cdanielmachado/carveme issues and pull requests

#215 - addConstr() takes at most 3 positional arguments (5 given)

Issue - State: open - Opened by Ming314 about 2 months ago

#214 - Reg the printRxnformula and Uptake

Issue - State: closed - Opened by NTDevika 3 months ago - 2 comments

#213 - Fix greedy cpu allocation

Pull Request - State: open - Opened by nickp60 3 months ago

#212 - Missing SBO Terms in XML Output with CarveMe

Issue - State: open - Opened by xuetingyue 4 months ago

#211 - Multi-process processing error

Issue - State: open - Opened by green34567 4 months ago - 1 comment

#210 - Too many charge unbalaced reactions

Issue - State: open - Opened by AnnyMais03 5 months ago

#209 - installation issue

Issue - State: open - Opened by ChenCongZ 5 months ago

#208 - Inconsistencies between reactions in universe file and in model generated from it

Issue - State: open - Opened by Brunokemon 5 months ago - 2 comments

#205 - Carveme not finishing with SCIP solver

Issue - State: open - Opened by ryan-boobybiome 8 months ago

#204 - Carveme 2.0

Issue - State: open - Opened by rhernandvel 8 months ago

#203 - Incomplete cyanobacteria universe - lacks photosynthesis related reactions

Issue - State: open - Opened by GediminasA 8 months ago - 1 comment

#202 - Advice on custom media and initialisation

Issue - State: closed - Opened by ryan-boobybiome 8 months ago - 1 comment

#201 - Location of gapfill outputs

Issue - State: open - Opened by AzizBenA 9 months ago

#200 - How to include new single species metabolic model in the model database

Issue - State: closed - Opened by Mushahid2521 9 months ago - 1 comment

#199 - SCIP with gap-filling and init

Issue - State: closed - Opened by tapj 10 months ago - 5 comments

#198 - First time installation issue

Issue - State: closed - Opened by Sail6666 11 months ago

#197 - Hidden universe?

Issue - State: open - Opened by NatashaJorge 11 months ago

#196 - Do not work with scipy 1.12.0

Issue - State: closed - Opened by GediminasA about 1 year ago - 2 comments

#195 - Having issues with cyanobacteria universe in latest version, and cplex installation for carveme version 1.4

Issue - State: open - Opened by marlaux about 1 year ago

#194 - Is it necessary to use a VNC server for the modeling process using CarveMe?

Issue - State: open - Opened by Thomas-tang880 about 1 year ago

#193 - I meet some errors when I use CarveMe for gap-filling

Issue - State: open - Opened by microbial-cookie about 1 year ago - 4 comments

#192 - How to create a universe?

Issue - State: open - Opened by kako-f about 1 year ago

#191 - ImportError: cannot import name 'SCIPSolver' from 'reframed.solvers'

Issue - State: closed - Opened by yqq-79 about 1 year ago - 9 comments

#190 - Error when giving user universe

Issue - State: open - Opened by NatashaJorge about 1 year ago

#189 - Biomass reaction in bacteria_universe sums to 1.03

Issue - State: open - Opened by sulheim over 1 year ago - 1 comment

#188 - incompatibility with BIGG formula

Issue - State: open - Opened by Shlomit840 over 1 year ago

#187 - 'BiGG_gene' is both an index level and a column label, which is ambiguous.

Issue - State: open - Opened by Baizhou12138 over 1 year ago - 1 comment

#186 - Diamond version incompatible / TypeError: sequence item 0

Issue - State: open - Opened by chumphati over 1 year ago

#185 - Problems gapfilling with CPLEX and Gurobi

Issue - State: closed - Opened by Brunokemon over 1 year ago - 4 comments

#184 - Where to find the biomass equation for FBA?

