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Open Source Science

https://github.com/biosimulations/biosimulations-runutils

Automation tools for running and comparing biosimulations from OMEX archives.

https://github.com/biosimulations/biosimulations-runutils

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Automation tools for running and comparing biosimulations from OMEX archives.

Basic Info
  • Host: GitHub
  • Owner: biosimulations
  • License: mit
  • Language: Python
  • Default Branch: dev
  • Size: 390 KB
Statistics
  • Stars: 0
  • Watchers: 7
  • Forks: 0
  • Open Issues: 3
  • Releases: 0
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Managed Biosim pipeline

Command Overview

  1. upload OMEX files
  2. refresh status
  3. download runs
  4. compare runs
  5. publish

Setup

create a .env file with the following. CLIENTID and CLIENTSECRET are only needed for publishing which is currently performed by site administrators.

```properties

for publication authentication

CLIENTID=<> CLIENTSECRET=<> AUTHHOST=auth.biosimulations.org AUTHAUDIENCE=api.biosimulations.org APIBASEURL=https://api.biosimulations.org|dev RUNAPPBASE_URL=https://run.biosimulations.org|dev

for pipeline

OMEXSOURCEDIR=<> OMEXOUTPUTDIR=<> ```

upload OMEX files

bash poetry run python main.py upload_omex --help

``` Usage: main.py upload_omex [OPTIONS]

upload and run OMEX files at BioSimulations

Options: --simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim] simulator to run [default: Simulator.vcell] --project-id TEXT filter by projectid --omex-src-dir PATH defaults env.OMEXSOURCEDIR --out-dir PATH defaults to env.OMEXOUTPUT_DIR --help Show this message and exit.

```

refresh status

bash poetry run python main.py refresh_status --help

``` Usage: main.py refresh_status [OPTIONS]

fetch status of runs and update biosimulations_runs.ndjson

Options: --out-dir PATH defaults to env.OMEXOUTPUTDIR --help Show this message and exit. ```

download runs

bash poetry run python main.py download_runs --help

``` Usage: main.py download_runs [OPTIONS]

download runs (results.zip) from BioSimulations

Options: --omex-src-dir PATH defaults env.OMEXSOURCEDIR --out-dir PATH defaults to env.OMEXOUTPUTDIR --project-id TEXT filter by project_id --simulator [tellurium|copasi|amici|vcell|pysces|libsbmlsim] filter by simulator --help Show this message and exit. ```

compare runs

bash poetry run python main.py compare_runs --help

``` Usage: main.py compare_runs [OPTIONS]

compare downloaded runs

Options: --omex-src-dir PATH defaults env.OMEXSOURCEDIR --out-dir PATH defaults to env.OMEXOUTPUTDIR --project-id TEXT filter by project_id --help Show this message and exit. ```

publish

bash poetry run python main.py publish --help

``` Usage: main.py publish [OPTIONS]

publish validated projects to BioSimulations

Options: --omex-src-dir PATH defaults env.OMEXSOURCEDIR --out-dir PATH defaults to env.OMEXOUTPUTDIR --project-id TEXT filter by project_id --help Show this message and exit. ```

Owner

  • Name: BioSimulations
  • Login: biosimulations
  • Kind: organization
  • Email: info@biosimulations.org
  • Location: United States of America

Enabling more comprehensive and more predictive biological models through enhanced reproducibility and reusability

GitHub Events

Total
  • Delete event: 5
  • Issue comment event: 1
  • Push event: 9
  • Pull request review comment event: 4
  • Pull request review event: 5
  • Pull request event: 7
  • Create event: 1
Last Year
  • Delete event: 5
  • Issue comment event: 1
  • Push event: 9
  • Pull request review comment event: 4
  • Pull request review event: 5
  • Pull request event: 7
  • Create event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 months
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.17
  • Merged pull requests: 4
  • Bot issues: 1
  • Bot pull requests: 4
Past Year
  • Issues: 1
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 months
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 1
  • Bot issues: 1
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (5)
  • luciansmith (2)
  • jcschaff (1)
  • renovate[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (5) enhancement (2) python (1)

Dependencies

poetry.lock pypi
  • annotated-types 0.6.0
  • certifi 2024.2.2
  • charset-normalizer 3.3.2
  • click 8.1.7
  • colorama 0.4.6
  • exceptiongroup 1.2.0
  • h5py 3.10.0
  • idna 3.6
  • iniconfig 2.0.0
  • mypy 1.8.0
  • mypy-extensions 1.0.0
  • numpy 1.26.4
  • packaging 23.2
  • pluggy 1.4.0
  • pydantic 2.6.3
  • pydantic-core 2.16.3
  • pytest 7.4.4
  • python-dotenv 1.0.1
  • requests 2.31.0
  • tomli 2.0.1
  • typer 0.9.0
  • types-requests 2.31.0.20240218
  • typing-extensions 4.10.0
  • urllib3 2.2.1
pyproject.toml pypi
  • mypy ^1.4.1 develop
  • pytest ^7.4.0 develop
  • types-requests ^2.31.0.10 develop
  • h5py ^3.10.0
  • pydantic ^2.5.2
  • python ^3.9
  • python-dotenv ^1.0.0
  • requests ^2.31.0
  • typer ^0.9.0