CovertLab wcEcoli issues

CovertLab / wcEcoli

Whole Cell Model of E. coli

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Add analysis output for table of genes involved in transertion

#1453 ggsun opened 4 days ago
0
Change from Google Cloud Container Registry to Artifact Registry

#1452 1fish2 closed 1 week ago
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Skip rRNA gene RNAP density plot if rRNA IDs do not match

#1451 ggsun closed 1 month ago
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Add variant plot for RNAP densities on rRNA operons

#1450 ggsun closed 1 month ago
0
Balance out synthesis probabilities of rRNA promoters

#1449 ggsun closed 1 month ago
0
Add listeners for max_p in transcript and polypeptide initiation

#1448 rjuenemann closed 2 months ago
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Add multigen plot for components involved in rRNA regulation

#1447 ggsun closed 2 months ago
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Activate fewer ribosomes to resolve overcrowding if rescaling fails

#1446 rjuenemann closed 2 months ago
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EcoCyc 28.0

#1445 rjuenemann closed 3 months ago
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doc: how to update a shared pyenv virtualenv

#1444 1fish2 closed 3 months ago
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Skip rRNA operon structures analysis if using nonstandard rRNA operon structures

#1443 ggsun closed 4 months ago
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Add cohort analysis to generate table of subgenerationally expressed genes

#1442 ggsun closed 4 months ago
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Add ParCa analysis to plot rRNA operon positions and structures

#1441 ggsun closed 4 months ago
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Add variant analysis script for rRNA gene copy numbers

#1440 ggsun closed 4 months ago
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Analysis schematic

#1439 thalassemia closed 4 months ago
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Add comparison/variant analysis scripts for ribosome concentrations

#1438 ggsun closed 4 months ago
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Add variant analysis script for instantanous doubling times

#1437 ggsun closed 4 months ago
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Fix issues with the rRNA gene RNAP densities comparison plot

#1436 ggsun closed 4 months ago
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Combine New Gene Variants

#1435 rjuenemann closed 4 months ago
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Add variant version of ppGpp concentration timetrace plot

#1434 ggsun closed 4 months ago
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Update variant active ribosome count histogram plot

#1433 ggsun closed 4 months ago
1
Update variant doubling time histogram plot

#1432 ggsun closed 5 months ago
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Optional New Gene Data File Incorporation

#1431 rjuenemann closed 5 months ago
0
Style guide

#1430 1fish2 closed 5 months ago
0
Adding Gene Copy Numbers to EcoCyc Table Export

#1429 rjuenemann closed 5 months ago
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Debug “Blas libraries are not found” warnings. [TODO: Fix #1419]

#1428 1fish2 closed 5 months ago
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tRNA charging/FBA floating point precision

#1427 thalassemia closed 5 months ago
2
migrate off of numpy.distutils

#1426 1fish2 opened 5 months ago
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Optimizations

#1425 thalassemia closed 5 months ago
8
Add comparison plot for instantaneous doubling times

#1424 ggsun closed 6 months ago
0
Update list of removed TUs for remove-rrna-operons variant

#1423 ggsun closed 6 months ago
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Add comparison analysis for rRNA transcription completion rates

#1422 ggsun closed 6 months ago
0
Fix rRNA operon orientation variant

#1421 ggsun closed 6 months ago
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Use wildtype replication coordinates to calculate ppGpp-adjusted expression levels

#1420 ggsun closed 6 months ago
0
AnalysisParcaTask fizzling when running sims with COMPRESS_OUTPUT=1

#1419 rjuenemann opened 6 months ago
1
fix coverage error and a bunch of warnings

#1418 1fish2 closed 6 months ago
0
Anerobic simulation timed out at 7 hours sim time

#1417 1fish2 opened 6 months ago
0
Updating Jenkins version

#1416 ggsun opened 6 months ago
1
Introduction of Internal Shift Variant for New Gene Induction

#1415 rjuenemann closed 6 months ago
0
Remove the Numba JIT-compilation code

#1414 1fish2 closed 7 months ago
3
Optimize 2CS and equilibrium rate functions

#1413 thalassemia closed 7 months ago
0
Add media options for rRNA variants

#1412 ggsun closed 7 months ago
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Add new comparison analysis script for RNAP densities on rRNA operons

#1411 ggsun closed 7 months ago
0
Fix rRNA location variant

#1410 ggsun closed 7 months ago
0
Add comparison analysis script for rRNA gene copy numbers

#1409 ggsun closed 7 months ago
0
Add cohort plot for number of RNAP-replisome collisions per gene

#1408 ggsun closed 7 months ago
0
Limit number of monomers plotted in ribosome_crowding plot

#1407 ggsun closed 7 months ago
0
Turn off jit compiler

#1406 1fish2 closed 7 months ago
4
Balance out translation efficiencies for more ribosomal proteins

#1405 ggsun closed 7 months ago
0
Divide counts of ribosomal proteins by their stoichiometries in ribosome components plot

#1404 ggsun closed 8 months ago
0