Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / sysbiochalmers/yeast-gem issues and pull requests

#379 - Implement YAML-based curation

Issue - State: open - Opened by edkerk about 1 month ago

#378 - ~6 incorrect annotations

Issue - State: open - Opened by oxinabox about 2 months ago - 4 comments

#377 - fix: growth predictions under anaerobic conditions

Pull Request - State: open - Opened by edkerk 2 months ago

#376 - bugs in growth prediction plot and scripts

Issue - State: open - Opened by edkerk 2 months ago

#375 - yeast 9.0.2

Pull Request - State: closed - Opened by edkerk 2 months ago

#374 - fix: curate auxotrophy and correct

Pull Request - State: closed - Opened by edkerk 3 months ago

#373 - chore: remove identifier prefixes from XML and store test results

Pull Request - State: closed - Opened by edkerk 3 months ago

#371 - implement auxotrophy-based curation

Issue - State: closed - Opened by edkerk 5 months ago - 1 comment

#370 - non-working BioStudies URL in yeast9 paper

Issue - State: closed - Opened by egonw 6 months ago - 3 comments

#369 - yeast 9.0.1

Pull Request - State: closed - Opened by edkerk 6 months ago

#368 - chore: update citation

Pull Request - State: closed - Opened by mihai-sysbio 6 months ago

#367 - Yeast-GEM visualization?

Issue - State: open - Opened by forxhunter 6 months ago - 4 comments

#366 - Hardware suggestion

Issue - State: closed - Opened by Danyang95 8 months ago - 1 comment

#364 - Add mets concentration from ymdb

Pull Request - State: closed - Opened by cheng-yu-zhang 11 months ago - 1 comment

#361 - yeast 9.0.0

Pull Request - State: closed - Opened by edkerk about 1 year ago

#360 - fix: unbalanced reactions and incorrect metFormulas

Pull Request - State: closed - Opened by edkerk about 1 year ago

#358 - reactions r_0533, r_0534, r_0535 appear not balanced

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

#357 - fix: make standard-gem.md a hidden file

Pull Request - State: closed - Opened by mihai-sysbio over 1 year ago

#356 - yeast 8.7.1

Pull Request - State: closed - Opened by edkerk over 1 year ago - 2 comments

#355 - fix: reaction name r_1024

Pull Request - State: closed - Opened by edkerk over 1 year ago

#354 - bug:spelling error for r_1024 "enxyme"

Issue - State: closed - Opened by BjornFJohansson over 1 year ago - 2 comments
Labels: fixed in devel

#353 - feat: function to report if flux vector is ΔG-compatible

Issue - State: open - Opened by edkerk over 1 year ago
Labels: enhancement

#352 - Proposed changes to the anaerobic model

Issue - State: open - Opened by davidhcsic over 1 year ago - 2 comments

#350 - fix: failing workflows

Pull Request - State: closed - Opened by mihai-sysbio over 1 year ago - 1 comment

#349 - feat: add UniProt identifiers

Pull Request - State: closed - Opened by cheng-yu-zhang over 1 year ago

#347 - fix: correct spontaneous r_0029 and r_0030

Pull Request - State: closed - Opened by edkerk over 1 year ago

#346 - feat: correct fructose transport

Pull Request - State: closed - Opened by edkerk over 1 year ago

#345 - chore: add standard-GEM.md

Pull Request - State: closed - Opened by edkerk over 1 year ago - 3 comments

#344 - feat: add metabolite SMILES

Pull Request - State: closed - Opened by edkerk over 1 year ago

#343 - yeast 8.7.0

Pull Request - State: closed - Opened by edkerk over 1 year ago

#342 - chore: small updates in aux functions and files

Pull Request - State: closed - Opened by edkerk over 1 year ago

#341 - fix: install dependencies in workflow

Pull Request - State: closed - Opened by mihai-sysbio over 1 year ago

#340 - unable to locate model when running io.read_yeast_model() in Python

Issue - State: closed - Opened by qqqtomcat over 1 year ago - 1 comment
Labels: fixed in devel

