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CovertLab
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vEcoli
Whole cell model of E. coli implemented with Vivarium
https://covertlab.github.io/vEcoli/
MIT License
12
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3
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TimeLimitError despite setting config["fail_at_total_time"]: false
#242
arnabmutsuddy
closed
1 month ago
5
Minor bug fixes
#241
thalassemia
closed
1 month ago
1
Must manually check CI output logs for Nextflow failures
#240
thalassemia
closed
1 month ago
1
Option to skip baseline variant sim_data
#239
thalassemia
closed
1 month ago
1
Option to Skip ParCa in Workflows
#238
thalassemia
closed
1 month ago
1
Cofactors merging new plots.
#237
cyrus-bio
closed
1 month ago
1
Cofactors updates
#236
cyrus-bio
closed
2 months ago
1
New cofactor plots
#235
cyrus-bio
closed
2 months ago
0
Fix some documentation typos
#234
thalassemia
closed
3 months ago
1
Rework Documentation
#233
thalassemia
closed
3 months ago
1
More Jenkins tests
#232
thalassemia
closed
4 months ago
0
Jenkins and Github Actions
#231
thalassemia
closed
4 months ago
0
Fixes for Sherlock
#230
thalassemia
closed
4 months ago
0
Use DuckDB for analysis scripts
#229
thalassemia
closed
4 months ago
0
Added more entries to default json
#228
cyrus-bio
closed
5 months ago
0
Catch up to wcEcoli
#227
thalassemia
closed
5 months ago
0
Cleanup code using ruff linter and formatter
#226
thalassemia
closed
5 months ago
0
Workflow support and Parquet emitter
#225
thalassemia
closed
5 months ago
0
Small updates to cofactors
#224
cyrus-bio
closed
7 months ago
0
setup.py use cython with NPY_NO_DEPRECATED_API
#223
eagmon
closed
7 months ago
1
Optimizations
#222
thalassemia
closed
9 months ago
0
Create empty array when zero initial replisomes
#221
thalassemia
closed
9 months ago
0
Patched rich media patch
#220
cyrus-bio
closed
8 months ago
0
Rich condition patch
#219
cyrus-bio
closed
11 months ago
1
Documentation WIP
#218
thalassemia
closed
9 months ago
0
Fixing minor bug in metabolism_redux_classic
#217
cyrus-bio
closed
11 months ago
0
Set OPENBLAS_NUM_THREADS=1 on Github Actions
#216
thalassemia
closed
1 year ago
0
Documentation
#215
thalassemia
closed
1 year ago
0
Increase iteration cap for expressionConverge, add more informative print statements
#214
cyrus-bio
closed
1 year ago
1
Test for division with new metabolism
#213
cyrus-bio
closed
1 year ago
0
TableReader update
#212
thalassemia
closed
1 year ago
0
Reaction patch to remove incorrectly parsed reactions
#211
cyrus-bio
closed
1 year ago
0
Causality update
#210
thalassemia
closed
1 year ago
0
Sim with new metabolism / without growth rate control + some cofactor notebooks
#209
cyrus-bio
closed
1 year ago
0
ParCa and Initial State
#208
thalassemia
closed
1 year ago
0
Media ID Timeline
#207
thalassemia
closed
1 year ago
0
Operons and Growth Rate Control
#206
thalassemia
closed
1 year ago
0
Adding new environments analysis, an experiment file, and a test
#205
timzjing
opened
1 year ago
2
Patch to add test to metabolism_redux.py
#204
cyrus-bio
closed
1 year ago
0
Update requirements.txt to remove unnecessary packages
#203
cyrus-bio
closed
1 year ago
0
Fixed small things in metabolism redux (binary kinetics indices)
#202
cyrus-bio
closed
1 year ago
1
Warnings during make compile
#201
rgiessmann
closed
1 year ago
1
Cannot run notebook
#200
rgiessmann
closed
1 year ago
1
Default config gets lost during installation
#199
rgiessmann
closed
1 year ago
1
Create __init__.py to allow antibiotics module to be installed with setup.py
#198
rgiessmann
closed
1 year ago
1
Update README.md for conda based installation
#197
rgiessmann
closed
1 year ago
1
speedup ideas
#196
1fish2
opened
1 year ago
0
Inefficiencies in PyMongo Driver
#195
thalassemia
closed
1 year ago
40
Numpy conversion
#194
thalassemia
closed
1 year ago
1
Initial version of new, refactored metabolic process, metabolism_redux.py
#193
cyrus-bio
closed
1 year ago
3
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