bioinformatics
Bioinformatics and Computational Biology Topics, DBs, Challenges, etc.
Links
- Open Bioinformatics Foundation GSoC
- Graph theory: chemlambda
The Cycle
- data -> interpreation via "tool"
- tool -> interpret
- self -> tool
- go back to 1.
Criteria
- submitting code/plots to github before the presentation
- code inputs and outputs
- explanation related to interpretation of results
- references
- innovation
Workshops
- R (Bioconductor)
- Python
- bionode/R - Tutorial
Databases
- ENSEMBL
- NCBI
- UniProt, Pfam
- RNACentral, rfam
- SGD, other species specific DBs
- ontology DBs, FANTOM, GO
- microarray DBs
- RNASeq
- SWISS Model
- STRING, IntAct, MARA
Undeveloped Ideas
- "data modeling", SQL relations
- "FBA"
- "structure analysis" (+ ramachandran plots)
- "PPI"
Web Tools
- EMBOSS explorer
Challenges
[5] finding secondary structure of RNA
CSC373 6.5
[1~3] multiple sequence alignment
- (cancer) cell lines
- similar proteins across species
- domain, family
[3] expression analysis with GEO2R
Link to BCH441 assignment
[4] mass spec -> protein
Frequency -> amino acid
[3] Phylogenetic Tree
A -> B Tools
Simple, one step tools, that can be used together in an analysis pipeline.
- BLAST
- PSI-BLAST (iterative though)
- bowtie
- tophat2
- ~
Visualization Tools
- phylip
- d3
- plotly
- cytoscape.js
- R's
plot()