BioModels projects – Fall 2016

Potential models for MCB 315

Kollarovic 2016
To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage (2016) Aging
BioModels pagepaper

Bulik 2016
The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism -€“ insights from mathematical modeling (2016) BMC Biology
BioModels pagepaper

Rantasalo 2016
Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae (2016) PLoS ONE
BioModels pagepaper

Leber 2016
Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection (2016) Journal of Theoretical Biology
BioModels pagepaper

Mukhopadhyay 2013
Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity (2013) PLoS Computational Biology
BioModels page; paper

Validation using Copasi

For help, see the User Manual. Our example mode is BIOMD0000000009.

Annotation spreadsheets

To enable collaborative annotation, I have extracted the models to Google Spreadsheets. Access the spreadsheet for your model here:

Annotation databases


For Models: is, isDerivedFrom, isDescribedBy, isInstanceOf, hasInstance.
For Biological Entities: encodes, hasPart, hasProperty, hasVersion, is, isDescribedBy, isEncodedBy, isHomologTo, isPartOf, isVersionOf, occursIn, hasTaxon.
For details, see here.


The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

Small molecules

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

KEGG Compound
KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.

Genes and transcripts

Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.


Gene Ontology

KEGG Reaction
KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.

The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.


Gene Ontology


PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.


UniProt Taxonomy
Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree.


BRENDA Tissue Ontology
BTO provides terms, classifications, and definitions of tissues, organs, anatomical structures, plant parts, cell cultures, cell types, and cell lines of organisms from all taxonomic groups (animals, plants, fungis, protozoon) as enzyme sources. The information is connected to the functional data in the BRENDA enzyme information system.

Biological processes

Gene Ontology
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

Completed in MCB 572

Nair 2015
Sensing Positive versus Negative Reward Signals through Adenylyl Cyclase-Coupled GPCRs in Direct and Indirect Pathway Striatal Medium Spiny Neurons (2015) Journal of Neuroscience
BioModels page (1,2); paper

De Caluwe 2016
A Compact Model for the Complex Plant Circadian Clock (2016) Frontiers in Plant Science
BioModels page; paper

Spreadsheets at