm: Anandh
* 2:30 pm: Andrey
* 3:15 pm: Sam
* 4:00 pm: Break
* 4:15 pm: Ioannis
* 5:00 pm: Open
* 5:45 pm: Sumanth Dathathri
* 6:30 pm: Done for the day

| width=25% |

==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Yong
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:30 pm: Hold: DARPA telecon
* 1:30 pm: Richard C
* 2:15 pm: Vipul
* 3:00 pm: Miki
* 3:45 pm: Break
* 4:00 pm: James
* 4:45 pm: Karena
* 5:30 pm: Ania
* 6:15 pm: Done for the day

| width=25% |

==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:15 am: Tung
* 11:00 am: Hold: DARPA telecon
* 12:00 pm: Lunch
* 12:45 pm: Hold
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

Mar 2017 meeting schedule

2017-02-27T16:46:21Z

Vsinghal: /* 3 Mar (Fri) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Reed
* 11:45 am: Shaobin
* 12:30 pm: Lunch
* 1:00 pm: Hold: DARPA telecon
* 2:00 pm: Vipul
* 2:45 pm: Mark
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: Sumanth Dathathri
* 6:30 pm: Done for the day

| width=25% |

==== 5 Mar (Sun) ====
* 1:45 pm: Anandh
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Yong
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:30 pm: Hold: DARPA telecon
* 1:30 pm: Richard C
* 2:15 pm: Ioannis
* 3:00 pm: Miki
* 3:45 pm: Break
* 4:00 pm: James
* 4:45 pm: Karena
* 5:30 pm: Ania
* 6:15 pm: Done for the day

| width=25% |

==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:15 am: Tung
* 11:00 am: Hold: DARPA telecon
* 12:00 pm: Lunch
* 12:45 pm: Hold
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

Henrike Niederholtmeyer, Jan 2017

2017-01-18T05:52:07Z

Vsinghal: /* 24 Jan (Tue) */

Henrike Niederholtmeyer will visit Caltech on 23-24 January 2017 to help us out with some microfluidics work we are doing. If you would like to meet with her, please sign up below.

=== Schedule ===
{| border=1
|- valign=top
| width=50% |
==== 23 Jan (Mon) ====
* Arrive sometime before noon
* 12 pm: Michaelle Mayalu seminar, 121 Annenberg (lunch)
* 1 pm: meet with Mark Prator and Reed McCardell
* 3 pm: TX-TL extract prep discussion: Miki, Yong, Sam
* 4 pm: Open
* 4:45 pm: Open
* 5:30 pm: Meet Richard in 107 Steele. Walk to dinner.

| width=50% |
==== 24 Jan (Tue) ====
* Morning: work with Mark and Reed
* 12 pm: Seminar in 121 Annenberg (abstract below)
* 1 pm: Lunch with Mark and Reed
* 2 pm: Open
* 2:45 pm: [[Jan 2017 meeting schedule|Richard]]
* 3:30 pm: Yong
* 4:15 pm: Vipul
* 5:00 pm: Done for the day
|}

=== Seminar info ===
<center>
'''Gene expression in a synthetic tissue of artificial cells'''

Henrike Niederholtmeyer and Neal K. Devaraj 
Department of Chemistry and Biochemistry, University of California, San Diego, USA

Tuesday, January 24, 2017 
12:00 pm, 121 Annenberg
</center>

Living cells in tissues or biofilms communicate with neighboring cells through chemical and mechanical signals allowing them to organize spatially. To reduce the complexity of these natural systems we create synthetic tissues of non-living artificial cells. We use a microfluidic method to produce porous capsules with an artificial “nucleus” where DNA is immobilized. Upon addition of transcription and translation reagents capsules synthesize proteins, which localize to nuclei containing binding sites. Neighboring capsules communicate by producing transcription factors that diffuse through the artificial tissue suggesting that it can serve as a model system to study pattern formation.

