Difference between revisions of "SURF 2021: Modeling tools for design and analysis of synthetic biological circuits"
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'''[[SURF 2020|SURF 2020]] project description''' | '''[[SURF 2020|SURF 2020]] project description''' | ||
[[File:SynBioModelingPipeline.jpg|thumb|500px|right|Figure 1: Modeling and analysis tools in synthetic biology pipeline]] | [[File:SynBioModelingPipeline.jpg|thumb|500px|right|Figure 1: Modeling and analysis tools in the synthetic biology pipeline]] | ||
* Mentor: Richard Murray | * Mentor: Richard Murray | ||
* Co-mentor: Ayush Pandey | * Co-mentor: Ayush Pandey | ||
| Line 11: | Line 11: | ||
We are interested in both theoretical and computational directions for this project. | We are interested in both theoretical and computational directions for this project. | ||
'''References:''' | '''References:''' | ||
# Tuza, Zoltan A., et al. "An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system." 52nd IEEE Conference on Decision and Control. IEEE, 2013. [[An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System| Link]] | # Tuza, Zoltan A., et al. "An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system." 52nd IEEE Conference on Decision and Control. IEEE, 2013. [[An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System| Link]] | ||
# | # Swaminathan, Anandh, et al. "Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape." (2017). [https://github.com/ananswam/bioscrape/ Github link] | ||
# | # BioCRNPyler - Biomolecular Chemical Reaction Network Compiler : A Python toolbox to create CRN models in SBML for biomolecular mechanisms. [https://github.com/BuildACell/BioCRNPyler Github link] | ||
# Sub-SBML | # Sub-SBML : A Python based toolbox to create, edit, combine, and model interactions among multiple Systems Biology Markup Language (SBML) models. [https://github.com/ayush9pandey/subsbml Github link] | ||
Revision as of 06:25, 11 December 2019
SURF 2020 project description
- Mentor: Richard Murray
- Co-mentor: Ayush Pandey
Research directions for the SURF project include:
- Modeling of cell-free systems
- System identification by parts, global sensitivity analysis, model decomposition, reduced models
- Using extract and tx-tl data
We are interested in both theoretical and computational directions for this project.
References:
- Tuza, Zoltan A., et al. "An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular “breadboard” system." 52nd IEEE Conference on Decision and Control. IEEE, 2013. Link
- Swaminathan, Anandh, et al. "Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape." (2017). Github link
- BioCRNPyler - Biomolecular Chemical Reaction Network Compiler : A Python toolbox to create CRN models in SBML for biomolecular mechanisms. Github link
- Sub-SBML : A Python based toolbox to create, edit, combine, and model interactions among multiple Systems Biology Markup Language (SBML) models. Github link
