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Cell models
h1_hesc Closed MIT Latest Success Results 89.6% 0 / 5 7252 3763 0 0 Yin Hoon Chew 2019-07-18 08:56 8
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Success Results 73.0% 0 / 1 5845 3677 0 0 balazs1987 2019-07-10 13:28 5
Whole-cell model of the reduced gram-positive pathogenic bacterium Mycoplasma pneumoniae
rand_wc_model_gen Open MIT Latest Latest Failed Results 39.2% 3 / 3 3339 5105 0 0 Arthur Goldberg 2019-07-05 07:30 7
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 1861 919 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 43.6% 2 / 20 10240 7356 0 2 Zhouyang Lian 2019-07-19 15:03 9
Toolkit for discovering and aggregating data for whole-cell modeling
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 1145 5336 0 1 Jonathan Karr 2019-06-26 10:14 1
Tools for analyzing whole-cell knowledge bases, models, and simulation results
wc_cli Open MIT Latest Latest Success Results 98.2% 1 / 2 1243 1320 0 0 Jonathan Karr 2019-06-27 22:03 3
Framework for testing whole-cell knowledge bases and models
wc_env_manager Open MIT Latest Latest Success Results 22.0% 4 / 14 1506 918 0 0 Jonathan Karr 2019-06-27 21:16 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 91.9% 13 / 28 3563 8806 0 3 Arthur Goldberg 2019-07-04 11:13 6
Tools for building and describing knowledge bases for whole-cell models
wc_kb_gen Open MIT Latest Latest Failed Results 96.7% 6 / 6 2085 5022 0 0 Arthur Goldberg 2019-07-05 07:27 6
Framework for systematically and scalably building knowledge bases for whole-cell models
wc_lang Open MIT Latest Latest Fixed Results 100.0% 15 / 116 5478 13189 0 2 Arthur Goldberg 2019-07-19 13:49 5
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 92.3% 9 / 16 3737 6825 0 1 YinHoon 2019-07-17 16:27 7
Framework for systematically and scalably designing whole-cell models from large datasets such as wc_kb
wc_rules Open MIT Latest Latest Failed Results 42.7% 5 / 10 3586 2431 0 2 Jonathan Karr 2019-06-26 10:16 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Failed Results 94.0% 23 / 50 4984 8993 0 1 Arthur Goldberg 2019-07-06 07:37 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Success Results 78.7% 0 / 0 830 5036 0 0 Jonathan Karr 2019-06-26 10:17 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.8 Latest Success Results 79.3% 3 / 35 5335 25082 0 0 Jonathan Karr 2019-07-18 07:42 5
Whole-cell modeling utilities
Modeling and simulation tools
bpforms Open MIT 0.0.5 Latest Success Results 83.5% 0 / 91 2022 2789 0 1 Jonathan Karr 2019-07-19 15:11 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 1661 3754 0 0 1 Jonathan Karr 2019-06-26 10:10 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 / 0 168 311 0 0 Jonathan Karr 2019-06-26 10:11 2
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2121 7191 0 0 0 Jonathan Karr 2019-06-26 10:13 1
Converts nose-style XML test reports to UnitTH-style XML test reports
obj_model Open MIT 0.0.6 Latest Failed Results 35.6% 11 / 45 4632 14343 0 0 Arthur Goldberg 2019-07-06 15:13 4
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.4 Latest Success Results 99.7% 0 / 0 1204 22686 0 0 0 Jonathan Karr 2019-06-26 10:13 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 1959 1149 0 0 Jonathan Karr 2019-06-27 21:15 1
Unit test history server (tests.karrlab.org)
unitth Open MIT 0.0.14 Latest Success Results 100.0% 0 / 3 2171 1914 0 0 0 Jonathan Karr 2019-06-26 10:14 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 2924 2260 0 0 1 Jonathan Karr 2019-06-26 10:11 1
Command line programs to save Google documents to files
latex-grant Open MIT0.0.3 0.0.5 Latest 0 / 1 3447 694 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 1521 11317 0 0 Zhouyang Lian 2019-07-12 11:54 3
Private configuration (e.g., passwords) for the Karr Lab builds
karr_lab_build_utils Open MIT 0.0.11 Latest Success Results 86.2% 3 / 30 3140 23208 0 0 Jonathan Karr 2019-06-27 21:15 3
Utility functions for building, testing, and documenting software
karr_lab_website Open MIT Latest 1 / 1 1152 571 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 Success Results 99.2% 2 / 2 4962 2844 0 2 Arthur Goldberg 2019-07-05 06:27 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 / 0 405 475 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 / 0 226 302 0 0 Jonathan Karr 2017-12-14 10:04 2
Code associated with our 2018 review in Current Opinion in Systems Biology
Other
bcforms Open MIT Latest Latest Success Results 99.0% 0 / 0 567 113 0 0 Jonathan Karr 2019-07-18 22:41 3
Toolkit for concretely describing macromolecular complexes
minicell_website Open MIT Latest 0 / 0 100 153 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 84.6% 0 / 2 624 2967 0 0 Jonathan Karr 2019-06-26 10:16 4
Ontology for whole-cell modeling