Michaëlle Mayalu, Jan 2017

2017-01-18T05:49:31Z

Vsinghal: /* 24 Jan (Tue) */

Michaëlle Mayalu from MIT will visit on 23-24 January. __NOTOC__

=== Schedule ===
{| border=1
|- valign=top
| width=50% |
==== 23 Jan (Mon) ====
* 8 am: Breakfast with Richard (Ath)
* 9 am: Anandh (103 Steele?)
* 10 am: DARPA Biological Control program meeting, 168 Broad (walk over with Richard)
<hr>
* 12 pm: Seminar, 121 Annenberg (abtract below)
* 1 pm: lunch with TBD
<hr>
* 2 pm: Open
* 2:45 pm: Open
* 3:30 pm: Open
* 4:15 pm: Aaron Ames, 266 Gates-Thomas
<hr>
* 5:30 pm: Meet Richard in 107 Steele. Walk to dinner.

| width=50% |

==== 24 Jan (Tue) ====
* 9:00 am: Open
* 9:45 am: Open
* 10:30 am: Open
* 11:15 am: Open
<hr>
* 12 pm: Henrike Niederholtmeyer seminar, 121 Annenberg
<hr>
* 1:00 pm: Open
* 1:45 pm: [[Jan 2017 meeting schedule|Richard]]
* 2:30 pm: John Doyle
* 3:15 pm: Vipul (Keck 222)
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Done for the day
|}

=== Seminar info ===
<center>
'''Reduced-order Systems Approach to Prediction of Emergent Behaviors'''

Michaëlle N. Mayalu 
Massachusetts Institute of Technology

Monday, January 23, 2017 
12-1 pm, 121 Annenberg
</center>

Increased understanding of the physical and chemical principles that drive a biological process has led to the development of mathematical formulations that are used to simulate a rich variety of responses. As a result, a vast amount of simulation data can be created for analyzing single cell behavior numerically. However complex and extensive mechanisms involved in emergent behavior of multiple interacting cells may become intractable due to mathematical and computational complexity. This talk will address how we can exploit simulation data describing the nonlinear dynamics of single cell behavior to create a reduced- order linear state equation in latent variable space. Furthermore, the linearity of the reduced-order latent variable state equation allows for the superposition of multiple solutions to predict emergent behaviors of interacting cells.
The linear latent state equation describing the nonlinear dynamics of single cell is created in two steps. First the original independent state variables are augmented by adding auxiliary variables necessary to “sufficiently inform” the single cell nonlinear dynamics. This creates a high-dimensional state space where a linear description of the nonlinear system can be found. Second, latent variables extracted from the high-dimensional state space and used to create the reduced-order linear equation. While the resultant latent state equation is linear, complex nonlinearities are embedded in the compact model, leading to precise and global linearization of nonlinear dynamics. Furthermore, in order to predict multi-cell emergent behavior, the reduced-order linear models of single cells are used as agents in a comprehensive agent-based framework based on linear superposition of mutually shared variables. The approach is motivated by emergent behaviors in collective cell migration in order to gain insight for the study and control cancer metastasis and wound healing. However, the general approach may be applied to systems of interacting nonlinear agents, which would otherwise be prohibitively complex to compute.

Michaëlle N. Mayalu is a Ph.D. student at the Brit and Alex d’Arbeloff Laboratory for Information Systems and Technology in the Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge MA. She received the B.S., and M.S., degrees in Mechanical Engineering in 2010 and 2012 from Massachusetts Institute of Technology. Her thesis work is focused on modeling and predicting biological systems behavior by drawing on aspects of dynamic modeling and simulation, data analysis, statistical learning and control theory. Her thesis supervisor is Professor H. Harry Asada in the Department of Mechanical Engineering at MIT.

Jan 2017 meeting schedule

2017-01-13T20:41:46Z

Vsinghal: /* 23 Jan (Mon) */

Richard will be in town 20-24 Jan. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 20 Jan (Fri) ====
* Richard arrives on campus ~9:45 am
* 10:15 am: Mark
* 11:00 am: Yong
* 11:45 am: Anandh
* 12:30 pm: Lunch
* 1:30 pm: Yong and Frances A
* 2:30 pm: Sumanth Dathathri
* 3:15 pm: Reed
* 4:00 pm: Miki
* 4:45 pm: Break
* 5:00 pm: Cindy
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 22 Jan (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Rory
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 23 Jan (Mon) ====
* 8:00 am: Michaelle
* 9:00 am: Hold: Jaymie
* 10:00 am: BioCon meeting
* 12:00 pm: Seminar ([[Michaëlle Mayalu, Jan 2017|Michaelle]])
* 1:00 pm: Hold until needed
* 1:45 pm: Vipul
* 2:30 pm: CDS faculty meeting
* 4:15 pm: Tony Fragoso
* 5:00 pm: Ania
* 5:45 pm: William
* 6:30 pm: Dinner with visitors

