Issues

• Look into SBOL compatibility for DNA assemblies

  BuildACell/txtlsim-python#35 · Filter by author murrayrm opened on Sep 26, 2018

• 9-25 Meeting Recap: Code Clean-up

  BuildACell/txtlsim-python#34 · Filter by author WilliamIX opened on Sep 26, 2018
  2

  

• Why does the CDS part of a DNA Assembly have a dimerize parameter? A maturation time parameters?

  BuildACell/txtlsim-python#33 · Filter by author WilliamIX opened on Sep 24, 2018
  3

• Why is Concentration being passed around in update_species and update_reactions?

  BuildACell/txtlsim-python#32 · Filter by author WilliamIX opened on Sep 24, 2018
  1

• In Component.update_reactions parameters are being copied and re-updated in a way I don't understand

  BuildACell/txtlsim-python#31 · Filter by author WilliamIX opened on Sep 24, 2018
  1

• Why are we creating config files when components are instantiated?

  BuildACell/txtlsim-python#30 · Filter by author WilliamIX opened on Sep 24, 2018
  1

• Class Structure for DNA and DNA Assembly

  BuildACell/txtlsim-python#29 · Filter by author WilliamIX opened on Sep 20, 2018
  5

• Add component types as subclasses: mRNA, Protein, Small Molecule.

  BuildACell/txtlsim-python#28 · Filter by author WilliamIX opened on Sep 19, 2018
  5

• High Level Design Document

  BuildACell/txtlsim-python#25 · Filter by author WilliamIX opened on Sep 14, 2018

• What will our "Gold Standard Be" in terms of unit tests?

  BuildACell/txtlsim-python#23 · Filter by author WilliamIX opened on Sep 13, 2018
  2

• How do we detect compilation loops?

  BuildACell/txtlsim-python#22 · Filter by author WilliamIX opened on Sep 12, 2018
  7

• Decide how to best handle parameter files and implement

  BuildACell/txtlsim-python#19 · Filter by author murrayrm opened on Sep 12, 2018
  5

• Implement and test integrase.py example

  BuildACell/txtlsim-python#18 · Filter by author murrayrm opened on Sep 12, 2018

• Implement and test negautoreg.py (negative autoregulation example)

  BuildACell/txtlsim-python#17 · Filter by author murrayrm opened on Sep 12, 2018

• Implement energy-utilizing transcription and translation mechanisms

  BuildACell/txtlsim-python#16 · Filter by author murrayrm opened on Sep 12, 2018
  3

• Implement buffer component

  BuildACell/txtlsim-python#15 · Filter by author murrayrm opened on Sep 12, 2018

• Rename 'basic' mechanisms to 'simple'?

  BuildACell/txtlsim-python#14 · Filter by author murrayrm opened on Sep 12, 2018
  2

• Travis CI failing on tests/geneexpr_test.py even though it is OK on MacOS

  BuildACell/txtlsim-python#8 · Filter by author murrayrm opened on Aug 28, 2018

• Add unit tests for TX-TL interface

  BuildACell/txtlsim-python#2 · Filter by author murrayrm opened on Aug 13, 2018
  4