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BioSimulations

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

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More comprehensive and more predictive models have the potential to advance biology, bioengineering, and medicine. Building more predictive models will likely require the collaborative efforts of many investigators. This requires teams to be able to share and reuse model components and modeling tools. Despite extensive efforts to develop standards such as the COMBINE/OMEX archive format, the Kinetic Simulation Algorithm Ontology (KiSAO), the Systems Biology Markup Language (SBML), and the Simulation Experiment Description Markup Language (SED-ML) and repositories such as BioModels and the Physiome Model Repository, it is still often difficult to share, reuse, and combine models and modeling tools. One challenge to sharing and reusing models is the disparate formats, model repositories, and simulation tools for different types of models. The proliferation of numerous similar formats, repositories, and tools makes it difficult, especially for non-experts, to find models and to find an appropriate simulation tool for each model. In addition, the existing model repositories have limited capabilities for sharing associated resources such as training data, simulation experiments, and visualizations. BioSimulations addressses these challenges by making it easier for researchers to share and reuse modeling projects.

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  1. biosimulations biosimulations Public

    A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

    TypeScript 39 14

  2. status status Public

    📈 Uptime monitor and status page for BioSimulations, powered by @upptime

    Markdown 1

  3. deployment deployment Public

    Kubernetes Configuration for BioSimulations

    Shell 3 1

Repositories

Showing 10 of 20 repositories
  • .github Public

    GitHub profile for the BioSimulations organization

    biosimulations/.github’s past year of commit activity
    0 MIT 0 0 1 Updated Dec 1, 2024
  • biosim-client Public

    library for accessing biosimulations APIs.

    biosimulations/biosim-client’s past year of commit activity
    Jupyter Notebook 0 MIT 0 1 6 Updated Dec 1, 2024
  • biosimulations Public

    A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

    biosimulations/biosimulations’s past year of commit activity
    TypeScript 39 MIT 14 111 (3 issues need help) 13 Updated Dec 1, 2024
  • status Public

    📈 Uptime monitor and status page for BioSimulations, powered by @upptime

    biosimulations/status’s past year of commit activity
    Markdown 0 MIT 1 1 0 Updated Dec 1, 2024
  • deployment Public

    Kubernetes Configuration for BioSimulations

    biosimulations/deployment’s past year of commit activity
    Shell 3 MIT 1 6 5 Updated Nov 25, 2024
  • biosimulations-modeldb Public

    Command-line program and scheduled GitHub action for publishing the ModelDB model repository to BioSimulations

    biosimulations/biosimulations-modeldb’s past year of commit activity
    MATLAB 0 MIT 0 2 4 Updated Nov 15, 2024
  • biosimulations-bigg Public

    Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

    biosimulations/biosimulations-bigg’s past year of commit activity
    Python 1 MIT 0 3 4 Updated Nov 15, 2024
  • biosimulations-runutils Public

    Automation tools for running and comparing biosimulations from OMEX archives.

    biosimulations/biosimulations-runutils’s past year of commit activity
    Python 0 MIT 0 0 7 Updated Sep 24, 2024
  • biosimulations/eslint-plugin-exclude-strings’s past year of commit activity
    TypeScript 0 0 0 8 Updated Dec 15, 2023
  • static Public

    Repository for holding static files hosted at https://static.biosimulations.org

    biosimulations/static’s past year of commit activity
    CSS 0 Apache-2.0 0 0 1 Updated Dec 15, 2023

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