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Benchmarking#34

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JonahRileyHuggins wants to merge 230 commits intobirtwistlelab:masterbirtwistlelab/SPARCED:masterfrom ChocolateCharlie:benchmarkingChocolateCharlie/Birtwistle-SPARCED:benchmarkingCopy head branch name to clipboard

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Commits

Commits on Mar 13, 2024

• Radicaal quick restructuration

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• More quick organization

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• Quick clean of input and data structure

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• Remove Nextflow files from a specific user

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Commits on Mar 18, 2024

• Add common accessory Python files to .gitignore

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• Group files related to nextfow and kube in separate folder

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• Erase unecessary file

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• Update version file

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  f43c254

• Refactor Antimony model creation

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Commits on Mar 19, 2024

• Fix Antimony model creation in create_model script

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• Move temporarily previous documentation and create Sphinx docs

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• Generate basic documentation with PDJ theme

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• Move requirements to correct folder

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• Remove unnecessary config file

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Commits on Mar 21, 2024

• Autogenerate documentation with Sphinx

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• Create documentation page for model creation

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• Improve documentation for model creation

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• Add some documentation for antimony_utils

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Commits on Mar 22, 2024

• Separate SBML utils from rest of model creation script

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Commits on Apr 3, 2024

• First version to fully create a SPARCED model, from Antimony to AMICI

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• Clean input data files organization

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• Make arguments handling function reusable ; refactor utilities organization

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• Keep cleaning model creation script

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Commits on Apr 4, 2024

• Update documentation

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• Fix docs error in create_model ; attempt to fix layout for arguments

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• Clean command line antimony creation workflow

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• Ensure correctness of the generated Antimony file

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• Finish clean pipeline for Antimony model creation!

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• Remove unnecessary __init__.py files

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Commits on Apr 5, 2024

• Clean SBML model creation

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• Some work towards getting a similar SBML file than legacy - very close but not there yet

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Commits on Apr 8, 2024

• Fix conflict between ant_ and sbml_ prefixes

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  dab8481

• Create the wild flag to handle hard-coded values

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• Quick update of autodocumentation and fixing of all the bugs raised

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Commits on Apr 9, 2024

• Minor rearrangement of markdown files

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• Update documentation

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Commits on Apr 11, 2024

• Add some functions to handle AMICI compilation

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• Remove duplicate model name and add observables argument

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• Ongoing work with SBML

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• Ongoing work with AMICI compilation results

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• Create simulation folder

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• Fix SBML ; generate clean SBML model

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• Restore verbose default value

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Commits on Apr 12, 2024

• Update documentation

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• Remove SPARCED_Brep

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• Remove temporary documentation

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• Update documentation

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• Remove unnecessary file

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• Update SBML file

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• Make awesome docs

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• Add section for results replication in docs

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Commits on Apr 15, 2024

• Clear examples into subfolders

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• Add installation guide to docs

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• Update version number

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Commits on Apr 16, 2024

• Add license to docs

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• Update amici compilation file name

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• Add amici SPARCED standard model

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• Update requirements file and add an environment file

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• Add docs requirements

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• Add amici version number to installation guide

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Commits on Apr 17, 2024

• Clean Antimony file creation

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• Update documentation for Antimony

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• Update documentation for SBML

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• Update documentation for AMICI

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• Add SPARCED legacy model

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• Compare SPARCED standard with SPARCED legacy

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Commits on Apr 18, 2024

• Add requirements to run notebooks

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• Add SPARCED notebook model

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• AMICI models differences between legacy, notebook and standard versions

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• Update comparison between legacy and notebook models

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• Remove old unused files

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• Move Excel to TSV file conversion function to data folder

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• Add simulation arguments ; move file to main folder for better access

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• Move usefull data loading function to general utils

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Commits on Apr 19, 2024

• Fix typo in create_model imports

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• Update documentation

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• Remove unuseful and empty __init__ file

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• Make utils a module by adding an empty __init__ file

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• Add details to arguments helper

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• Add some ligands concentration handling for simulations

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• [BROKEN] Start cleaning run model simulation functions

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Commits on Apr 23, 2024

• Remove old and ambiguous AMICI model

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• Merge pull request #2 from birtwistlelab/master

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• Add missing verbose argument

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• The run script worksgit add simulation/run.py !

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• Latest file version

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• Dirty hard-coding to test quickly the simulation pipeline

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• Do no track simulation results

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Commits on Apr 24, 2024

• Remove old file that seemed unnecessary

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• Organize run model into several files

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• Read ligands from arguments

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Commits on Apr 25, 2024

• Set deterministic mode as default

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• Rename notebook files to ease simulation

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Commits on Apr 26, 2024

• Remove docker and kubernetes examples

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• Reorganize clean source

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• Update SPARCED's sbml model

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• Update documentation

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• Update README file

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• Attempt to fix internal links in README.md

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• Change link for papers reference in README.md

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• Move utility function from data folder to src folder

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• Update documentation

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• Remove Demo and Jupyter Notebook folders

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• Merge clean organization

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• Remove Docker file

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• Create Jupyter Notebook tutorial

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• Create Jupyter Notebook tutorial

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• Move output parameters to model folder instead of input data

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• Fix broken links in README.md

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• Improve docs index

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Commits on Apr 29, 2024

• Create arguments for GeneReg and OmicsData file paths

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• Fix tutorial

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• Add python-libsbml version number to installation guide

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• Add argument for simulation output directory

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• Add a todo

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Commits on May 1, 2024

• Update arguments help

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• Create IFNg model extension

