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23 Open 28 Closed
23 Open 28 Closed
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Issues list

Include default objective functions in COMO documentation during model building priority:normal state:open This is still being planned subsystem:documentation subsystem:jupyter-notebook Relates to the jupyter notebook type:cosmetics This is a visual issue type:usability This is impacting end-user usability
#114 opened Mar 31, 2023 by JoshLoecker
@JoshLoecker
Make GPLK and GUROBI available as options
#104 opened Mar 7, 2023 by JoshLoecker
Step 6 fails silently priority:major state:in-progress This is being worked on subsystem:jupyter-notebook Relates to the jupyter notebook type:bug This isn't working type:usability This is impacting end-user usability
#92 opened Feb 27, 2023 by JoshLoecker
Write a series of reports giving a summary of parameters used priority:normal state:open This is still being planned subsystem:jupyter-notebook Relates to the jupyter notebook subsystem:python Relates to Python files type:feature
#91 opened Feb 13, 2023 by JoshLoecker
6 tasks
Import common-name metabolites in model creation (step 4) priority:normal state:open This is still being planned subsystem:jupyter-notebook Relates to the jupyter notebook subsystem:python Relates to Python files type:feature
#90 opened Feb 2, 2023 by JoshLoecker
2
Allow reading of SBML models priority:normal state:open This is still being planned subsystem:python Relates to Python files type:feature
#78 opened Nov 7, 2022 by JoshLoecker
Update to Python 3.11 priority:normal state:open This is still being planned subsystem:python Relates to Python files type:development This is an issue with MADRID backend type:feature type:performance This isn't working as well or as fast as it should
#69 opened Oct 22, 2022 by JoshLoecker
Rerun flux balance analysis (cobra) priority:major state:open This is still being planned subsystem:jupyter-notebook Relates to the jupyter notebook type:bug This isn't working type:usability This is impacting end-user usability
#62 opened Oct 6, 2022 by JoshLoecker
Default regulation values should default to +/- 0.58 priority:normal state:open This is still being planned subsystem:python Relates to Python files type:performance This isn't working as well or as fast as it should type:usability This is impacting end-user usability
#58 opened Oct 6, 2022 by JoshLoecker
Linters and Type Checkers priority:minor state:open This is still being planned subsystem:other Relates to an unspecified part of the project type:development This is an issue with MADRID backend
#47 opened Sep 15, 2022 by JoshLoecker
1
Use CSV files instead of Excel Files priority:normal state:open This is still being planned subsystem:jupyter-notebook Relates to the jupyter notebook type:cosmetics This is a visual issue type:feature type:usability This is impacting end-user usability
#46 opened Sep 14, 2022 by JoshLoecker
[Cluster Sources] Cluster Transcriptomic and Proteomic Sources priority:normal state:in-progress This is being worked on subsystem:python Relates to Python files subsystem:R Relates to R files type:feature
#36 opened Sep 1, 2022 by JoshLoecker
2 of 6 tasks
Intermediate File Removal priority:normal state:open This is still being planned subsystem:other Relates to an unspecified part of the project type:feature
#34 opened Sep 1, 2022 by JoshLoecker
[Protein Transform] Split zFPKM Figures priority:normal state:open This is still being planned subsystem:R Relates to R files type:cosmetics This is a visual issue
#33 opened Sep 1, 2022 by JoshLoecker
Multistage Docker Builds priority:normal state:open This is still being planned subsystem:docker Relates to docker type:bug This isn't working
#32 opened Sep 1, 2022 by JoshLoecker
[Cluster Samples] Refactor boolean matrix creation priority:normal state:open This is still being planned subsystem:R Relates to R files type:bug This isn't working
#30 opened Sep 1, 2022 by JoshLoecker
File Paths in Jupyter Notebook priority:normal state:open This is still being planned subsystem:jupyter-notebook Relates to the jupyter notebook type:bug This isn't working
#27 opened Sep 1, 2022 by JoshLoecker
GitHub Actions Docker Caching priority:normal state:open This is still being planned subsystem:docker Relates to docker type:feature
#26 opened Sep 1, 2022 by JoshLoecker
R Log File not Created priority:normal state:in-progress This is being worked on subsystem:R Relates to R files type:bug This isn't working
#24 opened Sep 1, 2022 by JoshLoecker
[R scripts] Implement S4 Object Oriented Programming priority:minor state:open This is still being planned subsystem:R Relates to R files type:development This is an issue with MADRID backend type:performance This isn't working as well or as fast as it should
#22 opened Sep 1, 2022 by JoshLoecker
RPy2 Refactor priority:normal state:in-progress This is being worked on subsystem:python Relates to Python files subsystem:R Relates to R files type:development This is an issue with MADRID backend
#21 opened Sep 1, 2022 by JoshLoecker
8 of 9 tasks
Using Multiple Models for Drug Repurposing priority:major state:open This is still being planned subsystem:jupyter-notebook Relates to the jupyter notebook type:usability This is impacting end-user usability
#16 opened Sep 1, 2022 by JoshLoecker
Execute with Provided Example Data priority:normal state:open This is still being planned subsystem:other Relates to an unspecified part of the project type:cosmetics This is a visual issue type:usability This is impacting end-user usability
#14 opened Sep 1, 2022 by JoshLoecker
ProTip! Exclude everything labeled bug with -label:bug.