This is a tentative schedule at this point. Please check
back as it develops. Watch for announcements on the class
home page and in class for any significant changes. Since
this is an early voyage of this course and since it is
dependent on many different sources of input, including
yours, tolerance and patience is requested as we progress on
the cruise. Lecture/discussion: TTH 5:25-6:15 p.m.Dar 229 Name:
[*:
initials] e-mail: Dr. Barbara Chapman [BC] Dr. James Christmann [JC] Ms. Kim Cook [KC] Dr. Dan Crocker [DC] Dr. Derek Girman [DG] Dr. Bala Ravikumar [BR] Dr. Judy Sakanari [JS] Dr. Eileen Thatcher [ET] Dr. Richard Whitkus [RW] This schedule is under
construction and subject to change, but it should
give you a good idea of what to expect. Last updated
9/2/03. Date:
Topic:
Th 8/28 ET Introduction; Class mechanics Tu 9/2 ET What is bioinformatics?; Search strategies &
Boolean logic Th 9/4 ET Introduction to databases; Project
introduction: Literature analysis problem Tu 9/9 BR Database structure & design- useful
sites Th 9/11 KC ET BLAST; Project results: Literature
analysis problem Tu 9/16 ET Project introduction: Molecular database
problem Th 9/18 ET Analysis of search results; Refining
searches Tu 9/23 JS Project results: Molecular database
problem Th 9/25 BC Analysis of raw sequence data Tu 9/30 BC Gene finding & annotation Th 10/2 RW Project introduction: Genomic mapping
problem Tu 10/7 RW Project results: Genomic mapping
problem Th 10/9 ET Mapping disease genes; Linkage analysis;
Polymorphisms; Expression analysis &
microarrays Tu 10/14 JC Project introduction: Microarray
problem Th 10/16 KC Ethical issues in bioinformatics Tu 10/21 ET Project results: Microarray problem Th 10/23 Midsemester problem set Tu 10/28 ET Reconstructing history; Modes of evolution Th 10/30 DG Project introduction: Phylogenetic
reconstruction Tu 11/4 ET Statistical/probabilistic models Th 11/6 DG Project results: Phylogenetic
reconstruction Tu 11/11 ET Patterns in proteins; Motifs & profile
analysis; 3D structure determination Th 11/13 BC Project introduction: Protein structure
problem Tu 11/18 BC Model building techniques Th 11/20 BC Project results: Protein structure
problem Tu 11/25 ET Metabolic pathways & signaling networks Th 11/27 NO CLASS-
Happy
Thanksgiving!!! Tu 12/1 TBA Project introduction: Data mining
problem Th 12/4 ET Proteomics; Protein-protein interactions Tu 12/9 TBA Project results: Data mining problem Th 12/11 DCTBA Future bioinformatics- On the next wave Tu 12/16 Problem/project proposals due:
5:00 p.m. Selection of a suitable book will be discussed at the
first class meeting. Baxevanis & Ouellette, Bioinformatics: A
Practical Guide to the Analysis of Genes and Proteins
(2nd ed.), 2001, John Wiley & Sons, Inc. Mount, Bioinformatics: Sequence and Genome
Analysis, 2001, Cold Spring Harbor Laboratory
Press. Westhead, Parish & Twyman, Instant Notes:
Bioinformatics, 2002, BIOS Scientific Publishers
Ltd. Campbell & Heyer, Discovering Genomics,
Proteomics & Bioinformatics, 2003, Benjamin
Cummings. Claverie & Notredame, Bioinformatics for
Dummies, 2003, For Dummies. Date:
Topic:
Th 8/28 Introduction to problem based learning Tu 9/2 Review
tutorials; Internet as a research environment;
Search engines; Documentation requirements in
bioinformatics; Introduction to databases Th 9/4 Project: Literature analysis problem Tu 9/9 Molecular sequence databases; NCBI, NBIF, &
Biology Workbench interfaces; Key word, taxonomic,
and BLAST searches Th 9/11 Further exploration Tu 9/16 Project: Molecular database problem Th 9/18 Analysis of search results; Refining
searches Tu 9/23 Further exploration Th 9/25 Analysis of raw sequence data Tu 9/30 Gene finding & annotation Th 10/2 Submission of molecular sequences;
Project: Genomic mapping Tu 10/7 Further exploration Th 10/9 Plasmid mapping; Primer design Tu 10/14 Polymorphisms; Analysis of microarrays;
Project: Microarray problem Th 10/16 Further exploration Tu 10/21 Further exploration Th 10/23 Midsemester problem set Tu 10/28 Multiple sequence alignment; Analyzing drift vs.
selection; Th 10/30 Tree building by parsimony & maximum
likelihood; Tu 11/4 Further exploration Th 11/6 Further exploration Tu 11/11 SwissProt & PDB databases; Motifs
& profile analysis Th 11/13 Modeler; 3D structure viewers;
Project: Protein structure problem Tu 11/18 Secondary structure analysis Th 11/20 Further exploration Tu 11/25 Metabolic databases; data mining methods;
self-organizing maps Th 11/27 NO CLASS-
Happy
Thanksgiving!!! Tu 12/2 Project: Data mining problem Th 12/4 Comparative genomics & metabolic
pathways Tu 12/9 Further exploration Th 12/11 Fun & games 12/16 Problem/project proposal due: 5:00
p.m.
Lecture/discussion
schedule
Please note:
Computer laboratory: TTH 6:25-9:15 p.m. Dar 229
Faculty and guest presenters:
Fall, 2003 Lecture/discussion
Schedule:
Advances in computational biology
Text: [back]
Gibas & Jambeck, Developing
Bioinformatics Computer Skills, 2001, O'Reilly.
Fall, 2003 Laboratory
Schedule
.
Mid-semester problem set
due
Project: Phylogenetic reconstruction
Updated 9/2/03 by thatcher@sonoma.edu