cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction

cdanielmachado/carveme Issues

First time installation issue
Closed 2 months ago
SCIP with gap-filling and init
Updated 2 months ago3
Hidden universe?
Updated 4 months ago
Do not work with scipy 1.12.0
Closed 5 months ago2
I meet some errors when I use CarveMe for gap-filling
Updated 5 months ago4
Having issues with cyanobacteria universe in latest version, and cplex installation for carveme version 1.4
Updated 6 months ago
Is it necessary to use a VNC server for the modeling process using CarveMe?
Updated 6 months ago
ImportError: cannot import name 'SCIPSolver' from 'reframed.solvers'
Closed 6 months ago9
How to create a universe?
Updated 6 months ago
Error when giving user universe
Updated 7 months ago
[Feature request] Option to use non-proprietary solvers
Closed 8 months ago14
Biomass reaction in bacteria_universe sums to 1.03
Updated 8 months ago
Error encountered reading the model file
Updated 9 months ago2
incompatibility with BIGG formula
Updated a year ago
'BiGG_gene' is both an index level and a column label, which is ambiguous.
Updated a year ago
Diamond version incompatible / TypeError: sequence item 0
Updated a year ago
GPR rules and COBRA
Closed a year ago1
Problems gapfilling with CPLEX and Gurobi
Closed a year ago4
How to change the default solver cplex to gurobi？
Closed a year ago4
Where to find the biomass equation for FBA?
Closed a year ago
CarveMe ignores highly similar genes during the building of GPRs
Updated a year ago
CarveMe doesn’t satisfy the original protein complex definitions during the building of GPRs
Updated a year ago
Solver error: pip release not corresponding to latest release
Updated a year ago
Cplex Error
Closed a year ago8
cplex.exceptions.errors.CplexSolverError: CPLEX Error 1016: Community Edition. Problem size limits exceeded. Purchase at http://ibm.biz/error1016.
Closed a year ago5
The interested compound without BIGG id, could you help me add to the media components that Carveme can identify?
Updated a year ago
example codes
Updated a year ago
Setting cores
Updated a year ago
Inconsistencies in metabolite charges on pre-generated universe files.
Updated a year ago
[Feature request] Installable via bioconda
Updated a year ago
Gapfilling using a curated sbml?
Updated a year ago
Is it possible to predict auxotrophies from metabolic models generated by CarveMe?
Closed a year ago2
error about build model using example
Updated 2 years ago
Version issues and Solver 'cplex' not available
Closed 2 years ago2
example command meets with format mistak in py3
Updated 2 years ago1
GPR universe
Closed 2 years ago2
Carveme don't do gapfill for user defined medium
Closed 2 years ago3
The input genome did not match sufficient genes/reactions in the database.
Updated 2 years ago1
Database was built with a different version of Diamond and is incompatible. Failed to run diamond.
Updated 2 years ago
Basidiomycete fungi model
Updated 2 years ago2
SERVIDOR EN JUPYTER NOTEBOOK PARA CARVEME
Updated 2 years ago
Built my own media library
Closed 2 years ago3
Cplex academic license: problem size limits exceeded
Closed 2 years ago1
Does gap filling exclude new metabolite uptake reactions?
Updated 2 years ago
Error while creating community models
Updated 2 years ago
Warning: Gene association for reaction is not DNF
Updated 2 years ago
The '__init__.py' file is empty
Updated 2 years ago
inconsistencies and unconserved metabolites in MEMOTE results for carveme models
Closed 2 years ago2
documentation on using an open source solver?
Closed 3 years ago4
gapfill universe flavor
Closed 3 years ago2