Tutorials and Lecture Notes on Bioinformatics



A Guide to Molecular Sequence Analysis
A Guide to Structure Prediction
A Short Introduction to Biocomputing
Algorithms and Representations for Molecular Biology
Algorithms in Molecular Biology
Algorithms in Molecular Biology
Algorithms in biological sequence analysis
Applied Graph Theory and Algorithm
BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE
BioComputing Hypertext Coursebook
Bioinformatics
Bioinformatics
Bioinformatics
Bioinformatics
Bioinformatics Databases and Tools Guide
Bioinformatics and Computational Genomics
Bioinformatics and Genomic Analysis
Bioinformatics course at the GenZentrum, Muenchen.
Biosequence comparison tutorial
COMPUTATIONAL METHODS IN MOLECULAR BIOLOGY
CRI-MAP - Introduction
CompBio99 Home Page
Computational Genomics
Computational Molecular Biology
Computational Structural Biology: Protein Simulation and Structure Prediction
Computational and Biochemical Theories of the Origin of Life
Course in Computational Molecular Biology
DNA Sequence Analysis - Introduction
Data Entry Form Tutorials and Lecture Notes on Bioinformatics Database
Data Entry Form, Tutorials and Lecture Notes on Bioinformatics Database
EMBOSS Administrators Guide
EMBOSS Tutorial
FASTA MAN PAGES
GENOME ANALYSIS: A LABORATORY MANUAL
Gene Networks from Microarray Data
Genes, Genomes, and Bioinformatics Tutorial
Genomics and Computational Biology
Guide to Geometric Aspects of Protein Structure and Function
Homology modelling for beginners
Honours Computer & Bioinformatics Course
Human Molecular Genetics
Internet For Biologists - Introduction
Introduction to Computational Molecular Biology
Introduction to sequence analysis
Introductory Computer Course for the Life Sciences
Lectures by Professor M. Zuker
Lectures in Theoretical DNA and Protein analysis
MANT&EC Internet Skills for Bioinformatics: Information Publishing
MANT&EC Internet Skills for Bioinformatics: Tools and Methodologies
Making the most of your hidden Markov models
Molecular Biology Quiz
On-Line Mendelian Inheritance in Man - Introduction
Online Lectures on Bioinformatics
Primer on Molecular Genetics at John Hopkins
Principles of Computational Biology
Programming EMBOSS Applications
Programming for Bioinformatics and Internet (HTML, Perl, CGI)
Programming for Bioinformatics and Internet II (Perl, JavaScript, Java)
Protein Sequence Alignment and Database Scanning
Protein and DNA Sequence Analysis
Protein sequence and structure analysis: A practical guide "A taste of bioinformatics"
Representation of Molecular Models and Rendering Techniques
SANBI Bioinformatics class
The Virtual Lab
Tutorials and Lecture Notes on Bioinformatics Database
Using Computers for Molecular Biology" course
Using Computers in Molecular Biology
Using Internet Resources in Molecular Biology
Web Biochemistry

Title: A Guide to Molecular Sequence Analysis
WWW: http://www.sequenceanalysis.com/
Description: This guide will introduce the reader to molecular sequence analysis. In the context of this guide, sequence analysis is the process of trying to find out something about a nucleotide or amino acid sequence, employing in silico biology techniques. You may have sequenced a gene yourself, and wish to learn what the long string of letters representing bases, actually code for. You may want to confirm that you have indeed cloned a gene successfully, or you might want to learn about a sequence of DNA that you know absolutely nothing about. You may want to know if a worm has a similar protein to a human one. These, and many other situations, require that you employ sequence analysis.

Title: A Guide to Structure Prediction
WWW: http://bonsai.lif.icnet.uk/people/rob/CCP11BBS/
Description: This is by no means intended to be a comprehensive guide to predicting protein 3D structure. Rather, I have tried as best as possible to summarise my general approach to the problem in a manner that I hope is useful and not too difficult to follow. I apologise in advance for failing to include various references, WWW sites, etc. The assumption is that you have a sequence of a protein that you want to know more about. Before you start, remember that this approach will not always provide satisfying or complete answers. However, it is increasingly rare that the techniques described here fail to shed any light on a protein sequence. Just a little time to analyse a sequence can possibly save time and money by aiding experimental design. I should emphasise that the title of talk for the above meeting was "Secondary structure prediction and fold recognition". The contents of these pages are thus heavily biased towards these two subjects (e.g. there are no figures for most of the other sections). Mostly, however, there are links within the other sections that can give you more information about them.

