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draeger-lab
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ModelPolisher
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
MIT License
22
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6
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Scraping for invalid identifiers.org URLs
#126
Schmoho
opened
1 week ago
0
lenient miriam registry parsing
#125
Schmoho
closed
2 weeks ago
0
Draeger lab/model polisher/#121 polishing unit tests
#124
Schmoho
closed
1 month ago
0
Identifiers.org new identifiers pattern lead to identifier duplicates
#123
GwennyGit
opened
1 year ago
0
polishing of reaction participants is aborted halfway through
#122
Schmoho
closed
1 year ago
1
introduce polishing unit tests
#121
Schmoho
closed
1 week ago
1
introduce UnitPolishing class
#120
Schmoho
closed
2 years ago
1
polishListOfObjectives throws ConcurrentModificationException
#119
Schmoho
closed
2 years ago
1
the way we check for FBC strict is not compliant with the spec
#118
Schmoho
opened
2 years ago
4
write class and method docstrings
#117
Schmoho
closed
1 week ago
1
build and ship javadocs for the Project
#116
Schmoho
closed
2 years ago
2
update README and Wiki
#115
Schmoho
opened
2 years ago
1
release branch does not build
#114
Schmoho
closed
2 years ago
1
failing tests on master
#109
Schmoho
closed
2 years ago
1
issue #104 third party licenses
#108
Schmoho
closed
2 years ago
0
Add annotations for KEGG pathways and genes
#107
NantiaL
opened
2 years ago
4
MetaNetX annotations not added properly
#106
NantiaL
opened
2 years ago
8
ModelPolisher-2.0.1.jar is not available when running in docker container
#105
famosab
closed
2 years ago
2
Known security vulnerabilities detected in third-party library
#104
draeger
closed
2 years ago
3
Polished model read with errors in cobrapy
#103
EnuhBlaise
closed
1 year ago
17
Issue with opening model file
#102
alexander-alleman
closed
2 years ago
3
Update ModelPolisherOptions to allow for validation of unzipped output
#101
mephenor
closed
2 years ago
1
Conflict with SBML validation
#100
Biomathsys
closed
2 years ago
9
includeAnyURI not applied consequently across codebase
#99
mephenor
opened
4 years ago
0
Running with docker-compose run -u $(id -u):$(id -g) potentially locks up execution
#98
mephenor
closed
1 week ago
1
Adding Subsystem Annotation for models without Model BiGGId in BiGG
#97
mephenor
closed
4 years ago
1
Annotating models with the genome identifier
#96
draeger
opened
4 years ago
3
Update to JSBML 1.5
#95
draeger
closed
4 years ago
1
FbcPlugin and Reaction bounds/objective function/genes
#94
Linelili
closed
4 years ago
2
Refactoring
#93
mephenor
closed
4 years ago
0
How to handle queries with multiple return values
#92
mephenor
closed
2 years ago
2
Replace simple Connection with ConnectionPool for improved performance
#91
mephenor
closed
4 years ago
0
How to handle multiple gene_reaction_rules
#90
mephenor
closed
2 years ago
1
Spurious annotations
#89
mephenor
opened
4 years ago
4
GPR creation fails with ClassCastException
#88
mephenor
closed
4 years ago
4
Identifiers.org annotations are now https:, not http:
#87
mephenor
closed
4 years ago
0
Handling ncbigi annotations
#86
mephenor
closed
2 years ago
5
Rewriting BiGGId handling
#85
mephenor
closed
4 years ago
1
Current state
#84
mephenor
closed
2 years ago
9
Refactoring
#83
mephenor
closed
4 years ago
0
Error when running with docker-compose
#82
LisbethIsolde
closed
4 years ago
1
Remove remaining code pertaining to removed SQLite connector
#81
mephenor
closed
4 years ago
0
Update MIRIAM Registry to support new collections
#80
mephenor
closed
4 years ago
4
Make sure there is no hard dependency on AnnotateDB
#79
mephenor
closed
4 years ago
2
Allow for species/reactions/... to be processed directly
#78
mephenor
opened
4 years ago
2
Factor out helper functions, enums and inner classes into separate classes to improve readability
#77
mephenor
closed
4 years ago
1
COBRAparser partially fails to parse model
#76
mephenor
closed
1 year ago
4
Changing Travis, Gradle and Docker config to use Docker Hub images where possible
#75
mephenor
closed
4 years ago
0
Feature to produce CombineArchive, update Travis.
#74
codekaust
closed
4 years ago
1
fix #71
#73
codekaust
closed
4 years ago
2
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