Issue - State: closed - Opened by raysteven over 1 year ago

#183 - GPR rules and COBRA

Issue - State: closed - Opened by jiuchuyuan over 1 year ago - 1 comment

#182 - CarveMe doesn’t satisfy the original protein complex definitions during the building of GPRs

Issue - State: open - Opened by lazzarigioele over 1 year ago

#181 - Solver error: pip release not corresponding to latest release

Issue - State: open - Opened by Robaina over 1 year ago

#180 - CarveMe ignores highly similar genes during the building of GPRs

Issue - State: open - Opened by lazzarigioele over 1 year ago

#179 - Error encountered reading the model file

Issue - State: open - Opened by jiuchuyuan almost 2 years ago - 2 comments

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

Issue - State: open - Opened by microbial-cookie almost 2 years ago

#177 - example codes

Issue - State: open - Opened by parsanayyara almost 2 years ago

#176 - Setting cores

Issue - State: open - Opened by stephane-wang almost 2 years ago

#175 - How to change the default solver cplex to gurobi？

Issue - State: closed - Opened by wupeng1998 almost 2 years ago - 4 comments

#174 - Inconsistencies in metabolite charges on pre-generated universe files.

Issue - State: open - Opened by Gscorreia89 almost 2 years ago - 1 comment

#173 - [Feature request] Option to use non-proprietary solvers

Issue - State: closed - Opened by jolespin almost 2 years ago - 14 comments

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

Issue - State: closed - Opened by jolespin almost 2 years ago - 5 comments

#171 - [Feature request] Installable via bioconda

Issue - State: open - Opened by jolespin almost 2 years ago

#170 - Cplex Error

Issue - State: closed - Opened by PaulJames201 almost 2 years ago - 8 comments

#169 - Gapfilling using a curated sbml?

Issue - State: open - Opened by pushing2 about 2 years ago - 1 comment

#168 - Is it possible to predict auxotrophies from metabolic models generated by CarveMe?

Issue - State: closed - Opened by ilnamkang about 2 years ago - 2 comments

#167 - error about build model using example

Issue - State: open - Opened by Dodolove725 about 2 years ago

#166 - example command meets with format mistak in py3

Issue - State: open - Opened by Chenjlin28 over 2 years ago - 1 comment

#165 - GPR universe

Issue - State: closed - Opened by arianccbasile over 2 years ago - 2 comments

#164 - Carveme don't do gapfill for user defined medium

Issue - State: closed - Opened by NatashaJorge over 2 years ago - 3 comments

#163 - The input genome did not match sufficient genes/reactions in the database.

Issue - State: open - Opened by AnisMansouri over 2 years ago - 1 comment

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

Issue - State: open - Opened by AnisMansouri over 2 years ago

#161 - SERVIDOR EN JUPYTER NOTEBOOK PARA CARVEME

Issue - State: open - Opened by Rodriguez0101 over 2 years ago

#160 - Version issues and Solver 'cplex' not available

Issue - State: closed - Opened by bananabenana over 2 years ago - 2 comments

#159 - Cplex academic license: problem size limits exceeded

Issue - State: closed - Opened by Sanrrone over 2 years ago - 1 comment

#158 - Basidiomycete fungi model

Issue - State: open - Opened by shacharje1 over 2 years ago - 2 comments

#157 - Does gap filling exclude new metabolite uptake reactions?

Issue - State: open - Opened by behzadk over 2 years ago

#156 - Error while creating community models

Issue - State: open - Opened by NantiaL almost 3 years ago

#155 - Built my own media library

Issue - State: closed - Opened by zoelwl almost 3 years ago - 3 comments

#154 - Warning: Gene association for reaction is not DNF

Issue - State: open - Opened by franciscozorrilla almost 3 years ago

#153 - The 'init.py' file is empty

Issue - State: open - Opened by leopoldche almost 3 years ago

#152 - inconsistencies and unconserved metabolites in MEMOTE results for carveme models

Issue - State: closed - Opened by shumantov about 3 years ago - 2 comments

#151 - documentation on using an open source solver?