Title: A Short Introduction to Biocomputing
WWW: http://www.uni-mainz.de/~cfrosch/bc4s/example.html
Description: This introduction is thought to provide you with some basic information describing why biologists and biochemists become increasingly interested in using computational approaches for their daily work. You will be guided through an explicit example providing you with the chance to get hands-on experience in using advanced programs in the same way as modern biologists frequently do.

Title: Algorithms and Representations for Molecular Biology
WWW: http://smi-web.stanford.edu/projects/helix/mis214/
Description: Lecture notes and other material from the "Algorithms and Representations for Molecular Biology class" at Stanford University.

Title: Algorithms in Molecular Biology
WWW: http://www.cs.washington.edu/education/courses/590bi/98w/
Description: Slides and lecture notes on the "Algorithms in Molecular Biology" course at University of Washington .

Title: Algorithms in Molecular Biology
WWW: http://www.math.tau.ac.il/~shamir/algmb/algmb98.html
Description: Lecture notes on this course, taught in the Fall 1998-1999 at Tel Aviv University Department of Computer Science

Title: Algorithms in biological sequence analysis
WWW: http://bigbox/bio/bin
Description: Site for a course at the University of Nebraska, Spring 2000. Pages on amino acids, proteins, x-ray crystallography, sequence alignment, suffix trees, fragment assembly. Author: David Jaffe.

Title: Applied Graph Theory and Algorithm
WWW: http://www.cse.ucsc.edu/classes/cmpe177/
Description: Handouts for the this course held at Department of Computer Engineering, University of California, Santa Cruz.

Title: BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science

Title: BioComputing Hypertext Coursebook
WWW: http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html
Description: The following set of tutorial texts has been developed for the award-winning VSNS-BCD BioComputing Courses, aimed at a mixed audience of biologists, computer scientists, and students + researchers of related areas, on a late undergraduate / graduate level.

Title: Bioinformatics
WWW: http://bioinfo.mbb.yale.edu/mbb447b-99/
Description: Course material on the "Bioinformatics" course at Yale University. Computational analysis of gene sequences and protein structures, on a large-scale. Topics include sequence alignment, biological database design, comparative genomics, geometric analysis of protein structure, and macromolecular simulation.

Title: Bioinformatics
WWW: http://cecssrv1.cecs.missouri.edu/bioinformatics/index.html
Description: Lecture notes of the Bioinformatics Class, Winter 1999, at University of Missouri. This winter 1999 offering is to provide the necessary computational methodology and basic life science terminology for training computer science and life scineces graduate students interested in bioinformatics. No previous training in either life sciences or computer science will be required. The objectives of this course include the understanding of genome structure and funciton, discovery of new genes and useful variations, comparative genomics, and many others.

Title: Bioinformatics
WWW: http://bioinfo.mbb.yale.edu/mbb447b-99/
Description: Description: Course material on the "Bioinformatics" course at Yale University. Computational analysis of gene sequences and protein structures, on a large-scale. Topics include sequence alignment, biological database design, comparative genomics, geometric analysis of protein structure, and macromolecular simulation.

Title: Bioinformatics
WWW: http://www.cse.ucsc.edu/classes/cmp243/
Description: Class notes, handouts and more on this Bioinformatics held at Department of Computer Engineering, University of California, Santa Cruz.

Title: Bioinformatics Databases and Tools Guide
WWW: http://www.agr.kuleuven.ac.be/vakken/i287/bioinformatica.htm
Description: Bioinformatics links list at the Laboratory of Gene Technology, KULeuven, Belgium

Title: Bioinformatics and Computational Genomics
WWW: http://bioinformatics.weizmann.ac.il/courses/BCG/
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science In spring 1998, the Weizmann Institute of Science offered for the first time a local course that introduces principles and methods in bioinformatics, a discipline that deals with the computation of biological information. As many other related courses world-wide, this course focuses on sequence analysis and genomics.

