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Commits on Mar 26, 2026

• Complex listener merge (#1471)

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  mpg19

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  af2f53a

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Commits on Mar 23, 2026

• Jenkins GROUP_SCRATCH Storage Management (#1470)

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  rjuenemann

  and

  Copilot

  authored
  16c5076

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Commits on Mar 4, 2026

• Translation.py monomer data saving update. (#1469)

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  mpg19

  authored
  a4497e1

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Commits on Feb 14, 2026

• Added attributes to the MonomerCounts listener (#1466)

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  mpg19

  authored
  14201de

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Commits on Dec 5, 2025

• EcoCyc 29.5 (#1468)

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  rjuenemann

  authored
  302475a

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Commits on Nov 25, 2025

• add license to slurm jobs (#1467)

  rjuenemann

  authored
  9d85ad5

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Commits on Oct 27, 2025

• Creation of an optional protein degradation rate assignment combination ParCa parameter selection option (#1465)

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  mpg19

  authored
  609dd21

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Commits on Oct 9, 2025

• EcoCyc 29.1 (#1464)

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  rjuenemann

  authored
  06ee9d8

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Commits on Apr 2, 2025

• EcoCyc 29.0 (#1462)

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  rjuenemann

  authored
  b5128d0

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Commits on Dec 10, 2024

• team email: wholecellteam@lists.stanford.edu (#1460)

  1fish2

  authored
  23caa7e

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Commits on Nov 26, 2024

• plot at most the first 300 overcrowded monomers to prevent exceeding maximum figure size (#1459)

  rjuenemann

  authored
  a155791

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Commits on Nov 22, 2024

• EcoCyc 28.5 (#1458)

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  rjuenemann

  authored
  3ec41c6

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Commits on Oct 17, 2024

• Added supplemental source. (#1457)

  mpg19

  authored
  bad1bf6

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Commits on Oct 3, 2024

• update the pyenv setup steps (#1456)

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  1fish2

  authored
  26deae6

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Commits on Sep 13, 2024

• changed compartment of EG12298-MONOMER, and eliminated protein deg adjustments based on N-end rule for ADENYLATECYC-MONOMER and SPOT-MONOMER, which now have updated sequences. (#1455)

  nvivanco

  authored
  9f420e1

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Commits on Jul 29, 2024

• EcoCyc 28.1 (#1454)

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  rjuenemann

  authored
  dcf8b30

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Commits on Jul 8, 2024

• Add analysis output for table of genes involved in transertion (#1453)

  ggsun

  authored
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Commits on Jun 21, 2024

• Change from Google Cloud Container Registry to Artifact Registry (#1452)

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  1fish2

  authored
  9e03d05

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Commits on May 28, 2024

• Skip rRNA gene RNAP density plot if rRNA IDs do not match (#1451)

  ggsun

  authored
  b3b0272

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Commits on May 10, 2024

• Add variant plot for RNAP densities on rRNA operons (#1450)

  ggsun

  authored
  7b2976d

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Commits on May 6, 2024

• Balance out synthesis probabilities of rRNA promoters (#1449)

  ggsun

  authored
  36750cd

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Commits on May 2, 2024

• Add listeners for max_p in transcript and polypeptide initiation (#1448)

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  rjuenemann

  authored
  ef04f8d

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Commits on Apr 18, 2024

• Add multigen plot for components involved in rRNA regulation (#1447)

  ggsun

  authored
  fdaeb31

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Commits on Apr 16, 2024

• Activate fewer ribosomes to resolve overcrowding if rescaling fails (#1446)

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  rjuenemann

  authored
  ee68d57

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Commits on Mar 13, 2024

• EcoCyc 28.0 (#1445)

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  rjuenemann

  authored
  f724288

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Commits on Mar 10, 2024

• doc: how to update a shared pyenv virtualenv

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  1fish2

  authored
  7dc33a8

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Commits on Mar 1, 2024

• Skip rRNA operon structures analysis if using nonstandard rRNA operon structures (#1443)

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  ggsun

  authored
  eb8dd05

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• Add cohort analysis to generate table of subgenerationally expressed genes (#1442)

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  ggsun

  authored
  89e8417

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Commits on Feb 27, 2024

• Add ParCa analysis to plot rRNA operon positions and structures (#1441)

  ggsun

  authored
  d31e220

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Commits on Feb 23, 2024

• Add variant analysis script for rRNA gene copy numbers (#1440)

  ggsun

  authored
  11653e3

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• Analysis schematic (#1439)

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  thalassemia

  authored
  b6aebae

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Commits on Feb 21, 2024

• Add comparison/variant analysis scripts for ribosome concentrations (#1438)

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  ggsun

  authored
  d4c3801

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Commits on Feb 16, 2024

• Combine New Gene Variants (#1435)

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  rjuenemann

  authored
  471e5d2

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Commits on Feb 15, 2024

• Add variant analysis script for instantanous doubling times (#1437)

  ggsun

  authored
  81e9008

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Commits on Feb 13, 2024

• Fix issues with the rRNA gene RNAP densities comparison plot (#1436)

  ggsun

  authored
  24e01c9

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