BIOL Z620 Fall 2012

Selected Topics in Zoology (Section 34311):
Bioinformatics2Go

BIOL Z620 Fall 2012

Course description

BIOL Z620 Bioinformatics2Go

Lecture times and locations

Tues, Thur 10:00a-11:30a, Ballantine Hall (BH) 108

Tentative schedule

HTML version of this schedule

DAY DATE LECTURE TOPIC LECTURER

Tues Oct 30 1.1 Orientation
Introduction to WikiBCB
NCBI resources Volker Brendel

Thur Nov 1 1.2 Molecular Phylogeny
A list of Web-servers for molecular phylogeny analyses
Mobyle @ Pasteur Volker Brendel

Tues Nov 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 Nov 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 Nov 13 3.1 Gene structure prediction
GENSCAN
GeneMark
Augustus
GeneSeqer (spliced alignment) Volker Brendel

Thur Nov 15 3.2 Genome browsers and community genome annotation
yrGATE (annotation tool)
Gbrowse
FlyBase (Gbrowse instance) Volker Brendel

Tues Nov 20 THANKSGIVING BREAK n/a

Thur Nov 22 THANKSGIVING BREAK n/a

Tues Nov 27 4.1 Comparative Genomics
CoGE
CoGE Workshop links
CoGE Article Volker Brendel

Thur Nov 29 1:00pm Final Projects assigned
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 Nov 29 4.2 IU Connect URL for a guest presentation by
Dr. Eric Lyons of the University of Arizona Volker Brendel

Tues Dec 4 5.1 Gene expression analyses
NCBI GEO
NCBI Genotype-Tissue Expression
Motif finding in DNA and protein sequences
XXmotif
MOTIF Volker Brendel

Thur Dec 6 5.2 Workflow design and execution tools:
BioExtract Server
Galaxy
Taverna Volker Brendel

Tues Dec 10 11:59pm Final Projects due students

DAY	DATE	LECTURE	TOPIC	LECTURER
Tues	Oct 30	1.1	Orientation Introduction to WikiBCB NCBI resources	Volker Brendel
Thur	Nov 1	1.2	Molecular Phylogeny A list of Web-servers for molecular phylogeny analyses Mobyle @ Pasteur	Volker Brendel
Tues	Nov 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	Nov 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	Nov 13	3.1	Gene structure prediction GENSCAN GeneMark Augustus GeneSeqer (spliced alignment)	Volker Brendel
Thur	Nov 15	3.2	Genome browsers and community genome annotation yrGATE (annotation tool) Gbrowse FlyBase (Gbrowse instance)	Volker Brendel
Tues	Nov 20		THANKSGIVING BREAK	n/a
Thur	Nov 22		THANKSGIVING BREAK	n/a
Tues	Nov 27	4.1	Comparative Genomics CoGE CoGE Workshop links CoGE Article	Volker Brendel
Thur	Nov 29	1:00pm	Final Projects assigned 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	Nov 29	4.2	IU Connect URL for a guest presentation by Dr. Eric Lyons of the University of Arizona	Volker Brendel
Tues	Dec 4	5.1	Gene expression analyses NCBI GEO NCBI Genotype-Tissue Expression Motif finding in DNA and protein sequences XXmotif MOTIF	Volker Brendel
Thur	Dec 6	5.2	Workflow design and execution tools: BioExtract Server Galaxy Taverna	Volker Brendel
Tues	Dec 10	11:59pm	Final Projects due	students

Selected Topics in Zoology (Section 34311): Bioinformatics2Go