Title: Bioinformatics and Genomic Analysis
WWW: http://www.blc.arizona.edu/courses/bioinformatics/default.html
Description: Course material for the "Bioinformatics and Genomic Analysis" course at the University of Arizona

Title: Bioinformatics course at the GenZentrum, Muenchen.
WWW: http://www.lmb.uni-muenchen.de/Groups/Bioinformatics/Bioinfo.html
Description: Notes for this 1999 lecture course.

Title: Biosequence comparison tutorial
WWW: http://arep.med.harvard.edu/seqanal/index.html
Description: Welcome to the exciting world of biosequence comparison! These hypertext documents are intended to summarize the basic workings and concepts behind some popular programs, as well as to point out necessary cautions. It is not a substitute for reading the original literature. This document is intended to serve as a guide to using certain bioinformatics programs.

Title: COMPUTATIONAL METHODS IN MOLECULAR BIOLOGY
WWW: http://www.cs.huji.ac.il/~cbio/
Description: Slides and handouts on this course, taught at Hebrew University of Jerusalem Department of Computer Science

Title: CRI-MAP - Introduction
WWW: http://www.hgmp.mrc.ac.uk/Embnetut/Crimap/index.html
Description: CRI-MAP is a programme for the construction of genetic maps from gene linkage data. From the CRI-MAP Manual introduction by its author, Dr. Phil Green ... "The main purpose of CRI-MAP is to allow rapid, largely automated construction of multilocus linkage maps (and to facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). Although originally designed to handle codominant loci (e.g. RFLPs) scored on pedigrees "without missing individuals", such as CEPH or nuclear families, it can now (with some caveats described below) be used on general pedigrees, and some disease loci." In addition to its primary mapping function, CRI-MAP can also estimate recombination fractions & LOD scores between pairs of loci, perform multipoint likelihood calculations, and point out recombinant chromosomes in pedigrees. This tutorial is divided into three parts: 1. data input & formatting 2. mapping & LOD scores 3. map testing & X-overs Throughout, you will find links to: the CRI-MAP manual (World Wide Web version), its Table of Contents, and other references.

Title: CompBio99 Home Page
WWW: http://www.bio.cmu.edu/Courses/03510/
Description: Lecture notes, study aids and more from the Computational Biology course at Carnegie Mellon University.

Title: Computational Genomics
WWW: http://www.people.Virginia.EDU/~wrp/cshl98/cshl98.html
Description: Lecture notes from the 1998 "Computational Genomics" workshop at the University of Virginia

Title: Computational Molecular Biology
WWW: http://cmgm.stanford.edu/biochem218/
Description: Lectures notes, slides, references and more from Prof. Douglas L. Brutlag's course on "Computational Molecular Biology" - is a practical, hands on approach to the field of computational molecular biology. The course is recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning representation and analysis of biological sequences and structure. Various existing methods will be critically described and the strengths and limitations of each will be discussed. Future directions for development of new methods will also be discussed. There will be practical assignments utilizing the tools described. While no computer experience or programming skills are required, prior exposure to personal computers, e-mail, and the World Wide Web is essential.

Title: Computational Structural Biology: Protein Simulation and Structure Prediction
WWW: http://csb.stanford.edu/levitt/sb228/
Description: Course notes and assignments from Mike Levitt's class in Computational Structural Biology: Protein Simulation and Structure Prediction

Title: Computational and Biochemical Theories of the Origin of Life
WWW: http://www.weizmann.ac.il/~bmsegre/course.html
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science The origin of life is one of the major remaining mysteries facing science. The course will review computer science, biological and chemical literature related to this question, including the work of computer science pioneer John von Neumann, physicists such as Freeman Dyson and biological chemists such as Stuart Kauffman, Harold Morowitz and Manfred Eigen. Topics related to prebiotic evolution and to the emergence of life will be discussed. This will include theoretical models of self-reproducing automata, self-reproducing molecular assemblies, simulations of microscopic physico-chemical properties of mutually catalytic networks, homeostatic ensembles, quasi-species and hypercycles. Also to be included will be Artificial Life approaches involving formal languages (e.g. lambda-calculus), chemical kinetics simulations akin to molecular dynamics, as well as the origin of the genetic code (guest lecture by Prof. Edward Trifonov). The molecular version of the chicken-egg paradox will be reviewed in light of realistic prebiotic scenarios, on Earth and elsewhere. This interdisciplinary course and seminar is intended for students of Mathematics, Biology, Chemistry and Physics. Each interdisciplinary team of 2-3 students will be expected to deliver of a seminar and collaboratively carry out a computer simulation or analysis project.

