SEED 2024 - Revision history

Murray at 12:32, 26 June 2024

2024-06-26T12:32:44Z

← Older revision		Revision as of 12:32, 26 June 2024
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	<br>		<br>
	<font size="+0">Richard M. Murray <br> California Institute of Technology </font>		<font size="+0">Richard M. Murray <br> California Institute of Technology </font>
	~~</center>~~

	{\| align=center		{\| align=center
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	\|  style="text-  align=center;" \| Imperial College London		\|  style="text-  align=center;" \| Imperial College London
	\|}		\|}

			2024 Synthetic Biology: Engineering, Evolution & Design (SEED) Conference<br>
			25 June 2024
			</center>

	[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/synthetic_cells-seed_25Jun2024.pdf]]		[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/synthetic_cells-seed_25Jun2024.pdf]]

Murray at 14:28, 25 June 2024

2024-06-25T14:28:50Z

← Older revision		Revision as of 14:28, 25 June 2024
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	* [https://github.com/BuildACell/bioCRNpyler BioCRNpyler] - Biomolecular chemical reaction network compiler		* [https://github.com/BuildACell/bioCRNpyler BioCRNpyler] - Biomolecular chemical reaction network compiler
	* [https://github.com/biocircuits/bioscrape BioSCRAPE] - Biological stochastic simulation of single cell reactions and parameter estimation		* [https://github.com/biocircuits/bioscrape BioSCRAPE] - Biological stochastic simulation of single cell reactions and parameter estimation
	* [https://www.buildacell.org Build-A-Cell] - ~~An open source,~~ synthetic ~~cell community~~		* [https://www.buildacell.org Build-A-Cell] - Open collaboration supporting the science and engineering of building synthetic cells
	* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders		* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders
	* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery		* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery
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	* W. Poole, A. Pandey, A. Shur, Z. A. Tuza, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2020.08.02.233478v3\|BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts]], bioRxiv, 2022.		* W. Poole, A. Pandey, A. Shur, Z. A. Tuza, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2020.08.02.233478v3\|BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts]], bioRxiv, 2022.
	* Y. Zhang, Y. Qiu, M. Deveikis, Z. A. Martinez, T.-F. Chou, P. S. Freemont, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2024.06.19.599772v1\|Optimizing protein expression in the One-Pot PURE System: Insights into reaction composition and translation efficiency]], bioRxiv, 2024.		* Y. Zhang, Y. Qiu, M. Deveikis, Z. A. Martinez, T.-F. Chou, P. S. Freemont, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2024.06.19.599772v1\|Optimizing protein expression in the One-Pot PURE System: Insights into reaction composition and translation efficiency]], bioRxiv, 2024.

			=== Projects ===

			* [[Design and Implementation of Multi-Component Synthetic Cells]] (ARO/ICB)
			* [[Control of Functional Bioenabled Materials using Synthetic Cells]] (ICB/ASR)
			* [[Upscaling Engineering of Synthetic Biomachines]] (Schmidt Sciences)
			* [[Rules of Composition in Synthetic Biology Across Scales of Complexity: Theory and Tools]] (AFOSR)
			* [[Deciphering the Rules of Nucleus Architecture with Synthetic Cells and Organelles]] (NSF)
			* [[Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways]] (NSF)

Murray: /* Links to additional resources */

2024-06-25T13:49:03Z

Links to additional resources

← Older revision		Revision as of 13:49, 25 June 2024
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	* [https://github.com/BuildACell/bioCRNpyler BioCRNpyler] - Biomolecular chemical reaction network compiler		* [https://github.com/BuildACell/bioCRNpyler BioCRNpyler] - Biomolecular chemical reaction network compiler
	* [https://github.com/biocircuits/bioscrape BioSCRAPE] - Biological stochastic simulation of single cell reactions and parameter estimation		* [https://github.com/biocircuits/bioscrape BioSCRAPE] - Biological stochastic simulation of single cell reactions and parameter estimation
	* [https://www.buildacell.org Build-A-Cell] -		* [https://www.buildacell.org Build-A-Cell] - An open source, synthetic cell community
	* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders		* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders
	* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery		* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery

Murray at 13:47, 25 June 2024

2024-06-25T13:47:35Z

← Older revision		Revision as of 13:47, 25 June 2024
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	* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders		* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders
	* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery		* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery
	* [https://vivarium-collective.github.io Vivarium ] -		* [https://vivarium-collective.github.io Vivarium ] - Simulation engine for composing and executing integrative multi-scale models

	=== Papers and preprints ===		=== Papers and preprints ===

Murray at 13:44, 25 June 2024

2024-06-25T13:44:59Z

← Older revision		Revision as of 13:44, 25 June 2024
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	[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/synthetic_cells-seed_25Jun2024.pdf]]		[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/synthetic_cells-seed_25Jun2024.pdf]]
	The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.		The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.

