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Cell models
h1_hesc Closed MIT Latest Latest Success Results 91.6% 0 / 5 9470 5164 0 0 Zhouyang Lian 2020-04-03 13:36 9
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Success Results 72.9% 0 / 1 6206 4245 0 0 Jonathan Karr 2020-03-19 20:31 5
Whole-cell model of the reduced gram-positive pathogenic bacterium Mycoplasma pneumoniae
rand_wc_model_gen Open MIT Latest Latest Failed Results 37.9% 3 / 3 5595 7541 0 0 Jonathan Karr 2020-03-19 20:31 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 2294 1083 0 0 Jonathan Karr 2015-04-20 17:25 1
Software to generate synthetic dynamic transcriptomic and proteomic data
Cell modeling and simulation tools
datanator Open MIT Latest Latest Success Results 56.6% 3 / 36 11371 8921 0 2 Zhouyang Lian 2020-04-01 17:29 9
Toolkit for discovering and aggregating data for whole-cell modeling
datanator_flask_REST Closed MIT Latest Success Results 84.5% 0 / 1 403 202 0 0 Zhouyang Lian 2019-09-10 13:10 4
A REST API to for the Datanator toolkit server
datanator_frontend Closed MIT Latest Failed 88.2% 11 / 211 6745 2120 0 1 Jonathan Karr 2020-04-01 10:44 4
Finds the most relevant kinetic data for biochemical models
datanator_query_python Open MIT api Latest Success Results 76.9% 0 / 9 400 1251 0 0 Zhouyang Lian 2020-04-03 14:22 5
A package to query and format the data in the integrated Datanator database
datanator_rest_api Open MIT 0.0.1 Latest Success Results 83.6% 7 / 50 1205 2879 0 0 Zhouyang Lian 2020-04-01 09:12 4
A OAS3 compliant REST API for the Datanator integrated database
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 1420 8212 0 1 Jonathan Karr 2020-03-19 20:32 1
Tools for analyzing whole-cell knowledge bases, models, and simulation results
wc_cli Open MIT Latest Latest Success Results 98.2% 1 / 2 1599 2013 0 0 Jonathan Karr 2020-03-19 20:32 3
Framework for testing whole-cell knowledge bases and models
wc_env_manager Open MIT Latest Latest Success Results 21.6% 6 / 21 1775 1159 0 0 Jonathan Karr 2020-03-19 20:32 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 93.8% 12 / 31 3882 10647 0 4 Yin Hoon Chew 2020-03-23 09:06 6
Tools for building and describing knowledge bases for whole-cell models
wc_kb_gen Open MIT Latest Latest Success Results 96.5% 6 / 6 2289 6617 0 0 Jonathan Karr 2020-03-19 20:32 6
Framework for systematically and scalably building knowledge bases for whole-cell models
wc_lang Open MIT start_commi_for_round_trip_migration_test Latest Success Results 99.8% 24 / 133 6178 15153 0 2 Jonathan Karr 2020-03-19 20:32 6
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 93.9% 10 / 17 6108 11665 0 1 Yin Hoon Chew 2020-04-02 12:55 7
Framework for systematically and scalably designing whole-cell models from large datasets such as wc_kb
wc_onto Open MIT 0.0.2 Latest Success Results 100.0% 0 / 2 954 5224 0 0 Jonathan Karr 2020-03-19 20:33 5
Ontology for whole-cell modeling
wc_rules Open MIT Latest Latest Success Results 42.6% 5 / 10 3937 2891 0 2 Jonathan Karr 2020-03-19 20:33 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 94.8% 26 / 79 8371 13292 0 1 Arthur Goldberg 2020-04-01 10:48 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Failed Results 78.9% 0 / 0 947 7994 0 0 Arthur Goldberg 2020-03-31 14:09 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.15 Latest Success Results 82.6% 3 / 37 6448 35504 0 1 Arthur Goldberg 2020-04-01 09:19 5
