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Cell models
h1_hesc Closed MIT Latest Latest Success Results 89.1% 0 / 5 8629 4620 0 0 Yin Hoon Chew 2019-12-05 11:17 9
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Success Results 72.9% 0 / 1 6170 3802 0 0 Arthur Goldberg 2019-11-05 06:23 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 4708 6678 0 0 Jonathan Karr 2019-10-10 23:03 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 2163 1011 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 51.8% 2 / 25 10888 8432 0 2 zhouyang.lian 2019-12-09 14:38 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 0.0% 9 / 13 2923 1106 0 0 yosefdroth 2019-12-09 17:31 3
Finds the most relevant kinetic data for biochemical models
datanator_query_python Open MIT api Latest Success Results 81.6% 2 / 2 60 110 0 0 zhouyang.lian 2019-12-09 14:36 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 86.5% 1 / 10 301 583 0 0 zhouyang.lian 2019-12-04 15:00 4
A OAS3 compliant REST API for the Datanator integrated database
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 1314 7215 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 1505 1726 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 21.7% 6 / 20 1567 943 0 0 Yin Hoon Chew 2019-11-05 09:02 3
Tools for managing computing environments for WC modeling
wc_kb Open MIT Latest Latest Success Results 93.8% 12 / 31 3635 9282 0 4 Jonathan Karr 2019-10-29 11:09 6
Tools for building and describing knowledge bases for whole-cell models
wc_kb_gen Open MIT Latest Latest Success Results 96.5% 6 / 6 2090 5456 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 Fixed Results 99.8% 21 / 127 5746 13738 0 2 Arthur Goldberg 2019-11-09 07:26 6
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 94.3% 10 / 17 5201 10032 0 1 Yin Hoon Chew 2019-12-09 09:40 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 / 2 666 3544 0 0 Arthur Goldberg 2019-10-19 14:30 5
Ontology for whole-cell modeling
wc_rules Open MIT Latest Latest Failed Results 42.7% 5 / 10 3831 2597 0 2 Jonathan Karr 2019-09-18 13:05 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Failed Results 91.2% 27 / 72 7530 11820 0 1 Arthur Goldberg 2019-12-04 10:27 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Success Results 78.9% 0 / 0 900 7000 0 0 Arthur Goldberg 2019-11-05 06:30 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.10 Latest Failed Results 79.1% 4 / 37 5979 31665 0 1 Arthur Goldberg 2019-12-10 14:14 5
Whole-cell modeling utilities
Modeling and simulation tools
bcforms Open MIT 0.0.3 Latest Success Results 94.9% 0 / 0 1588 1620 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 3011 5962 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 2064 4709 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 97.7% 16 / 30 862 559 0 0 Arthur Goldberg 2019-12-10 15:00 3
Python framework for discrete event simulation
Software development tools
nose2unitth Open MIT 0.0.13 Latest Success Results 100.0% 0 / 0 2128 7230 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 97.7% 23 / 113 4716 14953 0 0 Jonathan Karr 2019-10-29 13:34 5
Database-independent Django-like object schema
pkg_utils Open MIT 0.0.4 Latest Success Results 99.7% 0 / 0 1315 23267 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 1964 1171 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
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