NIH P50 - Revision history

Murray: /* Drafts */

2006-11-19T21:07:35Z

Drafts

← Older revision		Revision as of 21:07, 19 November 2006
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	* Intro material + admin, training, etc (15 Nov 06, 10:30 pm): [[Media:nih06-systems.pdf\|pdf]] (154K)		* Intro material + admin, training, etc (15 Nov 06, 10:30 pm): [[Media:nih06-systems.pdf\|pdf]] (154K)
	* DBP #1 - Core Processes in Micro-Organisms: [[Media:nih06-dbp1.doc\|doc]] (3.0 MB), [[Media:nih06-dbp1.pdf\|pdf]] (1.3MB)		* DBP #1 - Core Processes in Micro-Organisms: [[Media:nih06-dbp1.doc\|doc]] (3.0 MB), [[Media:nih06-dbp1.pdf\|pdf]] (1.3MB)
			* NIH: [http://grants.nih.gov/grants/guide/rfa-files/RFA-GM-07-004.html RFA], [http://grants.nih.gov/grants/funding/phs398/phs398.html PHS 398]
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Murray: /* Drafts */

2006-11-16T06:41:35Z

Drafts

← Older revision		Revision as of 06:41, 16 November 2006
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	== Drafts ==		== Drafts ==
	* Intro material + admin, training, etc (15 Nov 06, 10:30 pm): [[Media:nih06-systems.pdf\|pdf]]		* Intro material + admin, training, etc (15 Nov 06, 10:30 pm): [[Media:nih06-systems.pdf\|pdf]] (154K)
	* DBP #1 - Core Processes in Micro-Organisms: [[Media:nih06-dbp1.doc\|doc]]		* DBP #1 - Core Processes in Micro-Organisms: [[Media:nih06-dbp1.doc\|doc]] (3.0 MB), [[Media:nih06-dbp1.pdf\|pdf]] (1.3MB)
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Murray: /* Goals */

2006-11-16T06:36:48Z

Goals

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	\| width=60% \|		\| width=60% \|
	== ~~Goals~~ ==		== Drafts ==
	* ~~To develop a complete and predictive understanding of the control systems that are responsible for core processes of metabolism~~, ~~polymerization~~, ~~assembly and signal transduction in microorganisms~~		* Intro material + admin, training, etc (15 Nov 06, 10:30 pm): [[Media:nih06-systems.pdf\|pdf]]
	* ~~To apply the techniques developed through the study of individual cells to the complementary problems of communication modes and probabilistic decision processes~~ in ~~multi~~-~~cellular systems~~		* DBP #1 - Core Processes in Micro-Organisms: [[Media:nih06-dbp1.doc\|doc]]
	* To develop a complete and predictive understanding of the control systems that are responsible for regulating the processes directing how mammalian cells interact with their environment.
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	== Timeline ==		== Timeline ==
	* 16-18 Nov: CDS out of town (online)		* 16-18 Nov: CDS out of town (online)

Murray: /* Program summary (5 pages) */

2006-11-16T06:00:09Z

Program summary (5 pages)

← Older revision		Revision as of 06:00, 16 November 2006
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	* Current owner: Richard		* Current owner: Richard
	* Sent out for comment on 13 Nov		* Sent out for comment on 13 Nov
			* Added paragraph from MBE in single cell imaging

	==== Organizational structure/decision making plan (2 pages) ====		==== Organizational structure/decision making plan (2 pages) ====

Murray: /* Core facilities (2 pages) */

2006-11-16T05:59:26Z

Core facilities (2 pages)

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	==== Core facilities (2 pages) ====		==== Core facilities (2 pages) ====

			==== Education and Training ====
			* Owner: Richard Murray
			* Initial version sent out for comment

	==== Intellectual property plan (1 page) ====		==== Intellectual property plan (1 page) ====

Murray: /* Center development and outreach plans (5 pages) */

2006-11-16T05:58:26Z

Center development and outreach plans (5 pages)

← Older revision		Revision as of 05:58, 16 November 2006
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	==== Center development and outreach plans (5 pages) ====		==== Center development and outreach plans (5 pages) ====
			* Current owner: Richard
			* Sent out for comment

	==== Research projects and preliminary studies (50 pages) ====		==== Research projects and preliminary studies (50 pages) ====

Murray: /* Organizational structure/decision making plan (2 pages) */

2006-11-16T05:58:07Z

Organizational structure/decision making plan (2 pages)

← Older revision		Revision as of 05:58, 16 November 2006
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	==== Organizational structure/decision making plan (2 pages) ====		==== Organizational structure/decision making plan (2 pages) ====
			* Current owner: Richard
			* Working on first iteration; sent to Christina then to group

	==== Center development and outreach plans (5 pages) ====		==== Center development and outreach plans (5 pages) ====

Murray: /* Program summary (5 pages) */

2006-11-16T05:57:45Z

Program summary (5 pages)

← Older revision		Revision as of 05:57, 16 November 2006
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	==== Program summary (5 pages) ====		==== Program summary (5 pages) ====
			* Current owner: Richard
			* Sent out for comment on 13 Nov

	==== Organizational structure/decision making plan (2 pages) ====		==== Organizational structure/decision making plan (2 pages) ====

Murray: /* Proposal Outline */

2006-11-16T05:56:12Z

Proposal Outline

← Older revision		Revision as of 05:56, 16 November 2006
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	== Proposal Outline ==		== Proposal Outline ==

	==== Program summary (2 pages) ====		==== Program summary (5 pages) ====
	* Statement of goals and objectives (milestones)
	* Build off of vision statement
	* What makes us unique? Bringing together three essential elements
	** Computational and theoretical infrastucture for pursuing regulatory architectures
	** Unique experimental platforms
	** Unique ''combination'' of driving biological problems
	* Move from small scale static to large scale, dynamic
	** Look across a class of biological applications
	** Make use of theory and computational tools to guide experiments
	** Spatial structure and stochastics become important (primarily affect the dynamics of regulation)

