Moore Notes 3 12 14
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Group Call
- Participants: Katie, Jonathan, Tom, Stacia, Stephen, Dongying, Guillaume, Josh, Sarah
- Guillaume did not find any new datasets in CAMERA or MG-RAST
- Tom: Data Driven Discovery early career investigator application (slides)
- Protein function annotation
- High-throughput experimental assays for proteins (enzymes) and organisms (Biolog colorametric assay)
- Sequence/phylogenetic inference
- Evolutionary (selection) annotation
- Ecological annotation (correlation with other proteins and with ecological properties)
- Graph databases enable network analyses (e.g., social network analysis)
- Protein graph with nodes (tables) and edges (annotated pointers)
- Extend Bio4j GraphDB (e.g., with SFams sequence similarity results)
- Phylogeny of genomes using GEBA markers
- Network neighborhood based inferences
- Functional annotation, potentially in collaboration with Ladan
- Horizontal gene transfer identification and quantification
- Lineage specific selection and gain/loss
- Computational issues
- Many graph algorithms implemented
- Most compute is up front with results (summary statistics) stored in db
- Relationship to regression problems, other types of regression models
- Protein function annotation
- Some related work worth looking at
