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de_sim
Python-based object-oriented discrete-event simulation tool for complex, data-driven modelinglatex-grant
LaTeX classes for formatting scientific documents, including US federal grant proposals.intro_to_wc_modeling
Whole-cell modeling tutorialsdatanator
Toolkit for discovering and aggregating data for whole-cell modelinggdoc_down
Command line programs to save Google documents to text and LaTeX fileswc_rules
Rule-based modeling for whole-cell models.wc_lang
Language for describing whole-cell models as reaction networksconv_opt
Python package for linear and quadratic programmingobj_tables
Tools for creating and reusing high-quality spreadsheetswc_model_gen
Framework for systematically and scalably designing whole-cell models from large datasetsbpforms
Toolkit for concretely describing non-canonical DNA, RNA, and proteinswc_sim
A multi-algorithmic simulator for whole-cell modelsSynNetGen
Software to generate synthetic dynamic transcriptomic and proteomic datawc_kb
Tools for building databases of experimental data for constructing whole-cell modelsWcModelingTutorial
unitth
Python interface for UnitTH unit test history report generatorpaper_2018_curr_opin_biotechnol
Code associated with the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnologywc_analysis
Tools for analyzing whole-cell knowledge bases, models, and simulation resultsrand_wc_model_gen
Generate random whole-cell modelswc_onto
Ontology for whole-cell modelingexamples_for_presentations
Examples for presentationswc_utils
Utilities for whole-cell modeling such as logging, plotting, managing git repos, random number generation and otherswc_sandbox
A public jupyter notebook server for live documentation of karr lab packagesLove Open Source and this site? Check out how you can help us