*** New-- Live ---See it & Hear it Now!! ***
Statistical Physics and Biological Information
Institute for Theoretical Physics, Santa Barbara
dates: January 16 - June 15, 2001
This program aims to bring physicists together with biologists and computational biologists, to provide a
medium such that physicists can learn from biologists of the outstanding issues of importance to biology, and
explore together with biologists and computational biologists to better detect, understand, and manipulate
biological information. Main topics of the program can be divided into the following 3 focus groups:
Bioinformatics: sequence comparison; gene finding; protein structure prediction; DNA and protein motif detection; gene expression profile clustering; and phylogenetic tree reconstruction.
Molecular interaction and networks: RNA and protein structure and function; DNA/RNA-protein, protein-protein, protein-ligand interaction; recombination, mutation, and repair; protein, genetic, and immune networks.
Evolution: chemical evolution; RNA and protein breeding; viral and bacteria evolution; and co-evolution of interacting species.
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Additional Courses and some are only partially accessable
1) http://www.bioinf.man.ac.uk/dbbrowser/bioactivity/
Preface : Welcome to our Bioinformatics Web practical.
This is an interactive exercise that aims to provide a taste of
bioinformatics resources around the world. We hope to give a flavour of sequence
analysis, by introducing a range of widely-used analysis tools and databases. In
this tutorial, brief instructions are given in the headers; their highlighted
phrases control the contents of the left- and right- hand frames. Frame contents
may be refreshed at any time using the left-hand menu
.
Commentaries in the right-hand frames provide more detailed information than the
header instructions - please read these
carefully. For further info, the
info icons offer a route to supporting text & diagrams that form an adjunct
to Introduction to bioinformatics
published by Addison
Wesley Longman.
2) http://cmgm.stanford.edu/biochem218/
Computational
Molecular Biology This year, Computational Molecular Biology will be offered as an Internet only course. All lectures are prerecorded and available via streaming video on the Internet. This course is designed for molecular biologists and computer scientists desiring a practical, hands on approach to the field of computational molecular biology. The course is recommended for those wanting to understand the major issues concerning representation and analysis of biological sequences and structure. Topics covered include: accessing molecular databases, pattern search, classification of sequence and structure, alignment of sequences, rapid similarity searching, phylogenies, automated pattern learning, representing protein structure, modeling protein structure by homology, protein-protein docking and protein-ligand docking. Existing methods will be described critically and the strengths and limitations of each will be discussed. Future directions for development of new methods will also be discussed. There will be 6 homework assignments utilizing the tools described in the lectures. Each student will also be required to submit a final project either utilizing the methods presented, critically evaluating an existing method, proposing or implementing a novel approach.
Introductory molecular biology at the level of Biology 42, or advanced molecular biology at the level of Biochemistry 201 or consent of instructor.
There will be 7 homework assignments utilizing the tools described in the lectures. While no computer programming experience is required, prior exposure to personal computers, e-mail, and the Internet is essential. All homework and final projects will be submitted in electronic form, generally as e-mail or e-mail attachments but submissions as Web pages are also encouraged. At the end of the course a project will be required which utilizes or analyzes the methods presented in the course. The project could also involve a novel application of existing tools or the development of some new or improved method. ****Examples of Final Projects Submitted Last Year ****
Not everything is open but some of the homework assignments are and give a flavor of the course, z.b. http://cmgm.stanford.edu/biochem218/02Homework.html and http://cmgm.stanford.edu/biochem218/03Homework.html http://cmgm.stanford.edu/biochem218/04Homework.html http://cmgm.stanford.edu/biochem218/05Homework.html
2a) Biol - 4490 Bioinformatics (version 2.0) http://cmgm.stanford.edu/classes/csuh/ B i o i n f o r m a t i c s: Beginning Fall 2000 the Biology certificate program at CSU Hayward will also include a course in bioinformatics. A working knowledge of Unix will be required for participation in the course. Training will be provided for those lacking Unix experience
Virtual School of Natural Sciences BioComputing Division (VSNS-BCD) is offering educational services over the Internet, in the area of Biocomputing / Computational Biology / Bioinformatics. It was organized to develop and conduct the VSNS-BCD Biocomputing Courses in 1995 and 1996. Gradually, the coordinators, course alumni/ae and contributors started related projects, and even participated in several competitions. Via computer networks, we are able to offer our material free of charge to a worldwide audience. The VSNS BioComputing Division is an interdisciplinary effort coordinated by Robert Giegerich and Georg Fuellen, now involving more than 50 researchers and consultants from academia and industry. It serves as a test-bed for virtual collaboration among scientists, using a minimum of technical and financial resources to achieve maximum service to the scientific community.