Title: Course in Computational Molecular Biology
WWW: http://www.ibc.wustl.edu/CMB/bio5495/
Description: Lecture slides from the "Bioinformatics and Computational Molecular Biology" at Washington University

Title: DNA Sequence Analysis - Introduction
WWW: http://www.hgmp.mrc.ac.uk/Embnetut/Gcg/index.html
Description: There are three popular sets of DNA and protein sequence analysis programmes available via most EMBnet nodes: The Staden Package, from Rodger Staden et al, MRC Cambridge, UK The Wisconsin Package (GCG), from the Genetics Computer Group, Inc. USA EGCG (Extended GCG), from a consortium of researchers mostly based in Europe at EMBnet Nodes Exploring the complete range of programmes in each package is beyond the scope of this tutorial. Fortunately, the three packages have substantial overlap in the function of their programmes, so that learning in one package speeds use of another. We will consider representative or important programmes from each package, starting with how to manage a sequencing project in the Staden package. Later, as GCG and EGCG programmes are introduced, most of the main functional groupings of all packages will be covered.

Title: Data Entry Form Tutorials and Lecture Notes on Bioinformatics Database
WWW: http://www.hgmp.mrc.ac.uk/CCP11/forms/tutorials_form.html

Title: Data Entry Form, Tutorials and Lecture Notes on Bioinformatics Database
WWW: http://www.hgmp.mrc.ac.uk/CCP11/forms/tutorials_form.html
Description: Try to learn bio database.

Title: EMBOSS Administrators Guide
WWW: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Admin_guide/adminguide/
Description: A system adminstrator's guide to installing the EMBOSS package, written by David Martin at EMBnet Norway.

Title: EMBOSS Tutorial
WWW: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Tutorial/
Description: Introduction to Sequence Analysis using EMBOSS, written by Val Curwen at HGMP. An introduction to the most useful applications in EMBOSS, with exercises.

Title: FASTA MAN PAGES
WWW: http://www.infobiogen.fr/
Description: FASTA MANUAL

Title: GENOME ANALYSIS: A LABORATORY MANUAL
WWW: http://clio.cshl.org/books/g_a/bk1ch7/
Description: This review is a contribution to the forthcoming book Genome Analysis: A Laboratory Manual (Bruce Birren, Eric Green, Phil Hieter, Sue Klapholz and Rick Myers, eds) to be published by Cold Spring Harbor Laboratory Press in 1996. The hypertext version of the review is linked to Medline records, software repositories, sequences, structures, and taxonomies via the Entrez system of the National Center for Biotechnology Information. The document will be updated at intervals and the latest version will be published in the first print edition of the manual.

Title: Gene Networks from Microarray Data
WWW: http://www-binf.bio.uu.nl/~dutilh/gene-networks
Description: Since the development of the microarray technique in 1995, there has been an enormous increase in gene expression data from several organisms. Based on the view of gene systems as a logical network of nodes that influence each other's expression levels, scientists dream of being able to reconstruct the precise gene interaction network from the expression data obtained with this large scale arraying technique. Computer science shows that inference of a logical regulatory network is possible solely from sets of expression data, and mathematicians are working on the question how much data is at least necessary for reverse engineering. Meanwhile, experimental biologists are experiencing problems in the field. The number of experiments that are necessary before attempting network reconstruction is a lot more than is generally possible in ``wet'' laboratories, so data compression algorithms are applied to reduce the number of nodes considered. This is however an extremely coarse representation of the intricate interconnections that exist between single genes. The resulting network of only a handful of nodes is therefore usually only sufficient to describe the experiments performed, while any possible predicting properties are absent. In this literature thesis, I attempt to give an update on the state of the art in computerised network reconstruction techniques, and explicitly relate this to actual biological gene networks. I will go into the model formalisms used to describe genetic networks, and explain their specific advantages and disadvantages. Also, a separate chapter will be dedicated to several experimental results obtained in the research of genetic networks, and finally, a short discussion and some hypothesising is added.

