Biological Circuit Design
=============================================================

This course focuses on quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Topics are approached from experimental, theoretical and computational perspectives. Our goals for the class are (a) to build understanding of key principles of systems biology and (b) to develop skills for modeling and analysis of genetic circuits.

Useful links
-------------

- `Ed <https://edstem.org/us/courses/5128/>`_ (used for course communications)
- `Course Zoom link <http://be150.caltech.edu/2021/zoom/>`_ 
- `"200 Broad" Gather link <http://be150.caltech.edu/2021/gather/>`_
- `Video recordings <http://be150.caltech.edu/2021/videos/>`_


People
------

- Instructors

   + `Justin Bois <http://bois.caltech.edu/>`_ (`bois at caltech dot edu`)
   + `Michael Elowitz <https://www.elowitz.caltech.edu>`_ (`melowitz at caltech dot edu`)

- TAs

   + John Marken (`jmarken at caltech dot edu`)
   + Ankita Roychoudhury (`aroychou at caltech dot edu`)


.. toctree::
   :maxdepth: 1
   :caption: Chapters

   chapters/00_setting_up_python_computing_environment
   chapters/01_intro_to_circuit_design
   chapters/02_intro_to_python_for_biological_circuits
   chapters/03_small_circuits
   chapters/04_finding_motifs
   chapters/05_cffls
   chapters/06_functions_of_iffls
   chapters/07_molecular_titration
   chapters/08_robustness
   chapters/09_kinetic_proofreading
   chapters/10_repressilator
   chapters/11_delay_oscillators
   chapters/12_noise
   chapters/13_bursty
   chapters/14_stochastic_simulation
   chapters/15_stochastic_differentiation
   chapters/16_bet_hedging
   chapters/17_time-based_regulation
   chapters/18_paradoxical
   chapters/21_turing
   chapters/22_scaling_morphogens
   chapters/appA_regulatory_functions


.. toctree::
   :maxdepth: 1
   :caption: Homework

   homework/01/index
   homework/02/index
   homework/03/index
   homework/04/index
   homework/05/index
   homework/06/index
   homework/07/index
   homework/08/index
   homework/09/index
   homework/10/index

.. toctree::
   :maxdepth: 1
   :caption: Schedule

   schedule


.. toctree::
   :maxdepth: 1
   :caption: Policies

   policies


.. toctree::
   :maxdepth: 1
   :caption: Resources

   resources

.. toctree::
   :maxdepth: 1
   :caption: Package docs 

   package_docs/index