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Benchmarking #34

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Benchmarking #34

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JonahRileyHuggins
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Benchmarking functionality for querying sparced model predictions to experimental datasets via PEtab.

@ChocolateCharlie
Radicaal quick restructuration
3c5bb16
@ChocolateCharlie
More quick organization
555cad7
@ChocolateCharlie
Quick clean of input and data structure
76fe81d
@ChocolateCharlie
Remove Nextflow files from a specific user
19ea7ce
@ChocolateCharlie
Add common accessory Python files to .gitignore
c71d0d9
@ChocolateCharlie
Group files related to nextfow and kube in separate folder
cf986fb
@ChocolateCharlie
Erase unecessary file
98d9095
@ChocolateCharlie
Update version file
f43c254
@ChocolateCharlie
Refactor Antimony model creation
a70b1e9
@ChocolateCharlie
Fix Antimony model creation in create_model script
bd111dc
@ChocolateCharlie
Move temporarily previous documentation and create Sphinx docs
99c6aad
@ChocolateCharlie
Generate basic documentation with PDJ theme
1216640
@ChocolateCharlie
Move requirements to correct folder
5673d44
@ChocolateCharlie
Remove unnecessary config file
7fcb2ea
@ChocolateCharlie
Autogenerate documentation with Sphinx
9f196b7
@ChocolateCharlie
Create documentation page for model creation
4c73d76
@ChocolateCharlie
Improve documentation for model creation
11df83e
@ChocolateCharlie
Add some documentation for antimony_utils
b72de32
@ChocolateCharlie
Separate SBML utils from rest of model creation script
793a5b8
@ChocolateCharlie
First version to fully create a SPARCED model, from Antimony to AMICI
a64a3a9
@ChocolateCharlie
Clean input data files organization
56fbc49
@ChocolateCharlie
Make arguments handling function reusable ; refactor utilities organi…
6ebd2a0 
…zation
@ChocolateCharlie
Keep cleaning model creation script
489fe18
@ChocolateCharlie
Update documentation
2e65c59
@ChocolateCharlie
Fix docs error in create_model ; attempt to fix layout for arguments
4be2c67
@ChocolateCharlie
Clean command line antimony creation workflow
419f22e
@ChocolateCharlie
Ensure correctness of the generated Antimony file
f5fa6c5
@ChocolateCharlie
Finish clean pipeline for Antimony model creation!
b81d2c3
@ChocolateCharlie
Remove unnecessary __init__.py files
2c7cbb2
@ChocolateCharlie
Clean SBML model creation
cd2e82b
ChocolateCharlie and others added 30 commits May 23, 2024 12:04
@ChocolateCharlie
Add full incubation pipeline
a1b4966 
This pipeline was tested on the SPARCED_standard model for a) no incubation specified at all b) an incubation defined to 0 hours and c) an incubation set to 24 hours.
Updated LINCS-RPPA-Abundance benchmark to include all experimental da…
b06fdde 
…ta for all observables currently within SPARCED
@ChocolateCharlie
Merge incubation pipeline into main
3384d18
Updated LINCS-RPPA-Abundance benchmark to include all experimental da…
0e3be65 
…ta for all observables currently within SPARCED
Merge remote-tracking branch 'origin/master' into benchmarking
4d0ad08 
 conforming with most recent development on master branch.
updated dynamic module finder to noMPI benchmark evaluator.
476472d
Altered the direct reference for Species.txt in the RunSPARCED funtio…
ed0b660 
…n, so that no local instance of the input file is needed
needed to add paths of f_genereg and f_omics to both _preequilibrate …
5e4f716 
…and heterogenize functions
LINCS-RPPA-Abundance/LINCS-RPPA-(a)bundance --> LINCS-RPPA-Abundance/…
f676cdd 
…LINCS-RPPA-(A)bundance
file correction
83f6cba
Modularized the benchmarking code to imporve operation and readability.
5a32506
Removed unnecessary print statement
9393e87
@JonahRileyHuggins
Tried adding in a progress bar, work in progress
1a61261
@JonahRileyHuggins
Update model-benchmark-validation.py
4a818fa
fixed deadlock issues related to results passing
5c94308
added 0-timepoint experimental data to benchmark
ee8ca13
@JonahRileyHuggins
Updated RPPA benchmark
dfbf9c1 
Experimental data in benchmark updated to reflect level 0 Normalized Linear data produced by the LINCS consortium
@JonahRileyHuggins
Updated Benchmark Analysis Notebook
9adeb2c 
Updated to reflect current names of benchmarks
@JonahRileyHuggins
updates to model validation script
56a31e1
@JonahRileyHuggins
Update utils.py
45bc542
@JonahRileyHuggins
Code Cleaning Friday ;)
681fc92
@JonahRileyHuggins
Update model-benchmark-validation.py
b047386
@JonahRileyHuggins
Code-cleaning Friday
5340492 
cleaning and general maintenance.
@JonahRileyHuggins
Fixing cell cycle benchmark
b59aedc 
Issue with gene value assignment, changed to reassign omicsdata file.
@JonahRileyHuggins
Update utils.py
e09616e
@JonahRileyHuggins
issues with transcription value assignment never fixed
e40a11a
@JonahRileyHuggins
added benchmark generator to the benchmark untils tool suite
ef0082a
@JonahRileyHuggins
Update sparced_simulation.py
0144706
fixed transcription setting changes in benchmark, solved cell cycle b…
8dadda9 
…enchmark issue
fixed transcription setting changes in benchmark, solved cell cycle b…
1c3a7bf 
…enchmark issue
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2 participants
@JonahRileyHuggins @ChocolateCharlie