| width=25% |

==== 24 Jan (Tue) ====
* 9:45 am: Henrike
* 10:30 am: Karena
* 11:15 am: Tung
* 12:00 pm: Seminar ([[Henrike Niederholtmeyer, Jan 2017|Henrike]])
* 1:15 pm: [[Michaëlle Mayalu, Jan 2017|Michaelle]]
* 2:00 pm: Anu
* 2:45 pm: [[Henrike Niederholtmeyer, Jan 2017|Henrike]]
* 3:30 pm: Depart for airport
|}

Nov 2016 meeting schedule

2016-11-03T21:08:12Z

Vsinghal: /* 14 Nov (Mon) */

Richard will be in town 13-16 Nov. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |

==== 13 Nov (Sun) ====
 
 
<hr>
* 2 pm: Hold until needed
* 2:45 pm: Hold until needed
* 3:30 pm: Hold until needed
* 4:15 pm: Break
* 5:00 pm: Hold until needed
* 5:45 pm: Hold until needed
* 6:30 pm: Done for the day

| width=25% |

==== 14 Nov (Mon) ====
* 10:30 am: Open
* 11:15 am: Tung
<hr>
* 1:30 pm: Vipul
* 2:15 pm: Andrey Shur
* 3:00 pm: Shaobin
* 3:45 pm: Break
* 4:00 pm: Miki
* 4:45 pm: Open
* 5:30 pm: Anu
* 6:15 pm: Done for the day
| width=25% |

====15 Nov (Tue) ====
* 10:30 am: Mark
* 11:15 am: Reed
<hr>
* 1:30 pm: Open
* 2:15 pm: Karena Cai
* 3:00 pm: Tony Fragoso
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Cindy
* 5:30 pm: Open
* 6:15 pm: Done for the day
| width=25% |

==== 16 Nov (Wed) ====
* 10:30 am: Ania
* 11:15 am: Open
<hr>
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: CDS tea
* Depart for airport at ~4 pm
|}

Sep/Oct 2016 meeting schedule

2016-09-24T04:24:08Z

Vsinghal: /* 2 Oct (Sun) */

Richard will be in town 29 Sept - 3 Oct 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 29 Sep (Thu) ====
* Flying in from SF in the morning
* 1:00 pm: George
* 1:45 pm: Andrey
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Richard C.
* 4:15 pm: Sam
* 5:00 pm: Mark
* 5:45 pm: Break
* 6:00 pm: Reed
* 6:45 pm: Rory
* 7:30 pm: Done for the day
| width=25% |

==== 30 Sep (Fri) ====
* Morning: busy with other meetings/phone calls
* 1:30-3:30 pm: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy, Jining)
* 3:30 pm: Miki
* 4:30 pm: break
* 4:45 pm: Andrew
* 5:30 pm: Anandh
* 6:15 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: YONG
* 2:30 pm: Vipul
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Sumanth
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 3 Oct (Mon) ====
* 10 am - 12 pm: DARPA BioCon meeting
* 12:00 pm: Candidacy exam
* 1:45 pm: Jaymie
* 2:45 pm: Tung
* 3:30 pm: Shaobin
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Daniel N
* 6:00 pm: William
* 6:45 pm: Ania
* 7:30 pm: Done for the day
|}

Aug 2016 meeting schedule

2016-07-31T00:12:46Z

Vsinghal: /* 9 Aug (Tue) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |
==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam)
* 1:00 pm: Open
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Open
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Open
* 2:30 pm: Leave for airport
|}

Research meetings, Jan/Feb 2016

2016-01-23T00:51:53Z

Vsinghal: /* 7 Feb 2016 (Sun) */

Please sign up for a slot below. __NOTOC__

{| border=1 width=100%
|- valign = top
|
=== 25 Jan 2016 (Mon) ===
* Richard in SF
|
=== 26 Jan 2016 (Tue) ===
* 1-2 pm: Andrey Shur
* 2-3 pm: Anders Knight
* 3-4 pm: Reed McCardell
* 5:30-6:30 pm: Ania Baetica
|

