cdanielmachado/carveme

Issues

• Multi-process processing error

  #211 opened a month ago by green34567
  1

• Missing SBO Terms in XML Output with CarveMe

  #212 opened a month ago by xuetingyue
  0

• Too many charge unbalaced reactions

  #210 opened 2 months ago by AnnyMais03
  0

• Inconsistencies in metabolite charges on pre-generated universe files.

  #174 opened 2 years ago by Gscorreia89
  1

• installation issue

  #209 opened 2 months ago by ChenCongZ
  0

• Inconsistencies between reactions in universe file and in model generated from it

  #208 opened 2 months ago by Brunokemon
  2

• Relax binary constraint for fast gapfill

  #206 opened 3 months ago by djinnome
  0

• 'BiGG_gene' is both an index level and a column label, which is ambiguous.

  #187 opened a year ago by Baizhou12138
  1

• Carveme not finishing with SCIP solver

  #205 opened 5 months ago by ryan-boobybiome
  0

• Carveme 2.0

  #204 opened 5 months ago by rhernandvel
  0

• Incomplete cyanobacteria universe - lacks photosynthesis related reactions

  #203 opened 5 months ago by GediminasA
  1

• Advice on custom media and initialisation

  #202 opened 5 months ago by ryan-boobybiome
  1

• Biomass reaction in bacteria_universe sums to 1.03

  #189 opened a year ago by sulheim
  1

• SCIP with gap-filling and init

  #199 opened 6 months ago by tapj
  5

• Location of gapfill outputs

  #201 opened 6 months ago by AzizBenA
  0

• How to include new single species metabolic model in the model database

  #200 opened 6 months ago by Mushahid2521
  1

• Gapfilling using a curated sbml?

  #169 opened 2 years ago by pushing2
  1

• First time installation issue

  #198 opened 7 months ago by Sail6666
  0

• Hidden universe?

  #197 opened 8 months ago by NatashaJorge
  0

• Do not work with scipy 1.12.0

  #196 opened 9 months ago by GediminasA
  2

• I meet some errors when I use CarveMe for gap-filling

  #193 opened a year ago by microbial-cookie
  4

• Having issues with cyanobacteria universe in latest version, and cplex installation for carveme version 1.4

  #195 opened 10 months ago by marlaux
  0

• Is it necessary to use a VNC server for the modeling process using CarveMe?

  #194 opened a year ago by Thomas-tang880
  0

• ImportError: cannot import name 'SCIPSolver' from 'reframed.solvers'

  #191 opened a year ago by yqq-79
  9

• How to create a universe?

  #192 opened a year ago by kako-f
  0

• Error when giving user universe

  #190 opened a year ago by NatashaJorge
  0

• [Feature request] Option to use non-proprietary solvers

  #173 opened a year ago by jolespin
  14

• Error encountered reading the model file

  #179 opened 2 years ago by jiuchuyuan
  2

• incompatibility with BIGG formula

  #188 opened a year ago by Shlomit840
  0

• Diamond version incompatible / TypeError: sequence item 0

  #186 opened a year ago by chumphati
  0

• GPR rules and COBRA

  #183 opened a year ago by jiuchuyuan
  1

• Problems gapfilling with CPLEX and Gurobi

  #185 opened a year ago by Brunokemon
  4

• How to change the default solver cplex to gurobi？

  #175 opened 2 years ago by wupeng1998
  4

• Where to find the biomass equation for FBA?

  #184 opened a year ago by raysteven
  0

• CarveMe ignores highly similar genes during the building of GPRs

  #180 opened a year ago by lazzarigioele
  0

• CarveMe doesn’t satisfy the original protein complex definitions during the building of GPRs

  #182 opened a year ago by lazzarigioele
  0

• Solver error: pip release not corresponding to latest release

  #181 opened a year ago by Robaina
  0

• Cplex Error

  #170 opened 2 years ago by PaulJames201
  8

• cplex.exceptions.errors.CplexSolverError: CPLEX Error 1016: Community Edition. Problem size limits exceeded. Purchase at http://ibm.biz/error1016.

  #172 opened 2 years ago by jolespin
  5

• The interested compound without BIGG id, could you help me add to the media components that Carveme can identify?

  #178 opened 2 years ago by microbial-cookie
  0

• example codes

  #177 opened 2 years ago by parsanayyara
  0

• Setting cores

  #176 opened 2 years ago by stephane-wang
  0

• [Feature request] Installable via bioconda

  #171 opened 2 years ago by jolespin
  0

• Is it possible to predict auxotrophies from metabolic models generated by CarveMe?

  #168 opened 2 years ago by ilnamkang
  2

• error about build model using example

  #167 opened 2 years ago by Dodolove725
  0

• example command meets with format mistak in py3

  #166 opened 2 years ago by Chenjlin28
  1

• GPR universe

  #165 opened 2 years ago by arianccbasile
  2

• Carveme don't do gapfill for user defined medium

  #164 opened 2 years ago by NatashaJorge
  3

• The input genome did not match sufficient genes/reactions in the database.

  #163 opened 2 years ago by AnisMansouri
  1

• Database was built with a different version of Diamond and is incompatible. Failed to run diamond.

  #162 opened 2 years ago by AnisMansouri
  0