This lecture consists of six chapters. In each chapter one problem is treated. Here is an overview over the problems and the academic goals, addressed.
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Problem |
Academic goals |
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position of an aircraft |
nonlinear least squares, errors, sensitivity analysis, minimization |
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secondary structure prediction |
modelling, LS, SVD, best basis, NN, LP |
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molecular dynamics |
modelling, big sci. comp., But progr. generation, minimization |
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stock market prediction |
modelling, dynamic programming, discrete function minimization |
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phylogenetic tree construction |
dynamic programming, discrete optimization, genetic algorithms |
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puzzles |
combinatorial search, computing/estimating cardinality |
Raum RZ F21. Mo 16.15 - 17.00 Uhr
(Practical Exercises)
Lars
Ellgaard
- CHN L 33.1, Tel. 01 632 3027
Institut fuer Biochemie
(Lectures)
Prof. Gaston H. Gonnet
- IFW D 28.1, Tel. 01 632 74 70
Michael T. Hallett
- IFW D 29.1, Tel. 01 632 74 75
Computational Biochemistry Research Group, E.T.H. Zürich
The course will be 13 weeks long with 1 hours of lecture per week. The course takes place in a computer lab in order to facilitate a "hands-on" approach.
Abstract: The intention of this course is to provide biochemists with a practical guide to bioinformatics. This will be achieved by examining various software tools currently available to the community. Our focus will lie both on how one uses these tools and on the underlying algorithms. Covered topics include sequence alignment, phylogenetic trees, multiple sequence alignments, secondary structure prediction (de Novo and threading techniques), and the identification of proteins by mass.
Prequisities: We will not assume that students have any background in
computer science. Some familiarity with PCs and software such as Netscape
would be helpful. Computing
Resources: PC machines running NT, Netscape, Darwin, BLAST, and several
other packages.
Core topics covered in the course:
1. Introduction to existing datasets and tools.
2. Sequence alignment.
3. Phylogenetic trees.
4. Multiple sequence alignments.
5. Predictions of secondary structure.
6. Proteomics.
Discussion: IFW E42 Thursday
14:00-15:00
Lecture: IFW E42 Thursday 15:00-17:00
Professor Gaston Gonnet
Dr. Gina Cannarozzi
Computational Biochemistry Research Group, E.T.H. Zürich
Ch-8092 Zürich, Switzerland
gonnet,cannaroz@inf.ethz.ch
Email Gina cannaroz@inf.ethz.ch if you have questions or want to be added to the mailing list for the class.
Books No books will be required but much of the material will come
from CBRG papers and the Darwin
Manual.
We will also follow closely some chapters from the book by Dan Gusfield entitled
Algorithms on Strings, Trees, and Sequences . An introduction to biology
can be found in the Cartoon Guide to Genetics by Larry Gonick.
Core computer science/mathematics topics covered in the course:
1.Basic probability and statistics theory, Markov processes, jackknifing, bootstrapping (models of evolution),
2.Dynamic programming (string alignment),
3.Local and global search techniques for problems modelled discretely (phylogenetic tree construction),
4.Exact algorithms for discrete problems (parsimony, Bunneman trees),
5 Parameterized algorithms for discrete problems (character compatability),
6.Basic approximation techniques and heuristic design (tree construction, genome level events),
7.Fundamental/advanced data structures (patricia and suffix trees),
8.Numerical techniques (Brent's algorithm, least squares fit, ultrametrics),
9.Programming with the specialized interpreted language Darwin,
10.Molecular computing (time permitted).
Biological concepts covered in the course:
1.Models of evolution,
2.Aligning an amino acid sequence against amino acid sequences,
3.Aligning an amino acid sequence against a nucleotide sequence,
4.Phylogenetic (evolutionary) tree construction,
5.the use of multiple sequences alignments to predict a proteins secondary structure,
6.protein domains and protein domain families,
7.evolutionary events at the genomic level (inversions, duplications, lateral transfers).