#339 - yeast 8.6.3

Pull Request - State: closed - Opened by edkerk over 1 year ago - 8 comments

#338 - duplicate metabolites identified

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

#337 - Volatile Esters & Polyphosphate Reactions

Pull Request - State: closed - Opened by edkerk over 1 year ago - 5 comments

#336 - Volatile Esters & Polyphosphate Reactions

Pull Request - State: closed - Opened by uliebal over 1 year ago - 1 comment

#334 - reaction references

Issue - State: open - Opened by mihai-sysbio almost 2 years ago

#333 - chore: update workflows

Pull Request - State: closed - Opened by mihai-sysbio almost 2 years ago

#332 - Fructose transport is represented as a symporter instead of facilitated diffusion

Issue - State: closed - Opened by davidhcsic almost 2 years ago
Labels: fixed in devel, bug

#331 - check Lys2 and Leu2 gene associations

Issue - State: closed - Opened by edkerk almost 2 years ago - 1 comment

#330 - feat: add metDeltaG and rxnDeltaG fields

Pull Request - State: closed - Opened by cheng-yu-zhang almost 2 years ago - 4 comments

#328 - Update according to genome update in 2021

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

#327 - some memote workflows are failing

Issue - State: closed - Opened by mihai-sysbio over 2 years ago - 3 comments
Labels: fixed in devel, bug

#326 - fix: add missing standard-GEM file

Issue - State: closed - Opened by mihai-sysbio over 2 years ago
Labels: fixed in devel

#325 - References for anaerobic benchmarking

Issue - State: closed - Opened by mperisin-lallemand over 2 years ago - 11 comments

#324 - yeast 8.6.2

Pull Request - State: closed - Opened by edkerk over 2 years ago

#323 - ATP synthase mitochondrial complex curation

Pull Request - State: closed - Opened by ae-tafur over 2 years ago - 4 comments

#322 - cerevisiae with radiation simulation is possible?

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

#321 - yeast 8.6.1

Pull Request - State: closed - Opened by edkerk over 2 years ago - 1 comment

#320 - feat: Uniprot annotations for all genes

Issue - State: closed - Opened by edkerk over 2 years ago - 5 comments
Labels: fixed in devel

#319 - feat: single ec-code annotation per reaction

Issue - State: open - Opened by edkerk over 2 years ago - 5 comments

#318 - feat: metSMILES annotation

Issue - State: closed - Opened by edkerk over 2 years ago - 1 comment
Labels: fixed in devel

#317 - feat: KEGG pathway annotation

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

#316 - chore(deps-dev): bump pip-tools from 6.6.1 to 6.6.2 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#315 - Correction of compartment reaction——peroxisome

Pull Request - State: closed - Opened by cheng-yu-zhang over 2 years ago - 1 comment

#314 - Correction of compartment reaction——lipid droplet

Pull Request - State: closed - Opened by cheng-yu-zhang over 2 years ago - 3 comments

#313 - feat: add 19 new GPR and consolidate curations between model releases

Pull Request - State: closed - Opened by cheng-yu-zhang over 2 years ago - 5 comments

#312 - fix: reduce dependency

Pull Request - State: closed - Opened by edkerk over 2 years ago

#311 - yeast 8.6.0

Pull Request - State: closed - Opened by edkerk over 2 years ago

#310 - Feat: A python function for anaerobic condition setup

Issue - State: open - Opened by feiranl over 2 years ago - 4 comments

#309 - refactor: reduce dependencies modelTests

Issue - State: closed - Opened by edkerk over 2 years ago - 1 comment
Labels: fixed in devel

#308 - Interoperability improvements for `yeast-GEM.mat`

Issue - State: closed - Opened by exaexa almost 3 years ago - 4 comments
Labels: fixed in devel

#307 - Unique subsystem of rxn

Pull Request - State: closed - Opened by cheng-yu-zhang almost 3 years ago - 12 comments

#306 - Transporter annotation for transport rxns

Pull Request - State: closed - Opened by cheng-yu-zhang almost 3 years ago - 9 comments

#305 - Complex annotation

Pull Request - State: closed - Opened by cheng-yu-zhang almost 3 years ago - 8 comments

#304 - add reactions based on KEGG and MetaCyc annotations

Pull Request - State: closed - Opened by cheng-yu-zhang almost 3 years ago - 11 comments

