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CSCI B490 Fall 2015

Seminar in Computer Science (Section 31119):
Fundamental Models and Algorithms in Bioinformatics

CSCI B490 Fall 2015


Course description

CSCI B490 FMAB

Lecture times and locations

Mon, Wed 1:00p-2:15p, Lindley Hall (LH) 008

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

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DAYDATELECTURETOPICLECTURER
Mon Aug 24 0.1 Orientation
Introduction: Topics in bioinformatics, scope of class, and resources

National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics

Current Topics in Genome Analysis 2012, a National Human Genome Research Institute lecture series:

The Genomic Landscape (Lecturer: Dr. Andy Green)
Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis)
Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis)
Volker Brendel
Wed Aug 26 0.2 Mapping biological question onto computational problems

Resources:
Wikipedia - DNA
Howard Hughes Medical Institute BioInteractive
Sample BioInteractive Video
Where to find sequences:
NCBI Nucleotide
RCSB Protein Data Bank
Volker Brendel
Mon Aug 31 1.1 Topic I: Parsing genome feature annotation records for simple bioinformatics tasks

Class notes

Generic Feature Format (GFF3)
Biopython
Daniel Standage
Wed Sept 2 1.2 Computer Lab (assignment details) Daniel Standage
Mon Sept 7 No class (Labor Day)
Wed Sept 9 1.3 Quiz I
Mon Sept 14 2.1 Topic II: Simple sequence models
Lecture
Volker Brendel
Wed Sept 16 2.2 Computer Lab
Mon Sept 21 2.3 Evaluation Volker Brendel
Wed Sept 23 2.4 Quiz II
Mon Sept 28 3.1 Topic III: Advanced sequence models
Lecture
Volker Brendel
Wed Sept 30 3.2 Computer Lab
Mon Oct 5 3.3 Evaluation Volker Brendel
Wed Oct 7 3.4 Quiz III
Mon Oct 12 4.1 Topic IV: Pairwise sequence alignment
Lecture
Volker Brendel
Wed Oct 14 4.2 Computer Lab
Mon Oct 19 4.3 Evaluation Volker Brendel
Wed Oct 21 4.4 Quiz IV
Mon Oct 26 5.1 Topic V: Hidden Markov Models
Lecture
Volker Brendel
Wed Oct 28 5.2 Computer Lab
Mon Nov 2 5.3 Evaluation Volker Brendel
Wed Nov 4 5.4 Quiz V
Mon Nov 9 6.1 Topic VI: Sequence analysis with scores
Lecture
Volker Brendel
Wed Nov 11 6.2 Computer Lab
Mon Nov 16 6.3 Evaluation Volker Brendel
Wed Nov 18 6.4 Quiz VI
Mon Nov 23 THANKSGIVING BREAK n/a
Wed Nov 25 THANKSGIVING BREAK n/a
Mon Nov 30 7.1 Applications I Volker Brendel
Wed Dec 2 7.2 Applications II
NCBI BLAST
The Statistics of Similarity Scores
Guide 1
Guide 2
Align
Webinar 1
Webinar 2
Mon Dec 7 8.1 Review Volker Brendel
Wed Dec 9 8.2 Review Volker Brendel
Fri Dec 18 12:30pm - 2:30pm Final Exam Students