8.Protein identification through mass spectrometry
homework problem sets, homework solutions, other helpful handouts
A project is required---this list gives some ideas.
class and section times, instructor and TA information
Old class web pages:
WWW resources for biosequence analysis
URLs for web sites containing biosequence analysis tools, but not well annotated. This is my personal list of interesting sites, but it needs some updating, organzing, and annotating.
International Society for Computational Biology
ISCB is the primary professional organiszation for bioinformatics, sponsoring (or co-sponsoring) several conferences and having Bioinformatics as its official journal. Membership pays off in reduced conference fees and journal subscriptions.
Class notes and www pages for other bionformatics classes (maintained by ISCB)
List of on-line text resources for biosequence analysis
See also the ISCB list.
The University of California, Santa Cruz, bioinformatics (computational biology) research group models the primary (sequence) and secondary structures of DNA, RNA, and protein sequences, using hidden Markov Models (SAM=Sequence Alignment and Modeling System) and stochastic context-free grammars. UCSC also pioneered the use of Dirichlet mixtures for regularizing distributions of amino acids. Several servers are provided for using SAM, particularly for remote-homology and fold-recognition of proteins.
Kevin Karplus research overview
UCSC's proposed (not yet approved) Bioinformatics Master's program
The main tool at UCSC for building
and using hidden Markov models---there is also the general
SAM info page.
Local Sam Parameter
descriptions chapter This is one chapter of the local manual for SAM---it is
only accessible from UCSC and may include features not in the released version.
Chem
200A -- Fall 1996
Chemistry 200A: Protein Biophysics
(Fall-1998)
A protein-structure class with a fair amount of Wolrd-wide Web usage.
This tutorial is intended for people who know what an HMM is but want to know
how to use them most effectively. It details the tricks used in the SAM-T98
method (in 1998 the best method for remote homology detection in proteins). One
feature of this tutorial is the use of sequence logos on a running example to
show how various operations change what is being searched for. Also see http://www.soe.ucsc.edu/centers/cbe/packard.html
and the software program designed by this group (http://www.cse.ucsc.edu/~dkulp/cgi-bin/genie).
I am facinated with the possibility to build a number of exercises around
the tools and algorithms on this USSC page
http://www.cse.ucsc.edu/~kent/intronerator/index.html
9) http://www.cs.jhu.edu/~salzberg/cs439.html
|
CS 600.439 Principles of
Computational Biology Professor: Steven
Salzberg, salzberg@tigr.org This course is co-listed in the Part-time Programs in Engineering, Department of Computer Science, as 605.491 Principles of Computational Sequence Analysis. |
Textbooks: Introduction
to Computational Molecular Biology by Joao Setubal and Joao Meidanis.
Publisher: PWS Publishing Company, Boston, 1997. (The website lists
errata for the text.) Abbreviated as SM below. Computational
Methods in Molecular Biology edited by Steven Salzberg, David Searls,
and Simon Kasif. Publisher: Elsevier Science B.V., Amsterdam, 1998.
Softcover edition. Abbreviated as SSK below.
10) http://www.math.tau.ac.il/~rshamir/algmb.html
11) http://www.cs.washington.edu/education/courses/527/00wi/
12) ********** http://www.rickhershberger.com/darwin2000/ *****Favorite and #1 Model for modules, presentation and organization
Darwin 2000
A Web Site
for Student Research in Bioinformatics, Molecular Biology, and Evolution
Dr. Rick Hershberger
The Bioactive Site
Overview
of Darwin2000
Background
Bibliography
Overview
Understanding the process of evolution requires an appreciation for its underlying molecular mechanisms. The model of natural selection Darwin proposed can now be explained by, and is entirely consistent with, what we've learned since Darwin's time about how genes work to encode the structure of proteins, and how the structure and function of proteins determine the physiology, and thus the traits, of any organism. Using the Darwin 2000 series of online exercises, you may explore how genetic variation and selection for protein function together represent the forces driving evolution at the molecular level. In addition, you may explore how the proper function of a protein is related to its three-dimensional structure, which in turn is determined by its sequence of subunits
13) http://www.bioinformatics.pe.kr/
This takes some looking because some of it is in Korean but is an excellent resource for course outline and problem sets in English and a very good set of links to other courses and reference materials
14)
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Bioinformatics Tools |
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WWW: |
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Institution: |
The Virtual School of Molecular Sciences |
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Certificated: |
NO |
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Description: |
The Virtual School of Molecular Sciences is proud to present the first virtual course to support Bioinformatics which combines two of the most exciting technologies: Biotechnology and Information Technology. The course is aimed at programmers in bioinformatics and related disciplines and uses the power of Java to show a vital new approach to the creation of applications and programs. |
Numerous software tools for sequence analysis are used daily in molecular
biology and bioinformatics. They are provided on different computer networks all
over the world and offer services like access to vast amounts of data (GenBank,
EMBL, SwissProt, ...), searching for homologous sequences, comparing sequence
families, determing secondary and tertiary structures. This web-based course
provides a guided introduction to some of the most important tools, using
realistic example problems from molecular biology.
