View source for SBtools Bootcamp, June 2020

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<font color='blue' size='+2'>Open Source Tools for Biological Circuit Design</font>__NOTOC__
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'''Instructors'''
* Richard Murray (CDS/BE), murray@cds.caltech.edu
* Lecturers: John Marken (BE), Ayush Pandey (CDS), William Poole (CNS), Rory Williams (BE)
* TAs: Liana Merk, Manisha Kapasiawala, Ankita Roychoudhury, Sophie Walton
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'''Class meeting times'''
* 16-19 June, 8:30a-12:00p PDT
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This is the course homepage for the Synthetic Biology (Modeling and Analysis) Tools [SBtools] bootcamp.

This bootcamp covers the use of open source tools developed at Caltech for use in modeling and simulation of engineered biological circuits.  Participants in the course will develop working knowledge of modeling, simulation, and design tools that are available for biological circuits and apply that knowledge to a circuit relevant to your research.  Students will also gain insights into modeling and design choices, including what level of detail to include in a model based on the questions you are trying to ask.  

=== Lecture Schedule ===

Each day of the course will cover a different topic and/or tool.  The class sessions will contain a mixture of lecture, hands-on demonstrations, and participatory exercises.

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| '''Date'''
| '''Topic'''
| '''Instructors'''
| '''Tools'''
| '''Notes'''

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| L1 - 16 Jun
| Chemical reactions, mass action → BioCRNPyler (species, reactions)
| Ayush, John, Ankita, Sophie
| [[http:www.anaconda.com|Anaconda]], [[http:jupyter.org|Jupyter]], [[http:github.com|GitHub]], [[http:github.com/BuildACell/BioCRNPyler|BioCRNpyler]], [[http:github.com/ananswam/bioscrape/wiki|Bioscrape]]
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| L2 - 17 Jun
| ODEs, Hill functions → BioCRNPyler (species, reactions)
| Ayush, John, Ankita, Sophie
| [[http:github.com/BuildACell/BioCRNPyler|BioCRNpyler]],  [[http:github.com/ananswam/bioscrape/wiki|Bioscrape]]
| Core processes: transcription, translation → BioCRNPyler (mixtures)
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| L3&nbsp;-&nbsp;18&nbsp;Jun
| Intro to SBML and non-mass-action propensities & rules in bioscrape
| Rory, William, Liana, Manisha
|[[http:github.com/BuildACell/BioCRNPyler|BioCRNpyler]],  [[http:github.com/ananswam/bioscrape/wiki|Bioscrape]]
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| L4 - 19 Jun
| Genetic circuits → BioCRNPyler (components, mechanisms)
| Rory, William, Liana, Manisha
| [[http:github.com/BuildACell/BioCRNPyler|BioCRNpyler]],  [[http:github.com/ananswam/bioscrape/wiki|Bioscrape]]
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| TBD
| Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML 
| Ayush
| [[http:github.com/BuildACell/subsbml|Sub-SBML]]
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| TBD
| Bioscrape Lineages as a well-mixed version of gro
| William
| [[http:github.com/ananswam/bioscrape/wiki/Lineage-Package|Bioscrape Lineages]]
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| TBD
| System ID: Bioscrape inference tools 
| Ayush
| [[http:github.com/ananswam/bioscrape/wiki/Parameter-Inference-and-Identification|Bioscrape Inference]]
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=== Course Preparation ===

The course will rely on working knowledge of Python.  Participants who are not familiar with using Python should consider taking the BE 203 bootcamp, offered by Justin Bois.

[[Category: Courses]]