bioinformatics

Bioinformatics and Computational Biology Topics, DBs, Challenges, etc.

Links

• Open Bioinformatics Foundation GSoC
• Graph theory: chemlambda

The Cycle

1. data -> interpreation via "tool"
2. tool -> interpret
3. self -> tool
4. 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

Tutorial here

• (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()