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MetabolicAtlas
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standard-GEM
The standard for open-source GEMs on GitHub
https://www.biorxiv.org/content/10.1101/2023.03.21.512712
Creative Commons Attribution 4.0 International
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GSMM as an alternative to GEM
#39
mihai-sysbio
opened
9 months ago
0
Clarify naming convention for model files
#38
mihai-sysbio
opened
9 months ago
0
Support for repositories with multiple GEMs (f. ex. strain collections)
#37
famosab
opened
1 year ago
1
Automated tests via github actions for repositories generated from this template
#36
famosab
opened
1 year ago
3
update language in .standard-GEM.md
#35
mihai-sysbio
closed
1 year ago
0
fix: templates for GitHub Issues and Pull Requests
#34
mihai-sysbio
closed
1 year ago
1
chore: rename master to main, including Yeast-GEM refs
#32
mihai-sysbio
closed
3 years ago
0
template for gh pages landing page in /docs on master
#31
mihai-sysbio
opened
3 years ago
0
Revise templates in .github
#29
mihai-sysbio
opened
3 years ago
0
standard-GEM 0.5
#28
mihai-sysbio
closed
3 years ago
0
Encourage the use of dedicated fields rather than semantic overloading
#27
draeger
opened
3 years ago
12
improved descriptions of url and releases fields
#26
mihai-sysbio
closed
3 years ago
0
add taxonomy id
#25
mihai-sysbio
closed
3 years ago
0
fix: allow Genome ID from any sources
#24
haowang-bioinfo
closed
3 years ago
0
Focus of the next release
#23
mihai-sysbio
opened
3 years ago
0
clarify usage of Zenodo
#22
mihai-sysbio
closed
3 years ago
0
add field for genome id to readme
#21
mihai-sysbio
closed
3 years ago
0
Documentation of model development
#20
sulheim
opened
3 years ago
16
External standard subsystem for each reaction to make it comparable from different GEMs
#19
hongzhonglu
opened
3 years ago
10
Encourage the use of COMBINE archives as exchange format for the model and its execution
#18
draeger
opened
3 years ago
6
Include genome (+ annotation)
#17
edkerk
closed
3 years ago
7
Make the model used by both cobrapy and cobra toolbox?
#16
hongzhonglu
closed
3 years ago
9
GitHub versus specialized platform (database)
#15
Midnighter
closed
3 years ago
15
Require tagged releases to Zenodo
#14
Midnighter
closed
3 years ago
7
Model organism description
#13
Midnighter
closed
3 years ago
3
Guidelines color code
#12
Midnighter
closed
3 years ago
2
Consider using more powerful templating, e.g., cookiecutter
#11
Midnighter
opened
3 years ago
10
manage dependencies
#10
mihai-sysbio
opened
4 years ago
0
automated validation
#9
mihai-sysbio
closed
2 years ago
7
0.4
#8
mihai-sysbio
closed
4 years ago
0
fix: 0.4 typos
#7
mihai-sysbio
closed
4 years ago
0
rename _master_ to _main_
#6
mihai-sysbio
closed
3 years ago
8
feat: rename modelFiles to model resolves #4
#5
mihai-sysbio
closed
4 years ago
0
name of folder with models
#4
edkerk
closed
4 years ago
4
refactor: guidelines
#3
mihai-sysbio
closed
4 years ago
0
docs: refactor readme
#2
mihai-sysbio
closed
4 years ago
0
v0.3 draft
#1
mihai-sysbio
closed
4 years ago
0