Issue - State: closed - Opened by nick-youngblut about 3 years ago - 4 comments

#150 - gapfill universe flavor

Issue - State: closed - Opened by JosuaCarl about 3 years ago - 2 comments

#149 - GPR not identified in Memote

Issue - State: closed - Opened by Duleosol about 3 years ago

#148 - Invalid SBML file

Issue - State: closed - Opened by stelmo about 3 years ago - 10 comments

#147 - Issues of output results from riptide

Issue - State: closed - Opened by Xingchen-Bian over 3 years ago - 2 comments

#146 - fix: universe extensions in gapfill.py

Pull Request - State: closed - Opened by BenjaSanchez over 3 years ago - 1 comment

#145 - Reconstructing a single model is pending

Issue - State: closed - Opened by iuliachiciudean over 3 years ago - 1 comment

#144 - Carveme EggNog mapper error

Issue - State: closed - Opened by fcastillo1993 over 3 years ago - 4 comments

#143 - CarveMe output interpretation

Issue - State: closed - Opened by iuliachiciudean over 3 years ago - 2 comments

#142 - RuntimeError: Solver cplex not available.

Issue - State: closed - Opened by iuliachiciudean over 3 years ago - 1 comment

#141 - containerizing CarveMe

Issue - State: open - Opened by zoey-rw over 3 years ago - 3 comments

#140 - error while reconstructing the model using mylibrary

Issue - State: closed - Opened by Xingchen-Bian over 3 years ago - 1 comment

#139 - soft constraints inconsistency

Issue - State: closed - Opened by rcolpo over 3 years ago - 2 comments

#138 - Adding another protein function annotation tool

Issue - State: open - Opened by PedroMTQ over 3 years ago - 3 comments

#137 - Cynobacteria universe

Issue - State: open - Opened by Buiboni over 3 years ago - 2 comments

#136 - Inconsistencies in chemical formulae

Issue - State: closed - Opened by leuschjanphilipp over 3 years ago - 2 comments

#135 - Carveme Error calling stat on file /generated/bigg_proteins.dmnd

Issue - State: open - Opened by jorgeln0 over 3 years ago - 4 comments

#134 - "Hard constraints" reactions not present in model

Issue - State: closed - Opened by rcolpo over 3 years ago

#133 - Unusually high growth rates in reconstructed models

Issue - State: closed - Opened by shreyanshumale over 3 years ago - 2 comments

#132 - CPLEX API of Python

Issue - State: closed - Opened by joelmhaske over 3 years ago - 3 comments

#131 - GPR information is missing in output file

Issue - State: open - Opened by aini-bio over 3 years ago - 6 comments

#130 - Return ensemble to save, and return from carving after saving. Closes…

Pull Request - State: closed - Opened by filrot over 3 years ago

#129 - Problems when building model ensembles in 1.5.0: AttributeError: 'NoneType' object has no attribute 'genes'

Issue - State: closed - Opened by filrot almost 4 years ago - 2 comments

#128 - --refseq flag fails

Issue - State: closed - Opened by franciscozorrilla almost 4 years ago - 1 comment

#127 - A question about GramPos/Neg template choose

Issue - State: closed - Opened by Ezio0o almost 4 years ago - 2 comments

#126 - Very different reconstructions with CarveMe 1.5

Issue - State: closed - Opened by cdanielmachado almost 4 years ago - 3 comments

#125 - Low objective_value with the latest Carveme version

Issue - State: closed - Opened by juz4karen almost 4 years ago - 7 comments

#124 - How to know which reactions have been added for gap-filling?

Issue - State: closed - Opened by PolTorrentTornos almost 4 years ago - 1 comment

#123 - Reactions missing in bacterial universe after 1.5.0

Issue - State: closed - Opened by dotPiano almost 4 years ago - 3 comments

#122 - No growth with CarveMe v.1.5.0

Issue - State: closed - Opened by lumlukwp almost 4 years ago - 7 comments

#121 - carveme 1.5 not finding cplex

Issue - State: closed - Opened by vrmarcelino almost 4 years ago - 3 comments

#120 - Reactions without GPR in carveme 1.5.0

Issue - State: closed - Opened by dotPiano almost 4 years ago - 4 comments

#119 - merge development branch

Pull Request - State: closed - Opened by cdanielmachado almost 4 years ago

#118 - No console output after running CarveMe

Issue - State: closed - Opened by NantiaL almost 4 years ago - 2 comments

GitHub / cdanielmachado/carveme issues and pull requests