=== 27 Jan 2016 (Wed) ===
* 8:30-9:30 am: Vipul Singhal
* 9:30-10:30 am: Anandh Swaminathan
* 4-5 pm: Shaobin
* 5-6 pm: Ivan (flexible)
|

=== 28 Jan 2016 (Thu) ===
* 5:30-6:30 pm: Michele Colledanchise
* 6:30-7:30 pm: Yutaka
|

=== 29 Jan 2016 (Fri) ===
* 9-10 am: Hold: Benson
* 2-3 pm: Victoria Hsiao
* 3-4 pm: Clare
* 4:30-5:30 pm: Ioannis Filippidis
* 5:30-6:30 pm: George Artavanis
|- valign = top
|

=== 25 Jan 2016 (Mon) ===
* Richard in Hartford
|
=== 2 Feb 2016 (Tue) ===
* 9-10 am: Yong W.
* 2-3 pm: Tony Fragoso
* 3-4 pm: Sean Sanchez
* 4-5 pm: James Parkin
* 5:30-6:30 pm: Daniel Naftalovich
* 6:30-7:30 pm: Anu Thubagere
|

=== 3 Feb 2016 (Wed) ===
* 8:30-9:30 am: Cat McGhan
* 9:30-10:30 am: Sam Clamons
|

=== 4 Feb 2016 (Thu) ===
* Richard in SF
|
=== 5 Feb 2016 (Fri) ===
* BE visiting day
|}

=== 7 Feb 2016 (Sun) ===
* 2-3 pm: Vipul Singhal
* 3-4 pm: open (if needed)
* 4-5 pm: open (if needed)
* 5-6 pm: open (if needed)

Research meetings, Jan/Feb 2016

2016-01-18T23:05:01Z

Vsinghal: /* 27 Jan 2016 (Wed) */

Please sign up for a slot below. __NOTOC__

{| border=1 width=100%
|- valign = top
|
=== 25 Jan 2016 (Mon) ===
* Richard in SF
|
=== 26 Jan 2016 (Tue) ===
* 1-2 pm: Andrey Shur
* 2-3 pm: Anders Knight
* 3-4 pm: Reed McCardell
* 5:30-6:30 pm: Ania Baetica
|

=== 27 Jan 2016 (Wed) ===
* 8:30-9:30 am: Vipul Singhal
* 9:30-10:30 am: open
* 4-5 pm: open
* 5-6 pm: open
|

=== 28 Jan 2016 (Thu) ===
* 5:30-6:30 pm: open
* 6:30-7:30 pm: open
|
=== 29 Jan 2016 (Fri) ===
* 2-3 pm: open
* 3-4 pm: open
* 4:30-5:30 pm: Ioannis Filippidis
* 5:30-6:30 pm: open
|- valign = top
|

=== 25 Jan 2016 (Mon) ===
* Richard in Hartford
|
=== 2 Feb 2016 (Tue) ===
* 9-10 am: Yong W.
* 2-3 pm: Tony Fragoso
* 3-4 pm: open
* 4-5 pm: open
* 5:30-6:30 pm: open
* 6:30-7:30 pm: open
|

=== 3 Feb 2016 (Wed) ===
* 8:30-9:30 am: open
* 9:30-10:30 am: open
|
=== 4 Feb 2016 (Thu) ===
* Richard in SF
|
=== 5 Feb 2016 (Fri) ===
* BE visiting day
|}

Soheil Feizi, Oct 2015

2015-10-09T08:48:34Z

Vsinghal: /* Schedule */

* Visitor: Soheil Feizi (MIT)
* Date: October 19th (Mon)
=== Schedule ===
* 9:15 am - Yutaka Hori (218 ANB; ex 3552)
* 10:15 am -
* 11 am - Vipul Singhal (Keck 139)
* 11:45 am - seminar set up
* 12-1:15 pm - seminar (121 ANB)
* 1:30 pm -
* 2:15 pm - Anandh Swaminathan (Steele 103)
* 3 pm - Enoch Yeung (Keck 139)
* 4 pm - Richard Murray (Steele 109)
* 4:45 pm - Done

=== Seminar ===
Title: Learning (from) networks: fundamental limits, algorithms, and applications

Abstract: Network models provide a unifying framework for understanding dependencies among variables in medical, biological, and other sciences. Networks can be used to reveal underlying data structures, infer functional modules, and facilitate experiment design. In practice, however, size, uncertainty and complexity of the underlying associations render these applications challenging.

