GuidesBrowse Models

Browse Models

Learn how to effectively search and discover biological models in the bsim catalog.

Time estimate: 10 minutes

Goal

By the end of this tutorial, you’ll be able to:

  • Search for models by name and keyword
  • Filter models by organism, type, and source
  • Understand model metadata and annotations
  • Save models to your favorites

The Model Browser

Navigate to Models in the top navigation to access the model browser.

Search Bar

The search bar supports:

  • Model names: “Lotka-Volterra”, “Glycolysis”
  • Keywords: “cancer”, “metabolism”, “signaling”
  • BioModels IDs: “BIOMD0000000012”
  • Authors: “Tyson”, “Goldbeter”

Use quotes for exact phrase matching: "cell cycle" vs cell cycle

Filtering Models

By Organism

Filter to specific species:

  • Human (Homo sapiens)
  • Mouse (Mus musculus)
  • Yeast (Saccharomyces cerevisiae)
  • E. coli (Escherichia coli)
  • And many more…

By Model Standard

  • SBML: Systems Biology Markup Language - biochemical pathway models
  • NeuroML: Neural models for computational neuroscience
  • CellML: Physiological models for cell biology
  • NMODL: NEURON MOD files for neural simulation
  • ONNX: Machine learning models for hybrid simulations

By Source

  • BioModels: Curated biochemical models from EMBL-EBI (SBML)
  • ModelDB: Computational neuroscience models from Yale (NMODL, NeuroML)
  • NeuroML-DB: Neural models in NeuroML format
  • CellML Repository: Physiological models in CellML format
  • User: User-uploaded models (any supported standard)

Model Details

Click on any model to see:

Overview Tab

  • Description: What the model represents
  • Authors: Who created the model
  • Publication: Associated papers with DOI links
  • License: Usage terms

Components Tab

  • Species: Variables in the model (e.g., protein concentrations)
  • Parameters: Configurable constants
  • Reactions: Biochemical transformations
  • Compartments: Physical locations

Annotations Tab

  • GO terms: Gene Ontology annotations
  • KEGG pathways: Metabolic pathway links
  • UniProt: Protein references
  • ChEBI: Chemical entities

Saving Favorites

  1. Click the star icon on any model card
  2. Access your favorites from the Dashboard
  3. Organize favorites into collections (coming soon)

Advanced Search

Boolean Operators

cancer AND metabolism
cell cycle OR mitosis
apoptosis NOT cancer

Field-Specific Search

organism:human
type:sbml
author:Tyson

Combining Filters

organism:human type:sbml "cell cycle"

Best Practices

  1. Start broad, then narrow: Begin with general terms, add filters as needed
  2. Check annotations: Model quality varies; curated models are more reliable
  3. Read publications: Understanding the biology helps interpret results
  4. Compare models: Multiple models may represent the same system differently

Next Steps

OverviewRun a Simulation