Selected Topics in Zoology (Section 15716):
Bioinformatics2Go
Bioinformatics2Go
BIOL L506 (Z620) Fall 2015
Course description
BIOL L506 (Z620) Bioinformatics2Go
Lecture times and locations
Tues, Thur 1:00p-2:15p, Ballentine Hall (BH) 118 (Tu), 107 (Th)
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Tues | Sept 29 | 1.1 | Orientation Introduction to WikiBCB NCBI resources | Volker Brendel |
| Thur | Oct 1 | 1.2 | Molecular Phylogeny A list of Web-servers for molecular phylogeny analyses Mobyle @ Pasteur BMPS Tutorial | Volker Brendel |
| Tues | Oct 6 | 2.1 | Genetic variation NCBI dbSNP How To NCBI dbVar How To 1000 Genomes Project Nature 491:56 Example: rs1131769 Recent paper of interest | Volker Brendel |
| Thur | Oct 8 | 2.2 | Protein structure RCSB PDB PDB-101 - a number of wonderful tutorials! SWISS-MODEL - what to do if my protein is not in PDB!? (start here) | Volker Brendel |
| Tues | Oct 13 | 3.1 | Gene structure prediction GENSCAN GeneMark Augustus GeneSeqer (spliced alignment) | Volker Brendel |
| Thur | Oct 15 | 3.2 | Genome browsers and community genome annotation yrGATE (annotation tool) Polistes dominula xGDB instance Gbrowse FlyBase (Gbrowse instance) | Volker Brendel |
| Tues | Oct 20 | 4.1 | Gene structure annotation: Evidence-based annotation GAEVAL | Volker Brendel |
| Thur | Oct 22 | 1:00pm | Final Projects - task and scope The final project should be a new page in your WikiBCB name space called "final_project". The page should be a document of your learning in the class, linking the various modules in a logical fashion. The document would include an introduction that gives the relevant biological background and states a biological question you have been exploring (e.g., something about a particular gene or set of genes). You would then describe how you gathered data concerning the problem area from public databases, followed by documentation of how you used the different tools we looked at in class. Try to emphasize the logical flow going from gene to gene product; from gene to genome context; from one species to multiple species; etc. The overall goal of the final project is for you to provide a comprehensive record of your class experience in such a way that it will be a meaningful resource to you in the future. Unless you request otherwise, your WikiBCB write-ups will be made read-accessible to the world for the benefit of your fellow students, current and future, in the spirit of Wiki. | Instructor |
| Thur | Oct 22 | 4.2 | Comparative Genomics CoGE CoGE Workshop links CoGE Article | Volker Brendel |
| Tues | Oct 27 | 5.1 | Gene expression analyses NCBI GEO Example: GSE29252 Motif finding in DNA and protein sequences XXmotif MOTIF | Volker Brendel |
| Thur | Oct 29 | 5.2 | Workflow design and execution tools: BioExtract Server Galaxy Taverna | Volker Brendel |
| Tues | Nov 3 | 11:59pm | Final Projects due | students |