In this talk, we illustrate the use of spectral, combinatorial, and statistical inference techniques in several significant network science problems. First, we consider the problem of network alignment where the goal is to find a bijective mapping between nodes of two networks to maximize their overlapping edges while minimizing mismatches. To solve this combinatorial problem, we present a new scalable spectral algorithm, and establish its efficiency theoretically and experimentally over several synthetic and real networks. Next, we introduce network maximal correlation (NMC) as an essential measure to capture nonlinear associations in networks. We characterize NMC using geometric properties of Hilbert spaces and illustrate its application in learning network topology when variables have unknown nonlinear dependencies. Finally, we discuss the problem of learning low dimensional structures (such as clusters) in large networks, where we introduce logistic Random Dot Product Graphs, a new class of networks which includes most stochastic block models as well as other low dimensional structures. Using this model, we propose a spectral network clustering algorithm that possesses robust performance under different clustering setups. In all of these problems, we examine underlying fundamental limits and present efficient algorithms for solving them. We also highlight applications of the proposed algorithms to data-driven problems such as functional and regulatory genomics of human diseases, and cancer.

Tom Ellis, May 2015

2015-05-11T03:59:34Z

Vsinghal: /* Schedule: 18 May (Mon) */

Tom Ellis from Imperial College will be visiting on 18 May (Mon). If you would like to meet with him, please sign up for a slot below.

=== Schedule: 18 May (Mon) ===

{{agenda begin}}
{{agenda item|12:00 pm|Lunch with Richard}}
{{agenda item|1:30 pm|Biosensors and multicellular circuits - Shaobin, Victoria, James}}
{{agenda item|2:30 pm|Vipul and Zach (others welcome): Predictive Silico -> Vitro -> Vivo methodology}}
{{agenda item|3:30 pm|Open}}
{{agenda item|4:15 pm|Metabolic engineering - Yong }}
{{agenda item|5:00 pm|Richard}}
{{agenda item|5:30 pm|Done for the day}}
{{agenda end}}

Tom Ellis, May 2015

2015-05-11T03:59:24Z

Vsinghal: /* Schedule: 18 May (Mon) */

Tom Ellis from Imperial College will be visiting on 18 May (Mon). If you would like to meet with him, please sign up for a slot below.

=== Schedule: 18 May (Mon) ===

{{agenda begin}}
{{agenda item|12:00 pm|Lunch with Richard}}
{{agenda item|1:30 pm|Biosensors and multicellular circuits - Shaobin, Victoria, James}}
{{agenda item|2:30 pm|Vipul and Zach (other welcome): Predictive Silico -> Vitro -> Vivo methodology}}
{{agenda item|3:30 pm|Open}}
{{agenda item|4:15 pm|Metabolic engineering - Yong }}
{{agenda item|5:00 pm|Richard}}
{{agenda item|5:30 pm|Done for the day}}
{{agenda end}}

Tom Ellis, May 2015

2015-05-11T03:58:38Z

Vsinghal: /* Schedule: 18 May (Mon) */

Tom Ellis from Imperial College will be visiting on 18 May (Mon). If you would like to meet with him, please sign up for a slot below.

=== Schedule: 18 May (Mon) ===

{{agenda begin}}
{{agenda item|12:00 pm|Lunch with Richard}}
{{agenda item|1:30 pm|Biosensors and multicellular circuits - Shaobin, Victoria, James}}
{{agenda item|2:30 pm|Vipul and Zach: Predictive Silico -> Vitro -> Vivo methodology}}
{{agenda item|3:30 pm|Open}}
{{agenda item|4:15 pm|Metabolic engineering - Yong }}
{{agenda item|5:00 pm|Richard}}
{{agenda item|5:30 pm|Done for the day}}
{{agenda end}}

Ed Vipul Model Reduction

2014-07-09T22:17:48Z

Vsinghal: Vsinghal moved page Ed Vipul Model Reduction to Model reduction verification in TXTL, with Edward Hancock: More descriptive name

