Systems Biology

Network Reconstruction

Genetic Content:

Data – Unique ORF(open reading frame) identifiers, Gene product function or name, Gene symbol, Enzyme commision number, and Cellular location of gene product.

Databases and Algorithms- Entrex Gene, BioCyc, RegulonDB, GOLD, KEGG, Microbes online, SEED, UniProtKB, IMG

Active Enzymes:

Data – Subunit composition, Protein complex composition, and Enzyme symbols.

Databases and Algorithms – BRENDA, KEGG, MetaCyc, Primary Literature, TransportDB

Network Reactions:

Data – Metabolite stoichiometry, Co-factor specificity, Substrate specificity, Directionality or reversibility, and Cellular location.

Databases and Algorithms – KEGG, BRENDA, MetaCyc, Published Literature, PSORTdb, PubChem, Entrez Gene, UniPortKB, TransportDB

Automated Reconstruction Tools:

Databases and Algorithms – Model SEED, MetaCyc pathway tools, Grow match, RAVEN

Prepping for Modeling Co-opetitions

Math Modeling

Submodels – GIMMIE, iMat, MBA, INIT

Biochemical Genetic and Genomic (BiGG) Database

CoBRA Toolbox

CoBRA Methods Catalog

Sparse Identification of Nonlinear Dynamics

RECON Map

Machine Learning

Graph Attention Networks

Gap-Filling and Validation

Databases and Algorithms – SMILEY, SEED, ADOMETA, GapFill, Grow match, OMNI, Pathologic

Structural System Biology

Databases and Algorithms – AlphaFold2, AutoDock Suite, LZerd Protein Docking Suite