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Cell models
h1_hesc Closed MIT Latest Latest Success Results 89.1% 0 / 4 6399 3404 0 0 YinHoon 2019-05-26 12:25 7
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Failed Results 51.1% 0 / 1 5643 3372 0 0 balazs1987 2019-05-23 08:16 5
Whole-cell model of the reduced gram-positive pathogenic bacterium Mycoplasma pneumoniae
rand_wc_model_gen Open MIT Latest Latest Failed Results 38.8% 3 / 3 3158 4428 0 0 Jonathan Karr 2019-04-02 12:22 7
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 1718 884 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 Failed Results 68.4% 1 / 7 9573 6837 0 2 Zhouyang Lian 2019-05-26 08:10 8
Toolkit for discovering and aggregating data for whole-cell modeling
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 954 4590 0 1 Jonathan Karr 2019-04-03 16:27 1
Tools for analyzing whole-cell knowledge bases, models, and simulation results
wc_cli Open MIT Latest Latest Success Results 98.2% 0 / 0 1048 1128 0 0 Jonathan Karr 2019-04-02 12:22 2
Framework for testing whole-cell knowledge bases and models
wc_env_manager Open MIT Latest Latest Success Results 21.3% 3 / 13 1347 805 0 0 Arthur Goldberg 2019-05-16 05:36 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 91.8% 9 / 22 3231 7649 0 3 YinHoon 2019-05-26 12:22 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 1847 4071 0 0 balazs1987 2019-05-22 13:52 5
Framework for systematically and scalably building knowledge bases for whole-cell models
wc_lang Open MIT Latest Latest Success Results 100.0% 13 / 113 5013 11683 0 2 Jonathan Karr 2019-04-16 09:47 5
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 85.7% 9 / 16 3065 5605 0 1 balazs1987 2019-05-23 07:16 7
Framework for systematically and scalably designing whole-cell models from large datasets such as wc_kb
wc_rules Open MIT Latest Latest Success Results 42.7% 5 / 10 3243 2265 0 2 Jonathan Karr 2019-03-27 10:05 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 93.9% 23 / 50 4704 7786 0 1 Jonathan Karr 2019-04-03 16:27 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Success Results 78.7% 0 / 0 778 4261 0 0 Jonathan Karr 2019-04-03 16:27 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.6 Latest Success Results 78.2% 3 / 29 4988 21424 0 0 YinHoon 2019-05-24 19:13 5
Whole-cell modeling utilities
Modeling and simulation tools
bpforms Open MIT 0.0.5 Latest Success Results 99.6% 4 / 66 1386 1268 0 1 Jonathan Karr 2019-04-25 14:25 3
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 82.3% 0 / 0 1545 3351 0 0 1 Jonathan Karr 2019-03-27 10:02 1
High-level Python package for solving linear and quadratic optimization problems using multiple open-source and commercials solvers
desim Open MIT Latest Latest Success Results 100.0% 0 / 0 168 224 0 0 Jonathan Karr 2019-03-27 10:03 2
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2075 7102 0 0 0 Jonathan Karr 2019-03-27 10:04 1
Converts nose-style XML test reports to UnitTH-style XML test reports
obj_model Open MIT 0.0.6 Latest Success Results 97.8% 9 / 39 4283 12687 0 0 Arthur Goldberg 2019-05-26 13:16 4
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.4 Latest Success Results 99.7% 0 / 0 1138 20646 0 0 0 Jonathan Karr 2019-03-27 10:04 2
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 1945 1087 0 0 Jonathan Karr 2019-03-27 10:04 1
Unit test history server (tests.karrlab.org)
unitth Open MIT 0.0.14 Latest Success Results 100.0% 0 / 3 2058 1832 0 0 0 Jonathan Karr 2019-03-27 10:04 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 2812 2154 0 0 0 Jonathan Karr 2019-03-27 10:03 1
Command line programs to save Google documents to files
latex-grant Open MIT0.0.3 0.0.5 Latest 0 / 1 3175 660 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 1282 9340 0 0 Arthur Goldberg 2019-05-16 17:19 2
Private configuration (e.g., passwords) for the Karr Lab builds
karr_lab_build_utils Open MIT 0.0.11 Latest Success Results 86.0% 3 / 30 2911 21244 0 0 Jonathan Karr 2019-04-24 10:10 3
Utility functions for building, testing, and documenting software
karr_lab_website Open MIT Latest 1 / 1 1100 558 0 0 Jonathan Karr 2018-09-21 08:37 1
Code for Karr Lab website (karrlab.org)
Training materials
intro_to_wc_modeling Open MIT Latest Latest Failed Results 99.2% 2 / 2 4284 2436 0 2 Arthur Goldberg 2019-04-04 20:48 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 / 0 383 462 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 / 0 201 295 0 0 Jonathan Karr 2017-12-14 10:04 2
Code associated with our 2018 review in Current Opinion in Systems Biology
Other
minicell_website Open MIT Latest 0 / 0 100 145 0 0 Jonathan Karr 2018-03-30 06:12 1
Code for the MiniCell consortium website (minicell.org)
wc_onto Open MIT Latest Latest Success Results 100.0% 0 / 2 390 1420 0 0 balazs1987 2019-05-23 07:15 4
Ontology for whole-cell modeling