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Cell models
h1_hesc Closed MIT Latest Latest Success Results 89.5% 0 / 5 7534 4036 0 0 Yin Hoon Chew 2019-08-22 11:49 8
Whole-cell model of H1-hESCs
mycoplasma_pneumoniae Closed MIT Latest Latest Failed Results 73.0% 0 / 1 5845 3766 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 Success Results 37.9% 3 / 3 4021 5641 0 0 xzheng902 2019-08-22 08:52 8
Random whole-cell model generator
SynNetGen Open MIT Latest Latest 0 / 0 1959 941 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 68.7% 2 / 21 10549 7796 0 2 Zhouyang Lian 2019-08-19 12:58 9
Toolkit for discovering and aggregating data for whole-cell modeling
wc_analysis Open MIT Latest Latest Success Results 95.2% 0 / 0 1174 6005 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 Failed Results 97.3% 1 / 2 1426 1446 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% 6 / 19 1532 932 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% 14 / 29 3589 9168 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 Fixed Results 96.5% 6 / 6 2090 5365 0 0 Yin Hoon Chew 2019-08-21 16:04 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 100.0% 17 / 120 5607 13638 0 2 Jonathan Karr 2019-08-16 06:12 5
Data-driven, rule-based language for describing whole-cell models
wc_model_gen Open MIT Latest Latest Success Results 83.1% 9 / 16 4346 7865 0 1 Yin Hoon Chew 2019-08-22 11:59 7
Framework for systematically and scalably designing whole-cell models from large datasets such as wc_kb
wc_rules Open MIT Latest Latest Success Results 42.7% 5 / 10 3743 2530 0 2 Jonathan Karr 2019-06-26 10:16 2
Rule-based language for describing whole-cell models
wc_sim Open MIT Latest Latest Success Results 90.8% 20 / 50 5410 10030 0 1 Arthur Goldberg 2019-08-19 18:42 5
Multi-algorithmic whole-cell model simulator based on discrete event simulation
wc_test Open MIT Latest Latest Failed Results 78.7% 0 / 0 830 5713 0 0 Jonathan Karr 2019-06-26 10:17 4
Framework for testing whole-cell knowledge bases and models
wc_utils Open MIT 0.0.9 Latest Success Results 79.3% 3 / 35 5458 26926 0 0 Arthur Goldberg 2019-08-13 07:49 5
Whole-cell modeling utilities
Modeling and simulation tools
bpforms Open MIT 0.0.9 Latest Success Results 96.1% 0 / 101 2549 4002 0 1 Jonathan Karr 2019-08-20 05:59 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 1740 4037 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