Whole-cell modeling utilities
Modeling and simulation tools
bcforms Open MIT 0.0.8 Latest Success Results 94.9% 0 / 0 1998 3214 0 0 Jonathan Karr 2020-03-19 20:28 3
Toolkit for concretely describing macromolecular complexes
bpforms Open MIT 0.0.15 Latest Failed Results 74.2% 2 / 106 3892 7685 0 1 Jonathan Karr 2020-03-19 20:28 4
Python package for unambiguously representing the structure of modified forms of biopolymers such as DNA, RNA, and protein
conv_opt Open MIT 0.0.12 Latest Success Results 76.1% 0 / 0 2300 5525 0 0 1 Jonathan Karr 2020-03-19 20:28 2
High-level Python package for solving linear and quadratic optimization problems using multiple open-source and commercials solvers
de_sim Open MIT Latest Latest Success Results 98.1% 17 / 38 1497 1883 0 0 Arthur Goldberg 2020-03-31 12:06 3
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2340 7494 0 0 0 Jonathan Karr 2020-03-19 20:31 1
Converts nose-style XML test reports to UnitTH-style XML test reports
OASTools Open MIT v0.0.2 Latest Failed 17.8% 2 / 8 0 0 0 1 Bilal Shaikh 2019-09-17 09:49 2
A python package to provide tooling for the Open API Specification
obj_tables Open MIT 0.0.9 Latest Success Results 35.6% 14 / 133 5530 16689 0 0 Jonathan Karr 2020-03-30 18:52 6
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.5 Latest Success Results 99.0% 0 / 1 1802 25878 0 0 0 Jonathan Karr 2020-03-19 20:31 4
Utilities for linking setuptools with package version metadata, GitHub README.md files, requirements.txt files, and restoring overridden entry points during for editable installations
test_history_server Open MIT 0.0.3 Latest 0 / 1 1973 1255 0 0 Jonathan Karr 2019-09-18 13:44 1
Unit test history server (tests.karrlab.org)
unitth Open MIT 0.0.14 Latest Success Results 100.0% 0 / 3 2737 2318 0 0 0 Jonathan Karr 2020-03-19 20:31 1
Generate HTML test history report
Other scientific and software tools
gdoc_down Open MIT 0.0.8 Latest Success Results 100.0% 0 / 1 3811 2746 0 0 1 Jonathan Karr 2020-03-19 20:30 1
Command line programs to save Google documents to files
latex-grant Open MIT0.0.3 0.0.5 Latest 0 / 1 4322 836 0 4 Jonathan Karr 2019-02-26 20:11 1
LaTeX classes for federal grant applications
Karr Lab utilities
karr_lab_build_config Closed MIT Latest 0 / 0 1940 17081 0 0 Zhouyang Lian 2020-04-03 08:42 3
Private configuration (e.g., passwords) for the Karr Lab builds
karr_lab_build_utils Open MIT 0.0.11 Latest Success Results 85.7% 1 / 40 4421 28583 0 0 Jonathan Karr 2020-03-19 20:27 4
Utility functions for building, testing, and documenting software
Training materials
intro_to_wc_modeling Open MIT Latest Latest Success Results 99.2% 2 / 2 6256 3776 0 3 Jonathan Karr 2020-03-19 20:30 3
Jupyter playground for learning about whole-cell modeling, https://sandbox.karrlab.org
Code used for papers
paper_2018_curr_opin_biotechnol Open MIT Latest 0 / 0 495 502 0 0 Jonathan Karr 2019-04-04 08:43 1
Code associated with the Karr Lab's 2018 whole-cell modeling review in Current Opinion in Biotechnology
paper_2018_curr_opin_sys_biol Open MIT Latest 0 / 0 229 329 0 0 Jonathan Karr 2017-12-14 10:04 2
Code associated with our 2018 review in Current Opinion in Systems Biology
Other