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


.. .. toctree::
..    :maxdepth: 1
..    :caption: Front matter

..    front_matter/preface.rst
..    front_matter/technique_toc.rst



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

   chapters/00_setting_up_python_computing_environment.ipynb
   chapters/01_intro_to_circuit_design.ipynb
   chapters/02_response_time.ipynb
   chapters/03_bistability.ipynb
   chapters/04_ffls.ipynb
   chapters/05_dosage_compensation.ipynb
   chapters/06_exact_adaptation.ipynb
   chapters/07_signal_amplification.ipynb
   chapters/08_kinetic_proofreading.ipynb
   chapters/09_repressilator.ipynb
   chapters/10_delay_oscillators.ipynb
   chapters/11_time-based_regulation.ipynb
   chapters/12_molecular_titration.ipynb
   chapters/13_promiscuous_binding.ipynb
   chapters/14_multifate.ipynb
   chapters/15_noise.ipynb
   chapters/16_bursty.ipynb
   chapters/17_bet_hedging.ipynb
   chapters/18_stochastic_differentiation.ipynb
   chapters/20_lateral_inhibition.ipynb
   chapters/21_turing.ipynb
   chapters/22_scaling_morphogens.ipynb

.. toctree::
   :maxdepth: 1
   :caption: Technical Appendices

   technical_appendices/02a_approximate_autorepression_dynamics.ipynb
   technical_appendices/02b_numerical_odes.ipynb
   technical_appendices/02c_interactive_plotting.ipynb
   technical_appendices/03a_nondimensionalization.ipynb
   technical_appendices/04a_numerical_solutions_of_ffls.ipynb
   technical_appendices/09a_composite_functions_to_find_fixed_point.ipynb
   technical_appendices/09b_linear_stability_analysis.ipynb
   technical_appendices/09c_1d_root_finding.ipynb
   technical_appendices/10a_brute_force_linear_stability_analysis.ipynb
   technical_appendices/10b_gershgorin.ipynb
   technical_appendices/10c_numerical_ddes.ipynb
   technical_appendices/10d_linear_stability_analysis_ddes.ipynb
   technical_appendices/16a_gillespie.ipynb
   technical_appendices/16b_profiling_for_speed.ipynb

.. toctree::
   :maxdepth: 1
   :caption: Appendices

   appendices/appA_math/index.rst
   appendices/appB_python/index.rst
   appendices/appC_numerical_odes.ipynb
   appendices/appD_regulatory_functions.ipynb


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

   package_docs/index