Title: Genes, Genomes, and Bioinformatics Tutorial
WWW: http://csm.jmu.edu/biology/courses/bio220/aotw7.html
Description: The goal of this tutorial is to strengthen your understanding of gene structure, genome organization, and how molecular biologists use computers. You will visit several internet databases containing sequence information and answer a series of questions. As in previous tutorials, print the accompanying answer form before starting the tutorial. You may work in pairs. While the specific answers are by themselves not that significant, by completing the tutorial you will have been exposed to databases used by researchers that use the tools of molecular biology, and will gain a better understanding of nucleotide and amino acid sequence information. The correct answers will be provided via a link at the bottom of this page.

Title: Genomics and Computational Biology
WWW: http://www.courses.fas.harvard.edu/~bphys101/lecturenotes/index.html
Description: Survey course of genomics and computational biology

Title: Guide to Geometric Aspects of Protein Structure and Function
Description: Questions of chemical reactivity can often be cast as questions of molecular geometry. In particular, space-filling models are often invoked to rationalize the chemical behavior of proteins. Examples include linking the driving force for protein folding to solvent accessible surface area and the affinity for ligand protein binding to the mechanical fit of a ligand within a protein receptor site. Current numerical techniques do not provide a unified approach to these key geometric aspects of protein structure and function. Questions inadequately treated by current techniques include: Classification of protein internal spaces and their connectedness to the outside. Dynamic evolution of protein geometric properties. Docking of macro-molecules to protein receptor sites. We have recently begun to develop new methods -- in part inspired by algorithms used in computer-aided design and visualization for calculating molecular geometric properties. These new methods apply a ray-casting formalism to the analysis of molecular structure.

Title: Homology modelling for beginners
WWW: http://swift.embl-heidelberg.de/course/
Description: A very thorough introduction to the subject by G.Vriend.

Title: Honours Computer & Bioinformatics Course
WWW: http://www.up.ac.za/academic/microbio/hons/bioinf/index.html
Description: Introduction to computers, digital photography and bioinformatics

Title: Human Molecular Genetics
WWW: http://margot.weizmann.ac.il:3188/~hmg/introduc/index.html
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science

Title: Internet For Biologists - Introduction
WWW: http://www.hgmp.mrc.ac.uk/Embnetut/Ifb/ifb_intr.html
Description: Marshall McLuhan once muttered something about a global village, and the contradiction in terms was startling enough - back in the late '60's - that it became a pop-culture concept. Today, the global village is HERE, in the form of the Internet. So what does this Internet global village mean for practicing biologists? Like every other special interest group with a large or international membership, we now have places to meet and chat with distant colleagues, forums for discussion of problems, opinions & dogma, and an ENORMOUS offering of information and data analysis tools. These tutorials are to help you learn about the Internet and its many tools that take you to these sources of information. The tool you are using right now to read this text is called the World Wide Web, and your computer is running a programme known as a web browser. A number of words in this text are both underlined and coloured, like this, and several pictures have coloured outlines, like this one. When you "click on" one of these words or pictures with your mouse (move the mouse arrow pointer over the word and press the [left] mouse button), a link to another piece of information - somewhere else on the Internet - is activated, and your web browser tries to take you there. Try it now!

Title: Introduction to Computational Molecular Biology
WWW: http://theory.lcs.mit.edu/~mona/18.417-home.html
Description: Lecture notes and problem excercises from Bonnie Berger and Mona Singh's course at MIT.

Title: Introduction to sequence analysis
WWW: http://margot.weizmann.ac.il:3188/~hmg/seqanal/intro.html
Description: A short introduction by Gustavo Glusman

Title: Introductory Computer Course for the Life Sciences
WWW: http://dapsas.weizmann.ac.il/bcd/bcd_parent/bcd_course/course.html
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science Main topics: Internet: WWW, Email, FTP, telnet Introduction to UNIX and HTML Introduction to sequence analysis (GCG package) GCG's command line format Databases and logical names Running programs in batch Printing graphics Locating sequences in the databases Whole genome informatics Pairwise sequence comparison Database similarity searches BLAST, Fasta etc. Bioccelerator Multiple sequence alignment Restriction mapping and PCR Introduction to DNA sequencing Phylogenetic analyses

Title: Lectures by Professor M. Zuker
WWW: http://www.ibc.wustl.edu/~zuker/Bio-5495/
Description: Lecture notes on Biomolecular sequences, Molecular sequence alignment, Multiple sequence alignment, RNA secondary structure prediction, Phylogenetic Reconstruction.

