zhanglab/psamm

Issues

• How to add reactions identified by gap fill to model

  #264 opened 5 years ago by mmundy42
  1

• psamm-import command not found

  #218 opened 8 years ago by arturomarin
  2

• YAML reaction incorrectly parsing decimal stoichiometry as float

  #124 opened 8 years ago by jonls
  1

• Make NativeModel constructor take string, dict or file object

  #80 opened 8 years ago by spikeliu
  0

• Consistently parse include statements in native module

  #87 opened 8 years ago by jonls
  0

• Allow reactions with fixed flux in the limits definition

  #89 opened 8 years ago by jonls
  1

• Extend compatibility with older Cplex versions by only using set_offset when available

  #71 opened 8 years ago by jonls
  1

• Move YAML writing code from psamm-import to psamm.datasource.native

  #101 opened 8 years ago by spikeliu
  0

• gapfill: Inform user that a lower epsilon value could be used

  #75 opened 8 years ago by jonls
  1

• Allow user to set value of epsilon used in gapfill command

  #73 opened 8 years ago by jonls
  1

• In commands, add a separate command error to signal execution errors

  #74 opened 8 years ago by jonls
  1

• No warning given when ID is not a string

  #62 opened 9 years ago by jonls
  1

• Allow additional features in medium table definition

  #39 opened 9 years ago by jonls
  0

• Split gene associations from reaction database

  #51 opened 9 years ago by jonls
  1

• When loading a medium YAML file the extracellular compartment should be the default compartment

  #68 opened 9 years ago by jonls
  1

• Produce a warning about missing exchange reactions

  #49 opened 9 years ago by jonls
  1

• Add support for open source LP solver

  #9 opened 9 years ago by jonls
  1

• Incorrect solution to Fastcore LP10 with GLPK

  #61 opened 9 years ago by jonls
  0

• Allow specification of extracellular compartment name

  #48 opened 9 years ago by jonls
  1

• Allow gapfill of specific compound(s)

  #43 opened 9 years ago by jonls
  0

• New command to perform a single gene deletion experiment

  #44 opened 9 years ago by jonls
  1

• SBML export of flux limits

  #21 opened 9 years ago by jonls
  1

• GapFind/GapFill python tests

  #2 opened 9 years ago by jonls
  1

• Performance regression with Cplex 12.6.2

  #34 opened 9 years ago by jonls
  0

• Rename --reaction options to --objective

  #30 opened 9 years ago by jonls
  3

• Support default value (-) in limits table parser

  #35 opened 9 years ago by jonls
  0

• Missing documentation for medium table format

  #36 opened 9 years ago by jonls
  0

• Combine entries in media key to produce the model medium

  #37 opened 9 years ago by jonls
  1

• KEGG reaction information parsing

  #3 opened 9 years ago by jonls
  0

• Port to Python 3

  #14 opened 10 years ago by jonls
  1

• Generalize FVA, flux minimization and consistency check

  #4 opened 10 years ago by jonls
  1

• Extend fastgapfill command line options

  #5 opened 10 years ago by jonls
  2

• Use python3 compatible print function

  #1 opened 10 years ago by jonls
  1

• Factor out parsing list and array files

  #6 opened 10 years ago by jonls
  2

• Allow exporting text-based model to SBML

  #12 opened 10 years ago by jonls
  0

• Move reaction parsers to separate data source module

  #10 opened 10 years ago by jonls
  1

• Add the current table-based model format as a separate data source module

  #11 opened 10 years ago by jonls
  2

• SBML parser test case

  #7 opened 10 years ago by jonls
  0

• Use Exception subclass instead of generic Exception

  #8 opened 10 years ago by jonls
  0