#REDIRECT [[Model reduction verification in TXTL, with Edward Hancock]]

Model reduction verification in TXTL, with Edward Hancock

2014-07-09T22:17:48Z

Vsinghal: Vsinghal moved page Ed Vipul Model Reduction to Model reduction verification in TXTL, with Edward Hancock: More descriptive name

==Skype meeting with Ed, Jul 7 2014==

1) Main project ideas:
# Test Uniform degradation
# Test Hill Function orders by varying loading of repressor etc.
# Identify Units (need more details on this)

2) Circuit set up:
* pconst--Repressor_Reporter1_fusion
* pRepressed1--Reporter2
# Repressor-Reporter fusion proteins can be sent over from Imperial: lacI-GFP fusion and tetR-mCherry fusion.
# Need RFU to nM conversion curves for these fusion proteins. Check how much effort this requires, and what the procedure is.
# Since tetR and lacI are multimer dominant, we would like some monomer dominant proteins as well. Figure 3 in the appendix of Ed's paper shows that GalR and Clambda are possibly such repressors. It would be good to obtain these Repressors in advance and test them out. What promoter des GalR repress? Check literature.
# One question is: How reasonable is it to just assume that GFP and lacI-GFP have the same fluorescence.

==Plan for materials prep==
Need Fusion proteins (at least 1, two preferred)
Need GalR and cLambda on const promoter.
Need the promoters for GalR and cLambda

2014-04-02T21:09:15Z

Vsinghal: /* 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 11-12, 200 BRD
|
'''Teaching Assistants'''
* Victoria Hsiao (BE)
* Vipul Singhal (CNS)
* Recitation: Fr 11-12, location TBD
| rowspan=2 width=20% align=right |
__TOC__
|-
| colspan=2 |
This is the course homepage for BE 150/Bi 250 for Spring 2014. 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'''
| 31 Mar 2 Apr MBE/RMM
| Course overview, gene circuit dynamics
* Introduction to the course
* Rate equations enable analysis of gene regulation circuits
* Degradation rates control response times in simple open-loop gene regulation
* Autoregulatory feedback loops modulate the response times of genetic circuits, limit variability, and can enable rate-responsive systems
* Cooperative responses can enable switch-like regulation and bistability
* Circuit motifs can help identify functional modules in complex circuits
Recitation section: 4 Apr
* [[Media:MatlabTutorial.pdf|MATLAB]] and [[Media:SimbiologyTutorial.pdf|SimBiology]] Tutorial
* Useful MATLAB commands: [http://www.cds.caltech.edu/~murray/courses/be150/sp14/matlab/useful_matlab.m useful_matlab.m]
* SimBiology example: [http://www.cds.caltech.edu/~murray/courses/be150/sp14/matlab/rec1_pos_regdemo.sbproj Simbiology Project File]
* MATLAB/ode45 example: [http://www.cds.caltech.edu/~murray/courses/be150/sp14/matlab/pos_reg_main.m pos_reg_main.m]
* [http://www.mathworks.com/help/simbio/gs/simbiology-command-line-tutorial.html 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|sp14|caltech/bfs-class-intro_31Mar14.pdf|BFS Ch 1}}: Introductory Concepts (skim)
* {{be150 pdf|sp14|caltech/bfs-class-coreproc_31Mar14.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/sp14/hw1.pdf HW1]

|- valign=top
|

'''2'''
| 7 Apr 9 Apr* MBE
| Circuit motifs
*Feed-forward loops enable temporal filtering and pulse generation
*‘Futile cycles’ generate zero-order ultrasensitivity (phospho-switches)
*Multi-gene positive feedback loops can enable toggle switch behaviors
*Positive feedback can generate hysteresis and irreversibility - example: Xenopus oocyte maturation
*Paradoxical regulation by cytokines could enable regulation of a population response
Recitation (11 Apr): sample problems
* MATLAB/curve fitting tool example: {{be150-sp14 matlab|cftools_example.m}}

|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:
* {{be150 pdf|sp14|caltech/bfs-class-coreproc_31Mar14.pdf|BFS Ch 2}}: Modeling of Core Processes
** Section 2.4: post-transcriptional regulation
** Section 2.5: cellular subsystems

