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Cell models
h1_hesc Closed MIT Latest Latest Success Results 78.2% 0 / 5 8110 4336 0 0 Yin Hoon Chew 2019-10-15 17:00 8
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Success Results 73.0% 0 / 1 5845 3766 0 0 Jonathan Karr 2019-10-10 23:05 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 / 3 4683 6229 0 0 Jonathan Karr 2019-10-10 23:03 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 2117 983 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 62.5% 2 / 22 10761 8185 0 2 zhouyang.lian 2019-10-15 14:13 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 Success 0.0% 3 / 7 2149 833 0 0 yosefdroth 2019-09-16 13:32 3
Finds the most relevant kinetic data for biochemical models
datanator_query_python Open MIT api Latest Success Results 83.0% 1 / 1 0 0 0 0 zhouyang.lian 2019-10-15 09:04 4
A package to query and format the data in the integrated Datanator database
datanator_rest_api Open MIT 0.0.1 Latest Success Results 88.8% 1 / 9 194 237 0 0 Bilal Shaikh 2019-09-27 12:18 4
A OAS3 compliant REST API for the Datanator integrated database
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 1249 6749 0 1 Jonathan Karr 2019-10-10 23:03 1
Tools for analyzing whole-cell knowledge bases, models, and simulation results
wc_cli Open MIT Latest Latest Success Results 98.2% 1 / 2 1489 1596 0 0 Jonathan Karr 2019-09-24 20:54 3
Framework for testing whole-cell knowledge bases and models
wc_env_manager Open MIT Latest Latest Success Results 22.0% 6 / 20 1532 932 0 0 Jonathan Karr 2019-09-25 12:26 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 93.8% 12 / 31 3589 9168 0 3 Jonathan Karr 2019-10-12 11:36 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 2090 5365 0 0 Jonathan Karr 2019-09-24 20:55 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 Success Results 99.8% 19 / 124 5607 13638 0 2 Jonathan Karr 2019-10-10 22:57 6
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 84.1% 10 / 17 4689 9104 0 1 Jonathan Karr 2019-10-10 23:14 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 84.6% 0 / 2 648 3436 0 0 Jonathan Karr 2019-09-18 13:46 4
Ontology for whole-cell modeling
wc_rules Open MIT Latest Latest Success Results 42.7% 5 / 10 3789 2575 0 2 Jonathan Karr 2019-09-18 13:05 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 91.9% 20 / 52 5896 11096 0 1 Jonathan Karr 2019-10-10 23:02 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Success Results 78.7% 0 / 0 857 6450 0 0 Jonathan Karr 2019-10-10 22:57 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.10 Latest Success Results 79.2% 3 / 36 5789 30144 0 0 Jonathan Karr 2019-10-14 12:38 5
Whole-cell modeling utilities
Modeling and simulation tools
bcforms Open MIT 0.0.3 Latest Success Results 94.9% 0 / 0 1275 1039 0 0 Jonathan Karr 2019-09-30 09:52 3
Toolkit for concretely describing macromolecular complexes
bpforms Open MIT 0.0.10 Latest Success Results 95.9% 2 / 106 2911 5414 0 1 Jonathan Karr 2019-10-07 09:58 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 82.3% 0 / 0 1915 4372 0 0 1 Yin Hoon Chew 2019-10-01 12:44 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 97.9% 12 / 23 772 445 0 0 Arthur Goldberg 2019-10-02 08:51 3
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2121 7215 0 0 0 Jonathan Karr 2019-09-18 13:43 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 Success Results 97.8% 14 / 103 4672 14851 0 0 Jonathan Karr 2019-10-12 14:00 5
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.4 Latest Success Results 99.7% 0 / 0 1210 23130 0 0 0 Jonathan Karr 2019-09-18 12:44 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 1157 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 2293 2075 0 0 0 Jonathan Karr 2019-09-18 13:44 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 3214 2414 0 0 1 Jonathan Karr 2019-09-18 13:42 1
Command line programs to save Google documents to files
latex-grant Open MIT0.0.3 0.0.5 Latest 0 / 1 3755 726 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 1793 14013 0 0 zhouyang.lian 2019-10-10 12:08 3
Private configuration (e.g., passwords) for the Karr Lab builds
karr_lab_build_utils Open MIT 0.0.11 Latest Success Results 85.6% 3 / 37 3382 25753 0 0 Jonathan Karr 2019-10-14 12:38 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 5266 3126 0 3 Jonathan Karr 2019-10-10 22:57 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 / 0 411 475 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 / 0 229 302 0 0 Jonathan Karr 2017-12-14 10:04 2
Code associated with our 2018 review in Current Opinion in Systems Biology
Other