This course was designed for early graduate students in bioinformatics or
molecular biology. At Bielefeld University, the course is offered regularly
within a 11-week class period.
16)******** http://www-biology.ucsd.edu/others/dsmith/bioinformatics.html ********* Outstanding Links and established course
Introduction to Bioinformatics by Doug Smith--- BGGN 220--- a valuable CSU resource!
17) **** http://www.sdsc.edu/~gribskov/bimm140/ **** related to above
Welcome to BIMM 140 and BIMM 141! For Spring, 2001, BIMM 140 is the Lecture Course and BIMM 141 is the Lab Course of two coordinated courses presenting an Introduction to Bioinformatics. This web page is the official source of information about both of these courses and you should frequently check here for updates and corrections. Also check the BIMM 140 Syllabus for changes in the lecture schedule.
18) ******* http://www.sonoma.edu/People/T/Thatcher/biol480/ and http://www.sonoma.edu/People/T/Thatcher/biol518/workbench1.htm
Introduction to Biology Workbench
Go to Biology Workbench from the class web site and set up your account, if you don't
already have one. I suggest running the tutorial in one window, and Workbench in a second
window. That way you can toggle between them. Although you will be saving sequences on
your account, you'll still want to keep a log for making notes, recording ideas, results, and most
importantly- questions which you want to follow up in discussions.
AND ******** http://www.sonoma.edu/People/T/Thatcher/biol383/computing.htm ******
Virology Home page
Dr. Eileen Thatcher
Home Page
Office: Darwin 230A
v-mail: 707-664-2931
Office hours: Spring, 2001
T 10-12; Th 11-12 or by appt.
e-mail: thatcher@sonoma.edu
Introduction
A balanced approach to deliver a broad introduction to the field of molecular virology is my
aim. This will include some basic molecular biology along with an emphasis in studying the
molecular aspects of viruses. Bacteria phage, plant viruses, and insect viruses will be
discussed in addition to animal and human pathogens. Based on the surveys, the lectures and
discussion topics will be tailored to fit the class as much as possible. [Some restrictions do
apply. J]
19)**** http://www.iacr.bbsrc.ac.uk/notebook/courses/ *****
Very useful collection of primers, tutorials and resources such as:
A comprehensive package for the hands-on teaching of Molecular Biology.
Molecular Biology Notebook
MBN Online Courses
The Beginner's guide to molecular biology: a short course on the central dogma of molecular biology.
The beginner's guide will give you some simple information on the cell, DNA, RNA, and proteins, and how to make proteins. It is the prototype of Dr Chromo's school.
Famous Lives
A collection of links to the bibliographies of some of the scientists who established most of the actual knowledge. List is growing!
Other biology courses on the Web
A Level Biology Notes
The following is a collection of lecture notes for the AEB A level Modualr syllabus: 1998 Examination. they are arranged according to the four main modules. Select
the appropriate link to locate the notes of you choice.
BioChemNet
Biology and Chemistry educational resources online
20) **** http://www.sdsc.edu/pb/edu/pharm207/pharm207.html#timetable *******
21) http://www.sciencemag.org/feature/plus/sfg/education/index.shtml *************
 
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22) http://www.cellbio.com/courses.html
24) Secret passage to onlline journals