	==== Organizational structure/decision making plan (2 pages) ====		==== Organizational structure/decision making plan (2 pages) ====

	~~{\| border~~=~~1 width~~=~~100%~~		==== Center development and outreach plans (5 pages) ====
	\|-
	~~\| colspan~~=~~3 align~~ = ~~center\| '''Christina Smolke (PI)'''~~
	~~\|- valign=top~~
	~~\| width=33% \| '''Thrust I: Theory and computation''' <br> JD?~~
	* Model-checking and SOS methods for analysis of regulatory networks (John)
	* Stochastic simulation/SBML with spatial structure (John, CACR)
	* Feedback design of synthetic regulatory structures (Richard, John)
	~~\| width=33% \| '''Thrust II: Experimental Platforms''' <br> RP?~~
	* FRET-based molecular sensors (Christina)
	* Cryo-EM (Grant)
	* Single-cell measurements (Rob, Michael, Christina)
	~~\| width=33% \| '''Thrust III: Driving Biological Problems''' <br> DB?~~
	* NFkB, G-protein, MAPK signal transduction [& inflammation?] (David, Anand)
	* Multi-component phosphorelays in bacterial fate choice and development ~~(Michael)~~
	* Regulatory architectures in biofilms (Dianne)
	* Regulatory architectures in bacterial envelopes and ~~structures~~ (~~Grant, Rob, ???~~)
	* Re-engineering core microbial processes/metabolic engineering (Christina)
	\|-
	~~\| colspan=3 \|~~
	~~{\| width~~=~~100%~~
	~~\|- valign~~=~~top~~
	~~\| width~~=~~50% \|~~
	* Postdoc program
	* Seed funding?
	~~\| width~~=~~50% \|~~
	* Visitors
	* Workshops?
	\|}
	\|}

	==== ~~Center development~~ and ~~outreach plans~~ (5 pages) ====		==== Research projects and preliminary studies (50 pages) ====
	* Postdocs - what we were thinking here was something like the BI fellows program, which is nicely described on the web at
	~~<center>~~
	~~http://www.its.caltech.edu/~bi/fellows.html~~
	~~</center>~~
	~~:(basically: $50K/year stipend, $25K/year research fund. BI fellows work either with a group (or groups) in the BI or with some other group at Caltech).~~

	* Workshops - for some of the theory tools, we could imagine running some 1-3 day workshops that provide an introduction to the use of those tools. What I'm imagining here is graduate students coming together and spending 6-8 hrs/day for a few days learning things like SBML, modeling and analysis tools, etc. We could run these for people inside and outside Caltech.		===== DBP #1 =====

	* Boot camp (?) - Rob: what do you think about the idea of incorporating the physical biology boot camp into the proposal. I think we could do this by essentially doing exactly what you are already planning - once per year for students in the BE and/or incoming students associated with CBSA plus a few times a year for outside people. The only change would be that we could use CBSA resources to help cover costs, purchase equipment, etc. All: more info on the boot camp at		===== DBP #2 =====
	~~<center>~~
	~~http://www.rpgroup.caltech.edu/courses/PBL/bootcamp0206.htm~~
	~~</center>~~
	* Summer school (?) - within IST, we have run a "computing beyond silicon" summer school that ran for 4 weeks and brought in students and lecturers from around the country. We had lectures on various aspects of information science and technology (ranging from fundamental limits of computing to molecular electronics to information theory) and students did a small research project. We could do something similar in systems biology (but perhaps this is already covered by MBL and/or CSHL)?

	* SURF support		===== DBP #3 =====
	* Visiting scientists

	==== ~~Research projects and preliminary studies (30 pages)~~ ====		===== Experimental Platforms =====

	===== ~~RMM: Design of feedback systems in engineered biological circuits~~ =====		===== Theory and Computation =====
	* Focus on developing appropriate mathematical abstractions for design of feedback circuits
	* Possible thrusts:
	** Developing components of feedback systems: amplifiers (ongoing work with Erik Winfree), sensing and actuation systems (joint with Christina). Example might be a bio-PID circuit.
	** Different mechanisms for feedback in biology. This is a topic that Christina, John and I have discussed. Starting a reading group with Eric Kelsic plus some of my students to look into this.

	==== Core facilities (10 pages) ====		==== Core facilities (2 pages) ====

	==== Intellectual property plan (1 page) ====		==== Intellectual property plan (1 page) ====

	==== Diversity (URM) plan (~~2 pages~~) ====		==== Diversity (URM) plan (1 page) ====

	==== Timeline (2 pages) ====		==== Timeline (2 pages) ====
	* List of milestones for years 1, 2, 3 and 4-5

	[[Category:Proposals]]		[[Category:Proposals]]

Murray at 05:53, 16 November 2006

2006-11-16T05:53:39Z

← Older revision		Revision as of 05:53, 16 November 2006
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	* To apply the techniques developed through the study of individual cells to the complementary problems of communication modes and probabilistic decision processes in multi-cellular systems		* To apply the techniques developed through the study of individual cells to the complementary problems of communication modes and probabilistic decision processes in multi-cellular systems
	* To develop a complete and predictive understanding of the control systems that are responsible for regulating the processes directing how mammalian cells interact with their environment.		* To develop a complete and predictive understanding of the control systems that are responsible for regulating the processes directing how mammalian cells interact with their environment.

	~~== Objectives ==~~
	* CDS: A modular platform for detecting activation through signalling pathways using FRED-basted molecular sensors applied to mapK signalling pathways.
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	== Timeline ==		== Timeline ==