opencobra/Medusa

Issues

• Is Medusa obsolete software?

  #103 opened 2 years ago by jeffkimbrel
  3

• Add utility functions for extracting useful information about an ensemble

  #33 opened 6 years ago by gregmedlock
  1

• base_model

  #59 opened 4 years ago by Basie12
  4

• Benchmarking: FBA

  #48 opened 4 years ago by gregmedlock
  1

• Benchmarking: ensemble memory

  #49 opened 4 years ago by gregmedlock
  1

• clarify batch_load_from_files docstrings, variable names, and SBML/json checking

  #50 opened 5 years ago by gregmedlock
  0

• Update for compatibility with newer cobrapy versions

  #47 opened 5 years ago by gregmedlock
  0

• Package-wide linting

  #46 opened 5 years ago by gregmedlock
  0

• Parametrize tests

  #45 opened 5 years ago by gregmedlock
  0

• Add wrapper for add_models to create ensemble from collection of files

  #11 opened 5 years ago by gregmedlock
  4

• Reassignment of member ids does not reindex

  #36 opened 5 years ago by gregmedlock
  1

• Order of min/max columns in cobrapy has changed

  #35 opened 5 years ago by gregmedlock
  0

• Implement multiprocessing for iterative gapfilling

  #32 opened 6 years ago by gregmedlock
  0

• implement multiprocessing for ensembleFBA

  #24 opened 6 years ago by gregmedlock
  1

• Expand on analogies between Medusa containers/objects and cobrapy objects

  #29 opened 6 years ago by gregmedlock
  0

• Enable AutoAPI creation from docstrings

  #31 opened 6 years ago by gregmedlock
  0

• Include simpler analyses in examples within documentation

  #30 opened 6 years ago by gregmedlock
  0

• Remove transporter search from gapfilling example

  #27 opened 6 years ago by gregmedlock
  0

• Add function for generating ensemble when gapfilling draft model for biomass production without biolog data

  #26 opened 6 years ago by Tjmoutinho
  0

• Implement randomization strategies for iterative gapfilling

  #25 opened 6 years ago by gregmedlock
  0

• Add dataframe state output function

  #22 opened 6 years ago by gregmedlock
  0

• Sort requirements into requirements, develop, and doc

  #21 opened 6 years ago by gregmedlock
  0

• Profile runtime of continuous gapfilling

  #20 opened 6 years ago by gregmedlock
  0

• Create "Gallery" section of examples of ensemble analyses

  #19 opened 6 years ago by gregmedlock
  0

• Setup Sphinx documentation

  #12 opened 6 years ago by gregmedlock
  0

• fix local sphinx vs. readthedocs rendering differences

  #18 opened 6 years ago by gregmedlock
  1

• Add documentation for updating documentation deployment in Sphinx/Readthedocs

  #17 opened 6 years ago by gregmedlock
  0

• Add documentation for updating deployed release to contribution guide

  #16 opened 6 years ago by gregmedlock
  0

• enable pip installation of development branch

  #15 opened 6 years ago by Tjmoutinho
  1

• Add json IO for ensembles

  #14 opened 6 years ago by gregmedlock
  0

• Setup coverage through codedev

  #13 opened 6 years ago by gregmedlock
  0

• Convert docstrings to PEP/numpy standard

  #1 opened 6 years ago by gregmedlock
  0

• Move reaction_diff to a class within medusa.core

  #6 opened 6 years ago by gregmedlock
  1

• Start tests for Travis CI

  #5 opened 7 years ago by gregmedlock
  0

• Refactor ensemble construction within medusa.core.Ensemble

  #8 opened 7 years ago by gregmedlock
  1

• Set up paths for access anywhere

  #10 opened 7 years ago by gregmedlock
  0

• Add contribution instructions

  #9 opened 7 years ago by gregmedlock
  0

• Port flux analysis functions from Ensemble class to independent submodule

  #4 opened 7 years ago by gregmedlock
  0

• Implement degrade functions

  #7 opened 7 years ago by gregmedlock
  0

• Design queuing process for parallelization

  #3 opened 7 years ago by gregmedlock
  0

• Implement multi-species class using micom

  #2 opened 7 years ago by gregmedlock
  0