|

|- valign=top
|

'''3'''
| 14 Apr+ 16 Apr+ MBE
| Robustness
''Critical features of genetic circuits may be robust to variation in their own components, and the principle of robustness can be used to select identify likely circuit architectures:''
*In the bacterial chemotaxis circuit, perfect adaptation is robust to fluctuations in key cellular components
*Bifunctional kinases can generate ideal linear amplifiers with robustness to component concentrations
*Cosubstrate compensation provides oxygen homeostasis across a broad range of oxygen levels (Kueh)
Recitation (1 Feb): sensitivity analysis
*Demo of sensitivity analysis and how to add events in simbio: {{be150-sp14 matlab|I1FFL_sens_event_demo.sbproj}}
*Demo of how to use compartments within one model: {{be150-sp14 matlab|multiple_compartments.sbproj}}

|
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
BE 150:
* {{be150 pdf|sp14|caltech/bfs-class-dynamics_31Mar14.pdf|BFS Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
* {{be150 pdf|sp14|caltech/bfs-class-chemotaxis_31Mar14.pdf|BFS Sec 5.2}}: Bacterial chemotaxis

|

|- valign=top
|

'''4'''
| 21 Apr 23 Apr+ MBE
| Guest lecture: Joe Markson
''Clock-like oscillations can be implemented in cells:''
* Delayed negative feedback can enable clock-like oscillations in individual cells (Repressilator)
* Combined positive/negative feedback enables relaxation oscillation whose period and amplitude can be tuned independently
* A simple three-protein system can generate accurate clock-like oscillations of phosphorylation state
April 25: Course Project Assignments
|

BE 150:
* {{be150 pdf|sp14|caltech/bfs-class-dynamics_31Mar14.pdf|BFS Ch 3}}: Analysis of Dynamic Behavior
** Sections 3.5: Oscillatory Behavior

|

|- valign=top
|

'''5'''
| 28 Apr 30 Apr RMM
| ''Stochasticity, or ‘noise’ is ubiquitous in genetic circuits:''
* Intrinsic noise (stochasticity) in gene expression limits the accuracy of gene regulation
* Variability can be controlled by altering burst parameters
|

BE 150:
* {{be150 pdf|sp14|caltech/bfs-class-stochastic_31Mar14.pdf|BFS Ch 4}}: Stochastic behavior
* {{be150 pdf|sp14|caltech/bfs-class-random_05Jan13.pdf|App B}}: Probability and random processes (optional)
| rowspan=2 |

|- valign=top
|

'''6'''
| 5 May* 7 May* RMM
| ''Stochastic pulsing provides multiple functions in cells, similar to the role of oscillatory signals in engineering''
* Frequency modulation coordinates the responses of diverse genetic targets (example: yeast stress response)
* Excitability is a noise-dependent mechanism that enables probabilistic control of transient, stereotyped differentiation events
* Pulsing can enable dynamic multiplexing (example: p53)
|

|-
|
| 9 May 
| colspan=3 | Course project discussion with TAs

|- valign=top
|

'''7'''
| 12 May 14 May MBE
| Guest Lecture: Sandy Nandagopal & Joe Markson
Patterning
* Self-enhanced degradation makes morphogen gradients robust to variation in morphogen production rates.
* Shuttling mechanisms enable morphogen-based patterning systems to scale with tissue size.
|
* Alon, Ch 8: Robust Patterning in Development

| rowspan=2 |

|- valign=top
|

'''8'''
| 19 May 21 May MBE
| colspan=3 | Project presentations
|- valign=top
|

'''9'''
| 28 May+ 30 May* 
| 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|wi13|caltech/bfs-class-stochastic_05Jan13.pdf|Ch 4}}, {{be150 pdf|wi13|caltech/bfs-class-chemotaxis_05Jan13.pdf|Sec 5.2}}, {{be150 pdf|wi13|caltech/bfs-class-random_05Jan13.pdf|App B}}, {{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 are posted [[BE 150/Bi 250b project ideas, Winter 2013|here]]. 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 4 Feb for consideration.

Course project timeline:
* 1 Feb (Fri): [[BE 150/Bi 250b project ideas, Winter 2013|course projects]] posted on home page and announced in class
* 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.

Course preference instructions
{{BE 150 project instructions, Winter 2013}}

=== 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]]