Title: Lectures in Theoretical DNA and Protein analysis
WWW: http://www.biokemi.su.se/~arne/kurser/kurs_96/kurs_96_lectures.html
Description: Lecture notes on the "Theoretical DNA and Protein Analysis" course at Stockholm Graduate School in Biophysics .

Title: MANT&EC Internet Skills for Bioinformatics: Information Publishing
WWW: http://www.man.ac.uk/hpctec/courses/Biocomputing/publishing/st-notes/Inet-Bio_1.html
Description: This course gives in depth coverage for information providers who wish to publish information, distribute training material, share software and provide repository searching facilities using the World Wide Web.

Title: MANT&EC Internet Skills for Bioinformatics: Tools and Methodologies
WWW: http://www.man.ac.uk/hpctec/courses/Biocomputing/tools/InetToolsBio_1.html
Description: This timely course gives a good practical understanding of the tools and techniques for making best use of the Internet and in particular the World Wide Web in modern Computational Molecular Biology.

Title: Making the most of your hidden Markov models
WWW: http://www.cse.ucsc.edu/research/compbio/ismb99.tutorial.html
Description: ISMB99 Tutorial Material. 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.

Title: Molecular Biology Quiz
WWW: http://www.medkem.gu.se/edu/
Description: These exercises are designed as a part of a basic course in molecular biology at the Department of Medical Biochemistry at the Göteborg University, Sweden. Most of the exercises are in the form of self-paced quizzes. Questions are presented one at a time; only by giving the right answer can the user proceed to the next question. The package is designed so as to cover the flow of genetic information, going from DNA to protein. Most questions are related to DNA and protein sequence information.

Title: On-Line Mendelian Inheritance in Man - Introduction
WWW: http://www.hgmp.mrc.ac.uk/Embnetut/Omim/index.html
Description: OMIM is a catalogue of medically important human traits, genes and disorders thought to have a genetic basis. From the OMIM home page at the NCBI ... "This database is a catalog of human genes and genetic disorders authored and edited by Drs. Moyra Smith, Victor A. McKusick and their colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information." In addition, OMIM contains links to several other relevant or allied databases, including: the Human Genome Database, GDB the Cardiff Human Gene Mutation Database, HGMD the Seldin/Debry Human/Mouse Homology Map, the Cedar-Sinai Medical Center Genetics Image Archive, CSMC-IA, and several mutation-specific databases. This tutorial is divided into four parts: 1. Asking Simple Questions 2. OMIM Document Format 3. OMIM Gene Map 4. Linked Databases Throughout, you will find links to: the Table of Contents for the tutorial, a bibliography, and other web sites.

Title: Online Lectures on Bioinformatics
WWW: http://dkfz-heidelberg/tbi/bioinfo/
Description: Lectures on Bioinformatics with a focus on sequence analysis. (Martin Vingron)

Title: Primer on Molecular Genetics at John Hopkins
WWW: http://www.gdb.org/Dan/DOE/intro.html
Description: A thorough introductory text to molecular genetics.

Title: Principles of Computational Biology
WWW: http://www.cs.jhu.edu/~salzberg/cs439.html
Description: Steven Salzbergs course at Johns Hopkins University

Title: Programming EMBOSS Applications
WWW: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Develop/program.html
Description: A guide to writing bioinformatics applications using the libraries in the EMBOSS package. Written by the project coordinator Alan Bleasby at HGMP.

Title: Programming for Bioinformatics and Internet (HTML, Perl, CGI)
WWW: http://bioinformatics.weizmann.ac.il/courses/prog/
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science This course provides a step by step, theoretical and practical introduction to the development of useful tools for automation of complex computer jobs, and making these tools accessible on the network from a Web browser. Examples will be given on sequence analysis, database management, Web publishing etc. Main topics: Introduction to Internet usage and writing Web pages using HTML. Perl programming - the scientists' favorite, a powerful, easy-to-learn language. Providing a Web interface to your programs using CGI scripts.

