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CovertLab
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wcEcoli
Whole Cell Model of E. coli
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Turn off jit compiler
#1406
1fish2
closed
11 months ago
4
Balance out translation efficiencies for more ribosomal proteins
#1405
ggsun
closed
11 months ago
0
Divide counts of ribosomal proteins by their stoichiometries in ribosome components plot
#1404
ggsun
closed
11 months ago
0
Fix issues with the ribosome components plot
#1403
ggsun
closed
11 months ago
0
Update EcoCyc files to version 28.0
#1402
ggsun
closed
11 months ago
0
Add MSD comparison for excess subunit production to rRNA-to-ribosome yield plot
#1401
ggsun
closed
11 months ago
0
Slow JIT compilation on Linux
#1400
thalassemia
closed
11 months ago
10
Enforce integer sampling from multinomial
#1399
thalassemia
opened
11 months ago
8
Add analysis scripts for replisome-RNAP collisions
#1398
ggsun
closed
11 months ago
0
Transcribe intergenic regions for remove-rrna-operons option
#1397
ggsun
closed
11 months ago
0
Move up RnaMaturation in process order
#1396
ggsun
closed
11 months ago
0
Simulation Initialization Order
#1395
rjuenemann
closed
11 months ago
0
Move back RnaMaturation in process order
#1394
ggsun
closed
11 months ago
0
Add stable-rrna ParCa variant to make mature rRNAs stable
#1393
ggsun
closed
11 months ago
0
Add stable single-gene transcription units for remove-rrna-operons variant
#1392
ggsun
closed
11 months ago
1
Add comparison plot for ppGpp concentration timetraces
#1391
ggsun
closed
11 months ago
0
Use per-cell counts in rRNA-to-ribosome yield comparison plot
#1390
ggsun
closed
11 months ago
1
Modify rRNA mass fraction for remove_rrff variant
#1389
ggsun
closed
11 months ago
0
Fix RNA degradation bugs
#1388
ggsun
closed
11 months ago
0
Update location of DNA sites after new gene chromosome insertion
#1387
rjuenemann
closed
11 months ago
1
Update new gene flat data file structure to be compatible with EcoCyc Version 27.5
#1386
rjuenemann
closed
12 months ago
0
Add Jenkins Tests for New Genes
#1385
rjuenemann
closed
1 year ago
0
Exclude failed sims for doubling time histogram comparison plot
#1384
ggsun
closed
1 year ago
1
Fix out-of-memory issue with rRNA to ribosome yield plot
#1383
ggsun
closed
1 year ago
0
Add comparison plot for rRNA-to-ribosome yields
#1382
ggsun
closed
1 year ago
0
Add multigen plot to track counts of ribosomal components
#1381
ggsun
closed
1 year ago
0
Add comparison analysis for active ribosome counts
#1380
ggsun
closed
1 year ago
0
Set degradation rates of uncomplexed rRNAs to be equal to the mean mRNA degradation rate
#1379
ggsun
closed
1 year ago
1
Update list of transcription units to remove when rRNA operons are removed
#1378
ggsun
closed
1 year ago
0
Update operon paper code/plots to revised versions
#1377
ggsun
closed
1 year ago
0
Variants and Parameter Shifts
#1376
rjuenemann
closed
9 months ago
4
Reading attributes from tables in `cell_paths[0]` fails if the cell wasn't simulated
#1375
ggsun
opened
1 year ago
1
Update raw data files to EcoCyc version 27.5
#1374
ggsun
closed
1 year ago
0
Fix matplotlib errors from PR #1369
#1373
rjuenemann
closed
1 year ago
0
Determination of number of active ribosomes
#1372
rjuenemann
closed
5 months ago
0
Remove replisome count limit during initialization if mechanistic replisome option is off
#1371
ggsun
closed
1 year ago
0
stochastic-arrow==1.0.0
#1370
1fish2
closed
1 year ago
0
New gene translation efficiency modification
#1369
rjuenemann
closed
1 year ago
4
Can wcEcoli be used to simulate other species?
#1368
Rabadash8820
opened
1 year ago
3
Update wcEcoli from Python 3.8 to 3.11.3 and up-to-date pip libraries
#1367
1fish2
closed
1 year ago
16
Fix matplotlib errors for anaerobic sims
#1366
ggsun
closed
1 year ago
0
M2 Apple Silicon
#1365
rjuenemann
closed
1 year ago
8
Test only with operons for PR builds
#1364
ggsun
closed
1 year ago
0
plot to calculate # of sub gen genes
#1363
nvivanco
closed
1 year ago
0
Update raw data files to EcoCyc version 27.0
#1362
ggsun
closed
1 year ago
1
New metabolic pathway
#1361
ioanagherman
opened
1 year ago
1
Anaerobic build failures
#1360
ggsun
closed
1 year ago
0
added metabolic model for vioa_e based on mass-action
#1359
ioanagherman
closed
1 year ago
8
Add sample paper runs file for rRNA operon paper
#1358
ggsun
closed
1 year ago
0
Remove regulation of rRNA genes by TFs
#1357
ggsun
closed
1 year ago
0
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