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Cell models
h1_hesc Closed MIT Latest Latest Success Results 91.9% 0 / 5 11630 6301 0 0 Yin Hoon Chew 2021-06-11 14:57 9
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Success Results 72.8% 0 / 1 6424 5232 0 0 Jonathan Karr 2021-05-28 09:56 5
Whole-cell model of the reduced gram-positive pathogenic bacterium Mycoplasma pneumoniae
rand_wc_model_gen Open MIT Latest Latest Success Results 37.9% 3 / 4 5888 9314 0 0 Jonathan Karr 2021-05-28 09:55 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 2776 1427 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 47.3% 2 / 70 14384 10032 0 2 Jonathan Karr 2020-10-07 20:36 11
Toolkit for discovering and aggregating data for whole-cell modeling
datanator_flask_REST Closed MIT Latest Success Results 84.5% 0 / 1 478 202 0 0 Zhouyang Lian 2019-09-10 13:10 4
A REST API to for the Datanator toolkit server
datanator_frontend Closed MIT Latest Success 74.5% 11 / 100 10039 4832 0 1 Jonathan Karr 2020-10-12 08:02 4
Finds the most relevant kinetic data for biochemical models
datanator_query_python Open MIT v1.0.0 Latest Failed Results 78.0% 1 / 18 1915 3270 0 1 Zhouyang Lian 2020-10-12 07:59 5
A package to query and format the data in the integrated Datanator database
datanator_rest_api Open MIT v1.0.0 Latest Success Results 75.2% 4 / 100 4211 5787 0 0 Zhouyang Lian 2020-12-01 06:23 4
A OAS3 compliant REST API for the Datanator integrated database
wc_analysis Open MIT Latest Latest Failed Results 89.5% 0 / 0 1773 10427 0 1 Jonathan Karr 2020-06-26 12:48 1
Tools for analyzing whole-cell knowledge bases, models, and simulation results
wc_cli Open MIT Latest Latest Success Results 98.2% 1 / 2 1897 2691 0 0 Jonathan Karr 2020-04-27 11:51 3
Framework for testing whole-cell knowledge bases and models
wc_env_manager Open MIT Latest Latest Success Results 21.4% 6 / 21 2455 1732 0 0 Jonathan Karr 2021-06-13 16:18 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 93.8% 12 / 31 5020 13146 0 5 Yin Hoon Chew 2020-12-18 15:49 6
Tools for building and describing knowledge bases for whole-cell models
wc_kb_gen Open MIT Latest Latest Success Results 96.4% 6 / 6 2820 8775 0 0 Jonathan Karr 2021-06-13 16:57 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% 27 / 100 7719 17714 0 4 Yin Hoon Chew 2021-05-24 14:57 6
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 93.6% 10 / 17 7319 14259 0 2 Yin Hoon Chew 2021-06-11 14:55 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 97.4% 0 / 2 1481 8115 0 0 Arthur Goldberg 2020-12-16 10:17 5
Ontology for whole-cell modeling
wc_rules Open MIT Latest Latest Success Results 80.8% 1 / 13 5309 3847 0 3 John Sekar 2021-06-08 19:49 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 97.2% 35 / 100 11626 16411 0 2 Yin Hoon Chew 2021-06-02 15:29 6
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Failed Results 71.3% 0 / 0 1110 9934 0 0 Jonathan Karr 2021-05-28 09:56 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.24 Latest Success Results 81.8% 3 / 37 7464 42513 0 1 Arthur Goldberg 2020-09-28 15:38 5
Whole-cell modeling utilities
Modeling and simulation tools
bcforms Open MIT 0.0.9 Latest Success Results 94.8% 0 / 0 2766 6149 0 0 Jonathan Karr 2020-07-09 06:55 3
Toolkit for concretely describing macromolecular complexes
bpforms Open MIT 0.0.16 Latest Failed Results 75.6% 4 / 100 5061 11022 0 2 Jonathan Karr 2020-10-05 15:01 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% 2 / 2 3507 7837 0 0 1 Jonathan Karr 2021-05-28 09:45 3
High-level Python package for solving linear and quadratic optimization problems using multiple open-source and commercials solvers
de_sim Open MIT 1.0.5 Latest Success Results 99.1% 14 / 66 4581 5328 0 3 Arthur Goldberg 2020-12-17 06:34 3
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2602 8011 0 0 0 Jonathan Karr 2020-06-26 12:41 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 1.0.14 Latest Success Results 97.2% 10 / 100 7619 19552 0 2 Jonathan Karr 2021-06-13 17:08 7
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.5 Latest Success Results 99.0% 0 / 1 2355 30280 0 0 0 Jonathan Karr 2020-06-26 12:45 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 2135 1594 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 3461 2857 0 0 0 Jonathan Karr 2020-06-26 12:49 1
Generate HTML test history report
Other scientific and software tools
gdoc_down Open MIT 0.0.10 Latest Success Results 100.0% 1 / 5 5215 3371 0 0 2 Jonathan Karr 2020-10-02 06:31 3
Command line programs to save Google documents to files
latex-grant Open MIT0.0.5 0.0.5 Latest 0 / 1 6159 1193 0 6 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 2224 21700 0 0 Jonathan Karr 2021-06-13 16:41 4
Private configuration (e.g., passwords) for the Karr Lab builds
karr_lab_build_utils Open MIT 0.0.11 Latest Success Results 85.5% 1 / 40 4942 32587 0 0 Jonathan Karr 2020-07-24 19:23 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 8321 5039 0 3 Jonathan Karr 2020-06-26 12:32 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 / 0 605 763 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 1 / 1 418 586 0 0 Arthur Goldberg 2020-04-27 09:47 3
Code associated with our 2018 review in Current Opinion in Systems Biology
Other