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Cell models
h1_hesc Closed MIT Latest Latest Success Results 91.8% 0 / 5 9118 4925 0 0 Yin Hoon Chew 2020-02-16 13:54 9
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Failed Results 72.9% 0 / 1 6198 4053 0 0 Jonathan Karr 2020-01-08 11:22 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 5427 7144 0 0 Jonathan Karr 2020-01-08 11:22 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 2184 1047 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 56.8% 3 / 31 11208 8730 0 2 Jonathan Karr 2020-02-12 08:56 9
Toolkit for discovering and aggregating data for whole-cell modeling
datanator_flask_REST Closed MIT Latest Success Results 84.5% 0 / 1 399 202 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 93.2% 15 / 179 5366 1546 0 1 Jonathan Karr 2020-02-14 15:32 4
Finds the most relevant kinetic data for biochemical models
datanator_query_python Open MIT api Latest Success Results 78.5% 1 / 4 251 726 0 0 zhouyang.lian 2020-02-14 09:35 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 86.6% 11 / 43 808 1976 0 0 zhouyang.lian 2020-02-14 09:45 4
A OAS3 compliant REST API for the Datanator integrated database
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 1350 7754 0 1 Jonathan Karr 2020-01-08 11:22 1
Tools for analyzing whole-cell knowledge bases, models, and simulation results
wc_cli Open MIT Latest Latest Success Results 98.2% 1 / 2 1574 1895 0 0 Jonathan Karr 2020-01-08 11:22 3
Framework for testing whole-cell knowledge bases and models
wc_env_manager Open MIT Latest Latest Success Results 21.6% 6 / 21 1720 1086 0 0 Jonathan Karr 2020-01-09 14:19 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 93.8% 12 / 31 3728 10018 0 4 Yin Hoon Chew 2020-02-14 09:36 6
Tools for building and describing knowledge bases for whole-cell models
wc_kb_gen Open MIT Latest Latest Failed Results 96.5% 6 / 6 2216 6070 0 0 Jonathan Karr 2020-01-08 11:22 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% 23 / 132 6058 14399 0 2 Yin Hoon Chew 2020-01-21 12:05 6
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 93.7% 10 / 17 5633 10912 0 1 Yin Hoon Chew 2020-02-14 12:04 7
Framework for systematically and scalably designing whole-cell models from large datasets such as wc_kb
wc_onto Open MIT Latest Latest Success Results 100.0% 0 / 2 940 4408 0 0 Yin Hoon Chew 2020-01-10 15:20 5
Ontology for whole-cell modeling
wc_rules Open MIT Latest Latest Success Results 42.6% 5 / 10 3905 2719 0 2 Jonathan Karr 2020-01-08 11:23 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 93.4% 24 / 76 8071 12570 0 1 Arthur Goldberg 2020-02-08 09:01 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Failed Results 78.9% 0 / 0 914 7526 0 0 Jonathan Karr 2020-01-08 11:23 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.10 Latest Fixed Results 80.2% 3 / 37 6158 33620 0 1 Arthur Goldberg 2020-02-07 15:15 5
Whole-cell modeling utilities
Modeling and simulation tools
bcforms Open MIT 0.0.3 Latest Success Results 95.0% 0 / 0 1865 2327 0 0 Jonathan Karr 2020-01-08 11:20 3
Toolkit for concretely describing macromolecular complexes
bpforms Open MIT 0.0.10 Latest Success Results 75.8% 2 / 106 3200 6773 0 1 Jonathan Karr 2020-01-08 11:20 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 76.2% 0 / 0 2182 5009 0 0 1 Jonathan Karr 2020-01-08 11:20 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 98.0% 16 / 33 1324 1230 0 0 Jonathan Karr 2020-01-08 11:21 3
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2134 7346 0 0 0 Jonathan Karr 2020-01-08 11:22 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 0.0.8 Latest Failed Results 35.6% 23 / 114 5095 15791 0 0 Yin Hoon Chew 2020-01-21 09:26 6
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.4 Latest Success Results 98.1% 1 / 1 1722 24724 0 0 0 Jonathan Karr 2020-01-08 11:22 3
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 1219 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 2521 2237 0 0 0 Jonathan Karr 2020-01-08 11:22 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 3642 2633 0 0 1 Jonathan Karr 2020-01-08 11:21 1
Command line programs to save Google documents to files
latex-grant Open MIT0.0.3 0.0.5 Latest 0 / 1 4166 809 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 1933 16052 0 0 zhouyang.lian 2020-01-23 09:01 3
Private configuration (e.g., passwords) for the Karr Lab builds
karr_lab_build_utils Open MIT 0.0.11 Latest Success Results 85.5% 5 / 39 3858 27603 0 0 Jonathan Karr 2020-01-08 11:21 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 6090 3582 0 3 Arthur Goldberg 2020-02-10 11:15 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 / 0 468 488 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 / 0 229 315 0 0 Jonathan Karr 2017-12-14 10:04 2
Code associated with our 2018 review in Current Opinion in Systems Biology
Other