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  43c3d42

• Remove SPARCED legacy model to avoid confusion

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Commits on May 2, 2024

• Add a bunch of useful general functions

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Commits on May 3, 2024

• Revert data files from IFNg to standard

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Commits on May 6, 2024

• Fix coefficients in StoicMat

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Commits on May 8, 2024

• Make input files model specific

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  56a054e

• Update .gitignore

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• Update .gitignore

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• Update .gitignore to let README of default results folder appear

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• Change population argument name to popsize

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• Replace population by popsize everywhere

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• Update data README

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Commits on May 9, 2024

• Update environment.yml

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• Restore original StoicMat file

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• Create SPARCED-legacy model

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• Remove data folder

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• Use Antimony compatible name for SPARCED standard

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• Update config file name

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• Remove SPARCED tutorial model

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• Create blank tutorial model folder

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• Remove unnecessary arguments

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• Update default perturbation name in config files

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Commits on May 10, 2024

• benchmarks directory added

  

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• benchmarks directory added

  

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• benchmarks directory added

  

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• Update arguments

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• Clarify yaml structure

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• Update version number

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  f37850b

• Clarifiy arguments for compilation

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• Add PyYAML to requirements

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• Update arguments

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• Add paths handling utility file

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• Update type hint of append_subfolder()

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• Fix typo in arguments

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• Create launcher file for model compilation

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• Update main script to use compilation launcher

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• Update append_subfolder() error handling

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• Update error handling in paths

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• Recompile SPARCED standard

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• Update create_model() to fit new arguments

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Commits on May 13, 2024

• Move functions into utils and restructure a bit

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• Fix typo

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  1763c77

• Update to integrate new functions

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  dbbb4fb

• Enhance arguments readability

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• Tidy compilation launcher

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• Update module name

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• Update variable name

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• Update simulation scripts

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• Re-write loading of initial conditions

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• Add function to ensure validity of popsize

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• Remove compound and dose

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• Implement perturbations

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• Update main script

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• Fix Path's import

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• Fix arguments mismatch

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  dcfbb85

• Fix typo

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• Fix another typo

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• Fix input files loading

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  22016d9

• Update SPARCED_standard sbml

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  ccf977a

• [BROKEN] Fix some issues in simulation launcher

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• Update documentation

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Commits on May 14, 2024

• Fix SPARCED_standard's config file

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• [FIXED] Working simulation pipeline

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• Update documentation

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Commits on May 15, 2024

• Benchmark code for model to model analysis is seemingly working -JRH

  

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  8a24ac9

• Built dynamic amici module finder to conform to user defined names

  

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  311f74a

• Fix bug in population check

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• Merge remote-tracking branch 'origin/master' into benchmarking

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• updated benchmark pipeline; uses config.yaml to locate simulation files.

  

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• updated benchmark pipeline; uses config.yaml to locate simulation files.

  

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• Revised robustness of code to potential breakpoints

  

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Commits on May 16, 2024

• created script to run all benchmarks given a provided model path

  

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Commits on May 17, 2024

• Downgrade swig version

  

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• Minor SBML changes

  

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Commits on May 20, 2024

• Add basic plotting script

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• Merge remote-tracking branch 'refs/remotes/origin/master'

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Commits on May 22, 2024

• Clean SPARCED_legacy

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• Add time for SPARCED_legacy control simulation

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  3f498da

• Clean SPARCED_standard

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  a051d17

• Add README to control simulation of SPARCED_legacy

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• Remove old IFNg model

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• Update & run SPARCED's interactive tutorial

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Commits on May 23, 2024

• Apply perturbations separately from loading initial conditions

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• Add possibility to simulate incubation

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• Add full incubation pipeline

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• Updated LINCS-RPPA-Abundance benchmark to include all experimental data for all observables currently within SPARCED

  

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• Merge incubation pipeline into main

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• Updated LINCS-RPPA-Abundance benchmark to include all experimental data for all observables currently within SPARCED

  

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• Merge remote-tracking branch 'origin/master' into benchmarking

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Commits on May 24, 2024

• updated dynamic module finder to noMPI benchmark evaluator.

  

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• Altered the direct reference for Species.txt in the RunSPARCED funtion, so that no local instance of the input file is needed

  

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• needed to add paths of f_genereg and f_omics to both _preequilibrate and heterogenize functions

  

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• LINCS-RPPA-Abundance/LINCS-RPPA-(a)bundance --> LINCS-RPPA-Abundance/LINCS-RPPA-(A)bundance

  

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• file correction

  

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Commits on May 30, 2024

• Modularized the benchmarking code to imporve operation and readability.

  

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• Removed unnecessary print statement

  

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Commits on May 31, 2024

• Tried adding in a progress bar, work in progress

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  1a61261

• Update model-benchmark-validation.py

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Commits on Jun 3, 2024

• fixed deadlock issues related to results passing

  

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Commits on Jun 5, 2024

• added 0-timepoint experimental data to benchmark

  

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Commits on Jun 6, 2024

• Updated RPPA benchmark

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Commits on Jun 24, 2024

• Updated Benchmark Analysis Notebook

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  9adeb2c

• updates to model validation script

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Commits on Jun 26, 2024

• Update utils.py

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Commits on Jun 28, 2024

• Code Cleaning Friday ;)

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Commits on Jul 1, 2024

• Update model-benchmark-validation.py

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Commits on Jul 5, 2024

• Code-cleaning Friday

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Commits on Jul 12, 2024

• Fixing cell cycle benchmark

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Commits on Jul 15, 2024

• Update utils.py

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• issues with transcription value assignment never fixed

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Commits on Jul 18, 2024

• added benchmark generator to the benchmark untils tool suite

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Commits on Jul 19, 2024

• Update sparced_simulation.py

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• fixed transcription setting changes in benchmark, solved cell cycle benchmark issue

  

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• fixed transcription setting changes in benchmark, solved cell cycle benchmark issue

  

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