draeger-lab/ModelPolisher

Issues

• Identifiers.org new identifiers pattern lead to identifier duplicates

  #123 opened 2 years ago by GwennyGit
  0

• MetaNetX annotations not added properly

  #106 opened 2 years ago by NantiaL
  8

• Polished model read with errors in cobrapy

  #103 opened 2 years ago by EnuhBlaise
  17

• update README and Wiki

  #115 opened 2 years ago by Schmoho
  1

• polishing of reaction participants is aborted halfway through

  #122 opened 2 years ago by Schmoho
  1

• COBRAparser partially fails to parse model

  #76 opened 2 years ago by mephenor
  4

• Conflict with SBML validation

  #100 opened 2 years ago by Biomathsys
  9

• Spurious annotations

  #89 opened 4 years ago by mephenor
  4

• Update MIRIAM Registry to support new collections

  #80 opened 4 years ago by mephenor
  4

• Update ModelPolisherOptions to allow for validation of unzipped output

  #101 opened 2 years ago by mephenor
  1

• introduce polishing unit tests

  #121 opened 2 years ago by Schmoho
  0

• Known security vulnerabilities detected in third-party library

  #104 opened 2 years ago by draeger
  3

• introduce UnitPolishing class

  #120 opened 2 years ago by Schmoho
  1

• build and ship javadocs for the Project

  #116 opened 2 years ago by Schmoho
  2

• the way we check for FBC strict is not compliant with the spec

  #118 opened 2 years ago by Schmoho
  4

• write class and method docstrings

  #117 opened 2 years ago by Schmoho
  0

• failing tests on master

  #109 opened 2 years ago by Schmoho
  1

• release branch does not build

  #114 opened 2 years ago by Schmoho
  1

• ModelPolisher-2.0.1.jar is not available when running in docker container

  #105 opened 2 years ago by famosab
  2

• FbcPlugin and Reaction bounds/objective function/genes

  #94 opened 4 years ago by Linelili
  2

• Handling ncbigi annotations

  #86 opened 2 years ago by mephenor
  5

• includeAnyURI not applied consequently across codebase

  #99 opened 4 years ago by mephenor
  0

• Running with docker-compose run -u $(id -u):$(id -g) potentially locks up execution

  #98 opened 4 years ago by mephenor
  0

• Annotating models with the genome identifier

  #96 opened 4 years ago by draeger
  3

• Rewriting BiGGId handling

  #85 opened 4 years ago by mephenor
  1

• How to handle multiple gene_reaction_rules

  #90 opened 2 years ago by mephenor
  1

• Allow for species/reactions/... to be processed directly

  #78 opened 5 years ago by mephenor
  2

• Add annotations for KEGG pathways and genes

  #107 opened 2 years ago by NantiaL
  1

• How to handle queries with multiple return values

  #92 opened 2 years ago by mephenor
  2

• Current state

  #84 opened 2 years ago by mephenor
  9

• Issue with opening model file

  #102 opened 2 years ago by alexander-alleman
  3

• Make sure there is no hard dependency on AnnotateDB

  #79 opened 4 years ago by mephenor
  2

• Adding Subsystem Annotation for models without Model BiGGId in BiGG

  #97 opened 4 years ago by mephenor
  1

• Update to JSBML 1.5

  #95 opened 4 years ago by draeger
  1

• GPR creation fails with ClassCastException

  #88 opened 4 years ago by mephenor
  4

• Identifiers.org annotations are now https:, not http:

  #87 opened 4 years ago by mephenor
  0

• Replace simple Connection with ConnectionPool for improved performance

  #91 opened 4 years ago by mephenor
  0

• Factor out helper functions, enums and inner classes into separate classes to improve readability

  #77 opened 4 years ago by mephenor
  1

• Remove remaining code pertaining to removed SQLite connector

  #81 opened 4 years ago by mephenor
  0

• Error when running with docker-compose

  #82 opened 5 years ago by LisbethIsolde
  1

• Adapt Travis configuration to recent changes

  #68 opened 5 years ago by mephenor
  2

• Add Table of Contents in README.

  #64 opened 5 years ago by codekaust
  1

• Produce a single COMBINE archive containing the annotated model and glossary.

  #62 opened 5 years ago by codekaust
  1

• Add documentation of all command line arguments in README

  #66 opened 5 years ago by matthiaskoenig
  0

• Remove SQLite version

  #67 opened 5 years ago by mephenor
  4

• Produce glossary only when BiGG Annotations added.

  #69 opened 5 years ago by codekaust
  1

• Production of output fails if `output` location is given as file and file not present.

  #71 opened 5 years ago by codekaust
  2

• Produce glossary from annotated models.

  #60 opened 5 years ago by codekaust
  0

• ModelPolisher cannot find any relations in ADB.

  #56 opened 5 years ago by codekaust
  10

• Separate instructions for developers and users for running and building ModelPolisher.

  #57 opened 5 years ago by codekaust
  0