BIOL L506 (Z620) Fall 2015

Selected Topics in Zoology (Section 15716):
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

HTML version of this schedule

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

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

Selected Topics in Zoology (Section 15716): Bioinformatics2Go