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BIOL Z620 Fall 2013

Selected Topics in Zoology (Section 34311):
Bioinformatics2Go

BIOL Z620 Fall 2013


Course description

BIOL Z620 Bioinformatics2Go

Lecture times and locations

Tues, Thur 1:00p-2:15p, Student Building (SB) 221

Tentative schedule (class notes can be viewed with Adobe Acrobat Reader)

btn_printerFriendly.gif version of this schedule

DAYDATELECTURETOPICLECTURER
Tues Oct 1 1.1 Orientation
Introduction to WikiBCB
NCBI resources
Volker Brendel
Thur Oct 3 1.2 Molecular Phylogeny
A list of Web-servers for molecular phylogeny analyses
Mobyle @ Pasteur
Volker Brendel
Tues Oct 8 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 10 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 15 3.1 Gene structure prediction
GENSCAN
GeneMark
Augustus
GeneSeqer (spliced alignment)
Volker Brendel
Thur Oct 17 3.2 Genome browsers and community genome annotation
yrGATE (annotation tool)
Polistes dominula xGDB instance

Gbrowse
FlyBase (Gbrowse instance)
Volker Brendel
Tues Oct 22 4.1 Gene structure annotation, continued Volker Brendel
Thur Oct 24 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 24 4.2 Comparative Genomics
CoGE
CoGE Workshop links
CoGE Article
Volker Brendel
Tues Oct 29 5.1 Gene expression analyses
NCBI GEO
NCBI Genotype-Tissue Expression
Motif finding in DNA and protein sequences
XXmotif
MOTIF
Volker Brendel
Thur Oct 31 5.2 Workflow design and execution tools:
BioExtract Server
Galaxy
Taverna
Volker Brendel
Tues Nov 5 11:59pm Final Projects due students