LCSB-BioCore/COBREXA.jl issues and pull requests

#827 - legacy & update notices in README for v2

Pull Request - State: closed - Opened by exaexa 5 months ago

#826 - update CI a bit

Pull Request - State: closed - Opened by exaexa 5 months ago

#825 - work-around equalities in coupling bounds in MAT

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

#824 - fix grr symbols

Pull Request - State: closed - Opened by exaexa 7 months ago - 2 comments
Labels: bug, minor

#823 - Genes not parsed if they have an "@" symbol

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

#822 - Solve convert(StandardModel, model::JSONModel) issue

Pull Request - State: closed - Opened by josePereiro 9 months ago - 7 comments

#821 - Add required compat entries for Base libs

Pull Request - State: closed - Opened by exaexa 10 months ago

#820 - Small fix to mmdf

Pull Request - State: closed - Opened by stelmo 10 months ago

#819 - Showcase: enzyme communities

Pull Request - State: closed - Opened by stelmo 10 months ago - 2 comments

#818 - Showcase: enzyme communities

Pull Request - State: closed - Opened by stelmo 10 months ago - 1 comment

#817 - Implement SMoment

Pull Request - State: closed - Opened by stelmo 10 months ago - 3 comments

#816 - Add resource balance tutorial

Pull Request - State: closed - Opened by stelmo 10 months ago - 1 comment

#814 - january cleanup of `next`

Pull Request - State: closed - Opened by exaexa 11 months ago - 1 comment

#813 - Open the enzyme builder functions

Pull Request - State: closed - Opened by stelmo 11 months ago - 6 comments

#812 - Restructure a little bit

Pull Request - State: closed - Opened by stelmo 11 months ago - 2 comments

#811 - Implement community models

Pull Request - State: closed - Opened by stelmo 11 months ago - 4 comments
Labels: feature

#810 - Add a loopless modification for v2

Pull Request - State: closed - Opened by stelmo 11 months ago - 3 comments
Labels: feature

#809 - Homogenize names of functions

Pull Request - State: closed - Opened by stelmo 11 months ago - 5 comments
Labels: quality

#808 - Add max min driving force capability

Pull Request - State: closed - Opened by stelmo 11 months ago - 7 comments

#807 - JUMP time limit

Issue - State: closed - Opened by exaexa 11 months ago - 5 comments
Labels: feature, :axe: code axing :axe:

#805 - Add enzyme constrained models

Pull Request - State: closed - Opened by stelmo 12 months ago - 8 comments
Labels: feature

#804 - Small fixes for CT 0.6

Pull Request - State: closed - Opened by stelmo 12 months ago - 2 comments

#803 - inconsistent parsing of subsystems

Issue - State: open - Opened by mihai-sysbio 12 months ago - 9 comments
Labels: quality, feature, minor

#802 - Implement quadratic functionality

Pull Request - State: open - Opened by stelmo about 1 year ago - 4 comments

#801 - Implement enzyme model

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

#800 - Start getting FBA to work

Pull Request - State: closed - Opened by stelmo about 1 year ago - 4 comments

#799 - Make a clean slate

Pull Request - State: closed - Opened by stelmo about 1 year ago - 1 comment
Labels: do not merge

#798 - CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment

#797 - Warning when reaction is added with metabolites not yet in model

Issue - State: closed - Opened by HettieC about 1 year ago - 2 comments
Labels: quality, minor

#796 - sudden outbreak of ConstraintTrees

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

#795 - Extend core functionality

Pull Request - State: closed - Opened by stelmo about 1 year ago - 2 comments
Labels: do not merge

#794 - Document forwarding the `--project` exeflag with ClusterManagers

Issue - State: closed - Opened by exaexa about 1 year ago - 1 comment
Labels: documentation

#793 - CompatHelper: bump compat for HDF5 to 0.17, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 2 comments

#792 - CompatHelper: bump compat for SBML to 1, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment

#791 - CompatHelper: bump compat for PikaParser to 0.6, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 2 comments

#790 - Neaten the summarize functions

Pull Request - State: closed - Opened by stelmo over 1 year ago - 7 comments

#789 - Implement Tables.jl interface for `ModelWithResult`

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

#788 - Import annotations better for SBML

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

#787 - Make duplicate reaction test stricter

Pull Request - State: closed - Opened by stelmo over 1 year ago - 4 comments

#786 - Extend the SBO identifiers and add isa_xxx functions

Pull Request - State: closed - Opened by stelmo over 1 year ago - 4 comments

#785 - `check_duplicate_reaction` does not consider reaction directionality

Issue - State: closed - Opened by stelmo over 1 year ago - 2 comments

#784 - Check that function return types inferred in documentation make sense

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

#783 - fix sparsevec

Pull Request - State: closed - Opened by exaexa over 1 year ago - 2 comments
Labels: bug

