SEED 2024: Difference between revisions
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<font size="+0">Richard M. Murray <br> California Institute of Technology </font> | <font size="+0">Richard M. Murray <br> California Institute of Technology </font> | ||
{| | {| align=center | ||
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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 | ||
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align=center | Ayush Pandey William Poole Yan Zhang | | style="text-
align=center;" | Ayush Pandey William Poole Yan Zhang | ||
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style="text-
align=center;" | Imperial College London | ||
|} | |} | ||
2024 Synthetic Biology: Engineering, Evolution & Design (SEED) Conference<br> | |||
25 June 2024 | |||
</center> | </center> | ||
[[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] - Open collaboration supporting the science and engineering of building synthetic cells | |||
* [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 ] - Simulation engine for composing and executing integrative multi-scale models | |||
=== 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. | |||
=== 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) | |||
Latest revision as of 12:32, 26 June 2024
Upscaling Engineering of Synthetic Biomachines via Synthetic Cells
Richard M. Murray
California Institute of Technology
| Anton Jackson-Smith Zoila Jurado Zachary Martinez | b.next Build-A-Cell | |
| Ayush Pandey William Poole Yan Zhang | Imperial College London |
2024 Synthetic Biology: Engineering, Evolution & Design (SEED) Conference
25 June 2024
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
- BioCRNpyler - Biomolecular chemical reaction network compiler
- BioSCRAPE - Biological stochastic simulation of single cell reactions and parameter estimation
- Build-A-Cell - Open collaboration supporting the science and engineering of building synthetic cells
- Nucleus - Open source package for synthetic cell builders
- TRILL - Sandbox for creative protein engineering and discovery
- Vivarium - Simulation engine for composing and executing integrative multi-scale models
Papers and preprints
- Z. Jurado, A. Pandey, and R. M. Murray, A chemical reaction network model of PURE, bioRxiv, 2023.
- Z. A. Martinez, R. M. Murray, and M. Thomson, 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, 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, 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)