#303 - feat: standardize and simplify curation of yeast-GEM

Issue - State: closed - Opened by edkerk almost 3 years ago - 10 comments

#302 - feat: function for reproducible and convenient model curation

Issue - State: closed - Opened by edkerk almost 3 years ago
Labels: enhancement, fixed in devel

#301 - refactor: reduce dependencies and remove metabolite ID suffixes

Pull Request - State: closed - Opened by edkerk almost 3 years ago - 5 comments

#300 - add-rxn.prop: Hydrogen Sulfide Addition

Pull Request - State: closed - Opened by wtscott31 almost 3 years ago - 8 comments

#297 - Feat-stoichiometry coefficients for subunits in the enzyme complex

Issue - State: open - Opened by feiranl about 3 years ago - 10 comments

#296 - feat: volatiles produced by S. cerevisiae

Issue - State: closed - Opened by feiranl about 3 years ago - 6 comments
Labels: enhancement

#295 - Feat-Polyphosphate metabolism

Issue - State: closed - Opened by feiranl about 3 years ago - 1 comment
Labels: enhancement, wip

#294 - Fix-amino acid pathways localization

Issue - State: open - Opened by feiranl about 3 years ago - 1 comment
Labels: bug, wip

#292 - Question about ferredoxin iron-sulfur cluster

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

#290 - fix-bug: update the reversibility of reaction r_0446

Pull Request - State: closed - Opened by feiranl about 3 years ago

#289 - feat: have SLIMEr as option

Issue - State: open - Opened by edkerk about 3 years ago

#288 - feat: curate grRules with GPRuler output

Issue - State: open - Opened by edkerk about 3 years ago

#287 - fix: use python 3.9.7 in GitHub Actions

Pull Request - State: closed - Opened by edkerk about 3 years ago

#286 - doc: tutorial for yeast-GEM

Issue - State: open - Opened by edkerk about 3 years ago

#285 - Develop

Pull Request - State: closed - Opened by edkerk about 3 years ago - 2 comments

#282 - bug: unnecessary invalid BiGG identifiers suggested

Issue - State: open - Opened by edkerk about 3 years ago - 1 comment
Labels: help wanted, bug

#281 - bug: inconsistency in metabolite identifiers and names between .yml, .txt and .xml files.

Issue - State: closed - Opened by edkerk about 3 years ago - 1 comment
Labels: bug

#280 - How to used the ID of metabolites correctly in COBRApy?

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

#279 - chore(deps): bump babel from 2.9.0 to 2.9.1 in /requirements

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#265 - Fix: no flux in TCA when maximizing ATP production

Issue - State: closed - Opened by feiranl over 3 years ago - 5 comments
Labels: fixed in devel, bug

#245 - fix-update MNX IDs according to MNX database latest release 4.0

Issue - State: open - Opened by feiranl over 4 years ago - 5 comments
Labels: bug

#231 - feat:Missing annotations for Rhea and ModelSEED database

Issue - State: open - Opened by feiranl over 4 years ago - 3 comments
Labels: help wanted

#217 - fix: avoid duplicity in gene name storage

Issue - State: closed - Opened by BenjaSanchez almost 5 years ago - 1 comment
Labels: format fix, standby

#212 - feat: yeast-GEM maps in caffeine platform

Issue - State: closed - Opened by BenjaSanchez almost 5 years ago - 10 comments
Labels: enhancement

#194 - fix: mass- and charge balance reactions

Issue - State: open - Opened by edkerk over 5 years ago - 2 comments
Labels: help wanted, bug

#193 - Empirical stoichiometry for oxidative phosphorylation

Issue - State: closed - Opened by avlant over 5 years ago - 11 comments
Labels: enhancement, question

#191 - feat: include glycolipids in biomass

Issue - State: closed - Opened by hvdinh16 almost 6 years ago - 7 comments

#160 - fix: correction of gene relation for transport reactions

Issue - State: closed - Opened by hongzhonglu over 6 years ago - 4 comments
Labels: fixed in devel

#100 - Feat/badges

Pull Request - State: closed - Opened by BenjaSanchez almost 7 years ago
Labels: enhancement

#99 - Revert "Feat/add Gitter badge"

Pull Request - State: closed - Opened by BenjaSanchez almost 7 years ago