#782 - Pretty print model semantics

Issue - State: closed - Opened by stelmo over 1 year ago - 2 comments

#781 - fix filename

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

#780 - Throw error if too many arguments supplied to enzyme models

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

#779 - Develop → master merge for 1.5.0

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

#778 - fixed merge of #777

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

#777 - implement expression-limited fluxes (E-Flux like algorihm)

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

#776 - make the semantics cut

Pull Request - State: closed - Opened by exaexa over 1 year ago - 4 comments
Labels: code axing, :x: breaking :x:

#775 - finalize the semantics

Pull Request - State: closed - Opened by exaexa over 1 year ago - 2 comments
Labels: feature, :x: breaking :x:

#774 - Fix EqualGrowthCommunityModel accessors

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

#773 - implement wrappy pFBA using the normal L2 wrappers

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

#772 - Extend simplified enzyme model to include multiple capacity constraints

Pull Request - State: closed - Opened by stelmo over 1 year ago - 16 comments

#771 - Rename GeneAssociation file

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

#770 - Make kwarg plural

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

#769 - unify L2-like QP handling

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

#768 - `removeReaction!` etc. doesn't update all fields in a `CoreModel`

Issue - State: open - Opened by htpusa over 1 year ago - 1 comment
Labels: bug

#767 - split wrappers off to a separate module

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

#766 - Add basic show for ModelWithResult

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

#765 - Mapping through delimited IDs into inner models

Issue - State: closed - Opened by stelmo over 1 year ago - 2 comments

#764 - Fix cFBA implementation

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

#763 - Result wrapper

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

#762 - Fix and extend reconstruction functions and pipes for objectmodel

Pull Request - State: closed - Opened by stelmo over 1 year ago - 11 comments

#761 - Add `Result` type

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 2 comments

#760 - Add plural to change_bounds and add change_constraints

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 1 comment

#759 - Make kwargs for convenience enzyme constrained consistent

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 9 comments

#758 - JSON model format incompatible with escher

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

#757 - Return enzyme concentrations in useful units

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 2 comments

#756 - Export MIN_SENSE and MAX_SENSE

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 2 comments

#755 - Fix model accessor bugs

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 1 comment

#754 - Remove unnecessary docstrings

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 3 comments
Labels: code axing

#753 - remove and clean up GeneAssociations alias

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment

#752 - port GRR parsing to 2.0, avoid DNF complexity explosions

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment

#751 - Add pipes to all the analysis functions

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 4 comments
Labels: do not merge

#750 - Add model annotation details

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 10 comments

#749 - Add another convenience constructor for enzyme constrained models

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 1 comment

#748 - Add test for multiple capacity enzyme bounds

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 1 comment

#747 - pFBA pipe

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 8 comments
Labels: do not merge

#746 - Homogenize bound kwargs

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 1 comment

#745 - Generalize loopless modification

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 5 comments
Labels: do not merge

#744 - clean up SBML unit-error throwing

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment

#743 - Add balance accessor to community model

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 3 comments

#742 - Add some more semantics to EnzymeConstrainedModel

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 15 comments

#741 - Remove double s from enzyme semantics

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 1 comment

#740 - Remove switching argument for reaction constructors

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 3 comments

#739 - Add more reconstruction functions to ObjectModel

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 3 comments

#738 - Develop → master merge for 1.4.4

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 2 comments

#737 - version bump for 1.4.4

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

#736 - Q-opt support

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment

#735 - extensible variable semantics

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 2 comments

#734 - fix GRA compat once more (and hopefully the last time)

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment

#733 - GPA ordering fix

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment
Labels: bug, minor

#732 - Fix test bugs in new parser

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 3 comments

#731 - add an actual GPA/GRR to DNF parser

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment
Labels: quality, feature

#730 - remove a config from local CI

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment
Labels: quality

#729 - CompatHelper: bump compat for SBML to 1, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment

#728 - `LICENSE` file type was not markdown

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment
Labels: minor

#727 - remove obsolete print_banner() from the SIF container

Pull Request - State: closed - Opened by exaexa almost 2 years ago - 1 comment

#726 - Generalize metabolites

Pull Request - State: closed - Opened by stelmo almost 2 years ago - 3 comments

GitHub / LCSB-BioCore/COBREXA.jl issues and pull requests