Difference between revisions of "BE 240, Spring 2020"
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 Ayush   Ayush  
 [[http:github.com/ananswam/bioscrape/wikiBioscrape]]   [[http:github.com/ananswam/bioscrape/wikiBioscrape]]  
−   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W3_sbml_p1.ipynb  +   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W3_sbml_p1.ipynbW3_sbml_p1.ipynb]], [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W3_sbml_p2.ipynbW3_sbml_p2.ipynb]] (Jupyter notebook), [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/repressilator_sbml.xmlrepressilator_sbml.xml]] 
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 W4  23 Apr   W4  23 Apr  
 BioCRNpyler for generating large CRN models from parts   BioCRNpyler for generating large CRN models from parts  
 William   William  
−   BioCRNpyler  +   [[http:github.com/BuildACell/BioCRNPylerBioCRNpyler]] 
−    +   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W4_biocrnpyler.ipynbW4_biocrnpyler.ipynb]] (Jupyter notebook), [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/parameters.txtparameters.txt]] 
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 W5  30 Apr   W5  30 Apr  
 Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML   Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML  
 Ayush   Ayush  
−   SubSBML  +   [[http:github.com/BuildACell/subsbmlSubSBML]] 
−    +   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W5_subsbml.ipynbW5_subsbml.ipynb]], [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/subsbml_generate_models.ipynbsubsbml_generate_models.ipynb]] (Jupyter notebooks), 
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 W6  7 May   W6  7 May  
 Spatial systems and signalling   Spatial systems and signalling  
 Cindy   Cindy  
−    +   [[http:/github.com/murrayrm/grogro]] 
−    +   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W6_gro07May2020.pdfW6_gro07May2020.pdf]] 
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 W7  14 May   W7  14 May  
 Cells and Growth/death regulation   Cells and Growth/death regulation  
 Cindy   Cindy  
−    +   [[http:/github.com/murrayrm/grogro]] 
−    +   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W7_gro14May2020.pdfW7_gro14May2020.pdf]] 
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 W8  21 May   W8  21 May  
+   Bioscrape Lineages as a wellmixed version of gro  
+   William  
+   [[http:github.com/ananswam/bioscrape/wiki/LineagePackageBioscrape Lineages]]  
+   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W8_lineages21May2020.ipynbW8_lineages21May2020.ipynb]],  
+  [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/RepressillatorCRN.sbmlRepressillatorCRN.sbml]],  
+  [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/ToggleCRN.sbmlToggleCRN.sbml]]  
+   valign=top  
+   W9  28 May  
 System ID: Bioscrape inference tools   System ID: Bioscrape inference tools  
 Ayush   Ayush  
−    +   [[http:github.com/ananswam/bioscrape/wiki/ParameterInferenceandIdentificationBioscrape Inference]] 
−  +   [[http:www.cds.caltech.edu/~murray/courses/be240/sp2020/W9_inference28May2020.ipynbW9_inference28May2020.ipynb]]  
−  
−  
−   Bioscrape  
−    
−  
−    
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 W10  4 Jun   W10  4 Jun  
−    +   TBD 
−    +   TBD 
−    +   TBD 
    
}  } 
Latest revision as of 14:50, 28 May 2020
Open Source Tools for Biological Circuit Design  
Instructors

Class meeting times

This is the course homepage for BE 240, Spring 2020.
This course 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. Finally, the course aims to expand the available applications of modelbased design of biological circuits and/or the available tools for biological circuit design through open source implementations.
Lecture Schedule
Each week of the course will cover a different topic and/or tool. The first class meeting of the week (Thu session) will be a description of the use of that tool on a representative problem, carried out using a Jupyter notebook that students can download and follow along with the instructor. The second class meeting of the week (the following Tue) will consist of problems brought forth by students in the class as they have tried to implement the tools on their own problems. These problems will be discussed and solved in a group setting. Weekly office hours will be offered between the lectures to allow students to ask questions about individual tools and problem and receive help via Slack and/or Zoom.
Date  Topic  Lecturer  Tools  Notes 
W1  31 Mar  Organizational week  Richard  Anaconda, Jupyter, GitHub  Computer setup instructions 
W2  7 Apr  CRNs and simulating them with Bioscrape  William  Bioscrape  W2_bioscrape.ipynb (Jupyter notebook) 
W3  16 Apr  Intro to SBML and nonmassaction propensities & rules in bioscrape  Ayush  Bioscrape  W3_sbml_p1.ipynb, W3_sbml_p2.ipynb (Jupyter notebook), repressilator_sbml.xml 
W4  23 Apr  BioCRNpyler for generating large CRN models from parts  William  BioCRNpyler  W4_biocrnpyler.ipynb (Jupyter notebook), parameters.txt 
W5  30 Apr  Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML  Ayush  SubSBML  W5_subsbml.ipynb, subsbml_generate_models.ipynb (Jupyter notebooks), 
W6  7 May  Spatial systems and signalling  Cindy  gro  W6_gro07May2020.pdf 
W7  14 May  Cells and Growth/death regulation  Cindy  gro  W7_gro14May2020.pdf 
W8  21 May  Bioscrape Lineages as a wellmixed version of gro  William  Bioscrape Lineages  W8_lineages21May2020.ipynb, 
W9  28 May  System ID: Bioscrape inference tools  Ayush  Bioscrape Inference  W9_inference28May2020.ipynb 
W10  4 Jun  TBD  TBD  TBD 
Grading
This class is graded pass/fail. To pass the class, you must participate in at least 80% of the lectures and recitations and submit a final project report consisting of a Jupyter notebook demonstrating the use of two or more of the tools in the class on a problem of interest to your research.
Collaboration Policy
Collaboration is encouraged in figuring out how to use all of the tools of this course. The final project report should represent your individual understanding of how to apply the tools demonstrated in this course to a problem of interest to your research. Obtaining feedback and advice from the instructors, course participants, or others on the final project is allowed, but the final code included in the project should be written up individually, citing any sources of code snippets that are included in the notebook.