			=== Links to additional resources ===

			* [https://github.com/BuildACell/bioCRNpyler BioCRNpyler] - Biomolecular chemical reaction network compiler
			* [https://github.com/biocircuits/bioscrape BioSCRAPE] - Biological stochastic simulation of single cell reactions and parameter estimation
			* [https://www.buildacell.org Build-A-Cell] -
			* [https://nucleus.bnext.bio Nucleus] - Open source package for synthetic cell builders
			* [https://github.com/martinez-zacharya/TRILL TRILL] - Sandbox for creative protein engineering and discovery
			* [https://vivarium-collective.github.io Vivarium ] -

			=== Papers and preprints ===

			* Z. Jurado, A. Pandey, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2023.08.14.553301v1\|A chemical reaction network model of PURE]], bioRxiv, 2023.
			* Z. A. Martinez, R. M. Murray, and M. Thomson, [[http:www.biorxiv.org/content/10.1101/2023.10.24.563881v2.abstract\|TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering]], bioRxiv, 2023.
			* W. Poole, A. Pandey, A. Shur, Z. A. Tuza, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2020.08.02.233478v3\|BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts]], bioRxiv, 2022.
			* Y. Zhang, Y. Qiu, M. Deveikis, Z. A. Martinez, T.-F. Chou, P. S. Freemont, and R. M. Murray, [[http:www.biorxiv.org/content/10.1101/2024.06.19.599772v1\|Optimizing protein expression in the One-Pot PURE System: Insights into reaction composition and translation efficiency]], bioRxiv, 2024.

Murray at 13:12, 25 June 2024

2024-06-25T13:12:27Z

← Older revision		Revision as of 13:12, 25 June 2024
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	[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/~~syncell_seed~~-~~25Jun2024~~.pdf]]		[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/synthetic_cells-seed_25Jun2024.pdf]]
	The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.		The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.

Murray at 13:06, 25 June 2024

2024-06-25T13:06:15Z

← Older revision		Revision as of 13:06, 25 June 2024
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	\|}		\|}

			[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/syncell_seed-25Jun2024.pdf]]
	The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.		The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.

	~~[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/syncell_seed-25Jun2024.pdf]]~~

Murray at 13:05, 25 June 2024

2024-06-25T13:05:52Z

← Older revision		Revision as of 13:05, 25 June 2024
Line 18:		Line 18:

	The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.		The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.

			[[Image:murray_seed2024-firstpage.png\|right\|thumb\|link=https://www.cds.caltech.edu/~murray/talks/syncell_seed-25Jun2024.pdf]]

Murray at 13:01, 25 June 2024

2024-06-25T13:01:33Z

← Older revision		Revision as of 13:01, 25 June 2024
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	<br>		<br>
	<font size="+0">Richard M. Murray <br> California Institute of Technology </font>		<font size="+0">Richard M. Murray <br> California Institute of Technology </font>
			</center>

	{\|		{\| align=center
	\|-		\|-
	\| style="text-  align=center;" \| Anton Jackson-Smith    Zoila Jurado    Zachary Martinez		\| style="text-  align=center;" \| Anton Jackson-Smith    Zoila Jurado    Zachary Martinez
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	\|  style="text-  align=center;" \| b.next    Build-A-Cell		\|  style="text-  align=center;" \| b.next    Build-A-Cell
	\|-		\|-
	\|   ~~style~~="text-  align=center;" \| Ayush Pandey    William Poole    Yan Zhang		\| style="text-  align=center;" \| Ayush Pandey    William Poole    Yan Zhang
	\|		\|
	\|  style="text-  align=center;" \| Imperial College London		\|  style="text-  align=center;" \| Imperial College London
	\|}		\|}
	~~</center>~~

	The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.		The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.

Murray at 12:58, 25 June 2024

2024-06-25T12:58:48Z

← Older revision		Revision as of 12:58, 25 June 2024
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	{\|		{\|
	\|-		\|-
	\|   align=center \| Anton Jackson-Smith    Zoila Jurado    Zachary Martinez		\| style="text-  align=center;" \| Anton Jackson-Smith    Zoila Jurado    Zachary Martinez
	\|		\|
	\|  ~~align~~=center \| b.next    Build-A-Cell		\|  style="text-  align=center;" \| b.next    Build-A-Cell
	\|-		\|-
	\|   align=center \| Ayush Pandey    William Poole    Yan Zhang		\|   style="text-  align=center;" \| Ayush Pandey    William Poole    Yan Zhang
	\|		\|
	\|  ~~align~~=center \| Imperial College London		\|  style="text-  align=center;" \| Imperial College London
	\|}		\|}
	</center>		</center>

	The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.		The goal of this project is to demonstrate a model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We are focused on proof-of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. A major element of our work is the development of open source tools that help “routinize” the creation of synthetic cells. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.