Title: Programming for Bioinformatics and Internet II (Perl, JavaScript, Java)
WWW: http://bioinformatics.weizmann.ac.il/courses/prog2/
Description: Course material from this BIOINFORMATICS and COMPUTATIONAL GENOMICS COURSE at Weizmann Institute of Science This course (offered for the first time in the Spring 1999 semester) unleashes the full potential of Perl, introducing the creation of sophisticated software by joining already available modules. Principles of Object Oriented programming with Java and creation of Java Applets. Examples will be given on data-mining and intelligent user interfaces. Main topics: Perl modules - where to get, how to understand and how to integrate them into your application. Generation of graphical representation (examples for genomic data). Direct database access from your scripts. Client-side data manipulation with JavaScript. Object Oriented programming with Java and Perl.

Title: Protein Sequence Alignment and Database Scanning
WWW: http://barton.ebi.ac.uk/papers/rev93_1/rev93_1.html
Description: This is a preprint of the chapter in: Protein Structure prediction - a practical approach, Edited by M. J. E. Sternberg, IRL Press at Oxford University Press, 1996, ISBN 0 19963496 3.

Title: Protein and DNA Sequence Analysis
WWW: http://engpub1.bu.edu/bioinfo/SeqAnal.html
Description: Lecture notes, slides etc from the "Protein and DNA Sequence Analysis" course at Boston University

Title: Protein sequence and structure analysis: A practical guide "A taste of bioinformatics"
WWW: http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/
Description: Welcome to UCL's Web practical on bioinformatics, a gentle introduction to global sequence and structure analysis facilities. We hope the experience will reveal the power and potential both of W3 and of bioinformatics, but most of all we hope you have fun!

Title: Representation of Molecular Models and Rendering Techniques
WWW: http://scsg9.unige.ch/eng/toc.html
Description: Definitions of molecular surfaces and descriptions of rendering techniques for molecules at Geneva University, Switzerland

Title: SANBI Bioinformatics class
WWW: http://www.sanbi.ac.za/page2.html
Description: Lecture notes from the South African National Bioinformatics Institute "Honours Bioinformatics Course"

Title: The Virtual Lab
WWW: http://www.novo.dk/vl/index.asp
Description: Welcome to The Virtual Lab, a multimedia learning environment sponsored by Novo Nordisk, a world leader in insulin and diabetes care. Here you can learn about the processes used by scientists in engineering new enzymes and proteins, discuss your discoveries with other explorers, and research other topics in our library.

Title: Tutorials and Lecture Notes on Bioinformatics Database
WWW: http://www.hgmp.mrc.ac.uk/CCP11/forms/tutorials_form.html

Title: Using Computers for Molecular Biology" course
WWW: http://mcrcr0.med.nyu.edu/rcr/course/index.html
Description: Lecture slides from the "Using Computers for Molecular Biology" course at New York University Medical Center. Mostly about the VMS Operating system and GCG programs.

Title: Using Computers in Molecular Biology
WWW: http://www.bio.cam.ac.uk/bioteach/index.html
Description: A series of lectures making up NYU Medical Center Course G16.2604. The original NYU site

Title: Using Internet Resources in Molecular Biology
WWW: http://www.sdsc.edu/pb/edu/pharm207/pharm207.html
Description: Lecture notes on the Pharm 207/Bio 207 1998 course at the San Diego Supercomputer Center, University of California, San Diego. Increasingly the Internet is a source both of data and analysis tools in the field of molecular biology. Knowing what is available, being able to use these resources, and to interpret results returned by these resources is important to principal investigators, fellows, and students alike. A hands-on series of instructional lectures is presented with emphasis on working through real problems. Graduate students taking this course select their "pet protein" based on their reserach projects and solve these problems using that protein. Assessment is based upon a student's Web page developed during the course which describes features of their protein deciphered using a variety of Internet resources.

Title: Web Biochemistry
WWW: http://wbiomed.curtin.edu.au/teach/biochem/
Description: Molecular Architecture and enzymatic Mechanisms

Please contribute by contacting me of any bioinformatics tutorials that are not listed here.


Yong Huang .. Textknowledge