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Cell models
h1_hesc Closed MIT Latest Latest Failed Results 91.9% 0 / 5 10409 5874 0 0 Yin Hoon Chew 2020-09-08 15:18 9
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Failed Results 72.8% 0 / 1 6276 4789 0 0 Jonathan Karr 2020-06-26 12:39 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 / 4 5845 8759 0 0 Jonathan Karr 2020-06-26 14:53 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 2420 1207 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 47.4% 6 / 67 13176 9592 0 2 VictoriaGao1 2020-08-18 16:46 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 Failed 74.8% 18 / 327 9001 3412 0 1 Zhouyang Lian 2020-09-15 18:43 4
Finds the most relevant kinetic data for biochemical models
datanator_query_python Open MIT v1.0.0 Latest Success Results 77.9% 1 / 16 1023 2647 0 0 Zhouyang Lian 2020-09-14 14:25 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 75.9% 4 / 121 2649 5258 0 0 Zhouyang Lian 2020-08-03 09:26 4
A OAS3 compliant REST API for the Datanator integrated database
wc_analysis Open MIT Latest Latest Failed Results 89.5% 0 / 0 1646 9588 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 1793 2347 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 1990 1393 0 0 Jonathan Karr 2020-06-26 12:50 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Failed Results 93.8% 12 / 31 4290 12276 0 5 Jonathan Karr 2020-07-09 06:50 6
Tools for building and describing knowledge bases for whole-cell models
wc_kb_gen Open MIT Latest Latest Failed Results 16.5% 6 / 6 2442 8093 0 0 Jonathan Karr 2020-06-26 17:55 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 Failed Results 99.8% 25 / 137 6919 16781 0 3 Yin Hoon Chew 2020-09-07 17:20 6
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 93.7% 10 / 17 6763 13511 0 2 Yin Hoon Chew 2020-09-07 14:49 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 1313 7122 0 0 Yin Hoon Chew 2020-06-10 12:39 5
Ontology for whole-cell modeling
wc_rules Open MIT Latest Latest Success Results 42.6% 5 / 10 4379 3275 0 3 Jonathan Karr 2020-06-26 13:00 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 97.6% 35 / 106 10220 15375 0 2 Arthur Goldberg 2020-08-21 14:50 6
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Failed Results 78.7% 0 / 0 1062 9389 0 0 Jonathan Karr 2020-06-26 13:01 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.22 Latest Success Results 81.8% 3 / 37 6950 40183 0 1 Jonathan Karr 2020-09-08 07:13 5
Whole-cell modeling utilities
Modeling and simulation tools
bcforms Open MIT 0.0.9 Latest Success Results 94.8% 0 / 0 2509 5068 0 0 Jonathan Karr 2020-07-09 06:55 3
Toolkit for concretely describing macromolecular complexes
bpforms Open MIT 0.0.16 Latest Success Results 75.6% 2 / 106 4413 9831 0 1 Jonathan Karr 2020-07-09 06:53 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 Failed Results 72.5% 0 / 0 2822 7080 0 0 1 Jonathan Karr 2020-06-26 11:46 2
High-level Python package for solving linear and quadratic optimization problems using multiple open-source and commercials solvers
de_sim Open MIT 0.1.1 Latest Success Results 99.2% 14 / 54 2818 4276 0 1 Arthur Goldberg 2020-09-17 13:01 3
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2449 7728 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% 19 / 159 6552 18568 0 0 Jonathan Karr 2020-09-08 07:16 6
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.5 Latest Success Results 99.0% 0 / 1 1957 28815 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 1380 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 3116 2547 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% 0 / 3 4273 3041 0 0 1 Jonathan Karr 2020-07-19 20:05 2
Command line programs to save Google documents to files
latex-grant Open MIT0.0.3 0.0.5 Latest 0 / 1 4953 965 0 5 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 2191 20179 0 0 Zhouyang Lian 2020-09-02 14:04 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 4843 31297 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 6873 4327 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 / 0 551 589 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 / 1 322 463 0 0 Arthur Goldberg 2020-04-27 09:47 3
Code associated with our 2018 review in Current Opinion in Systems Biology
Other