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This resource is maintained by and © Damian Counsell, UK Medical Research Council Rosalind Franklin Centre for Genomic Research (the RFCGR) 1998-2004. It is made available under a modified version of the Open Publication Licence. Latest changes
$Revision: 1.207 $ $Date: 2005/04/05 13:06:07 $ IntroductionMail your questions to me, Damian Counsell, and I'll try to bring you answers. Alternatively, if you have your own answers, mail them to me and I'll incorporate them. The practical section in particular is full of gaps so your contributions to that are particularly welcome; I am slowly completing and extending the entries when I have the time. Although I am happy to tackle questions of general interest to all visitors to the site, please note that:
I acknowledge the help of many other individuals in creating this part of the Bioinformatics.Org site. If you have contributed and I have forgotten to credit you, please email me and I will correct my oversight immediately. Bioinformatics is, I believe, a special kind of engineering discipline---it certainly isn't a "pure" science. It has been enormously successful in its short existence and I think its successes have been the result of a practical and rigorous approach which I hope to encourage in anyone interested in entering the field. This document is not a scientific paper or textbook (yet). You will find blunt opinions here. If you disagree with me about any of the following please tell me. I hope to learn a lot from your inevitable and welcome criticisms. There is certainly one sense in which I consider myself a pure scientist: I'm open to rational persuasion. I write this resource and hold the copyright for the purposes of protecting its content from intellectual property pirates. By that I mean I want to keep this out of the hands of people who steal the work of others for commercial gain, and those who abuse and extend the powers of IP law at the expense of the disadvantaged---rather than those who would like to copy or mirror this resource for educational reasons. (This may sound overdramatic, but the FAQ has already been pirated for doubtful purposes.) Overview
Contents
Definitions: What is Bioinformatics?Definition of Bioinformatics: What is bioinformatics?Roughly, bioinformatics describes any use of computers to handle biological information. In practice, the definition used by most people is narrower; bioinformatics to them is a synonym for "computational molecular biology"---the use of computers to characterize the molecular components of living things. What is Bioinformatics?---The Tight Definition"Classical" bioinformaticsMost biologists talk about "doing bioinformatics" when they use computers to store, retrieve, analyze or predict the composition or the structure of biomolecules. As computers become more powerful you could probably add simulate to this list of bioinformatics verbs. "Biomolecules" include your genetic material---nucleic acids---and the products of your genes: proteins. These are the concerns of "classical" bioinformatics, dealing primarily with sequence analysis. Fredj Tekaia at the Institut Pasteur offers this definition of bioinformatics: "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information." It is a mathematically interesting property of most large biological molecules that they are polymers; ordered chains of simpler molecular modules called monomers. Think of the monomers as beads or building blocks which, despite having different colours and shapes, all have the same thickness and the same way of connecting to one another. Monomers that can combine in a chain are of the same general class, but each kind of monomer in that class has its own well-defined set of characteristics. Many monomer molecules can be joined together to form a single, far larger, macromolecule. Macromolecules can have exquisitely specific informational content and/or chemical properties. According to this scheme, the monomers in a given macromolecule of DNA or protein can be treated computationally as letters of an alphabet, put together in pre-programmed arrangements to carry messages or do work in a cell. "New" bioinformaticsThe greatest achievement of bioinformatics methods, the Human Genome Project, is currently being completed. Because of this the nature and priorities of bioinformatics research and applications are changing. People often talk portentously of our living in the " post-genomic" era. My personal view is that this will affect bioinformatics in several ways:
Definitions of Fields Related to BioinformaticsWhat is Biophysics?Molecular biology itself grew out of biophysics.The British Biophysical Society defines biophysics as: "an interdisciplinary field which applies techniques from the physical sciences to understanding biological structure and function"More information about the various facets of the discipline can be found at the society's site hosted at Birkbeck College, London. Mike Goodrich wrote to ask what the status of biophysics was given the definition of computational biology submitted by Paul Schulte (below). A recent article in The Scientist [free registration required] dealt with this question---thanks to Jo Wixon (Managing Editor of Comparative and Functional Genomics) for the reference. What is Computational Biology?Computational biologists might object (please do), but, I find that people use "computational biology" when discussing that subset of bioinformatics (in the broadest sense) closest to the field of classical general biology. Computational biologists interest themselves more with evolutionary, population and theoretical biology rather than cell and molecular biomedicine. It is inevitable that molecular biology is profoundly important in computational biology, but it is certainly not what computational biology is all about (see next paragraph). In these areas of computational biology it seems that computational biologists have tended to prefer statistical models for biological phenomena over physico-chemical ones. This is often wise... One computational biologist (Paul J Schulte) did object to the above and makes the entirely valid point that this definition derives from a popular use of the term, rather than a correct one. Paul works on water flow in plant cells. He points out that biological fluid dynamics is a field of computational biology in itself. He argues that this, and any application of computing to biology, can be described as "computational biology" (see also the "loose" definition of bioinformatics below). Where we disagree, perhaps, is in the conclusion he draws from this---which I reproduce in full: "Computational biology is not a "field", but an "approach" involving the use of computers to study biological processes and hence it is an area as diverse as biology itself." Richard Durbin, Head of Informatics at the Wellcome Trust Sanger Institute, expressed an interesting opinion on this distinction in an interview: "I do not think all biological computing is bioinformatics, e.g. mathematical modelling is not bioinformatics, even when connected with biology-related problems. In my opinion, bioinformatics has to do with management and the subsequent use of biological information, particular genetic information." What is Medical Informatics?The Medical Informatics FAQ (no relation) provides the following definition: "Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information." That FAQ also points here Aamir Zakaria, the author of the FAQ, emphasises that medical informatics is more concerned with structures and algorithms for the manipulation of medical data, rather than with the data itself. This suggests that one difference between bioinformatics and medical informatics as disciplines lies with their approaches to the data; there are bioinformaticians interested in the theory behind the manipulation of that data and there are bioinformatics scientists concerned with the data itself and its biological implications. (I believe that a good bioinformatics researcher should be interested in both of these aspects of the field.) Medical informatics, for practical reasons, is more likely to deal with data obtained at "grosser" biological levels---that is information from super-cellular systems, right up to the population level---while most bioinformatics is concerned with information about cellular and biomolecular structures and systems. On both of these points I'd be happy for any medical informatics specialists to correct me. What is Cheminformatics?The Web advertisement for Cambridge Healthtech Institute's Sixth Annual Cheminformatics conference describes the field thus: "the combination of chemical synthesis, biological screening, and data-mining approaches used to guide drug discovery and development" but this, again, sounds more like a field being identified by some of its most popular (and lucrative) activities, rather than by including all the diverse studies that come under its general heading. The story of one of the most successful drugs of all time, penicillin, seems bizarre, but the way we discover and develop drugs even now has similarities, being the result of chance, observation and a lot of slow, intensive chemistry. Until recently, drug design always seemed doomed to continue to be a labour-intensive, trial-and-error process. The possibility of using information technology, to plan intelligently and to automate processes related to the chemical synthesis of possible therapeutic compounds is very exciting for chemists and biochemists. The rewards for bringing a drug to market more rapidly are huge, so naturally this is what a lot of cheminformatics works is about. Here is a page with a commercial slant which links to some interesting discussions of the term "cheminformatics", what it means, whether or not it exists as a distinct discipline, and even whether it should be replaced by "chemoinformatics". The span of academic cheminformatics is wide and is exemplified by the interests of the cheminiformatics groups at the Centre for Molecular and Biomolecular Informatics at the University of Nijmegen in the Netherlands. These interests include:
Trinity University's Cheminformatics Web page, for another example, concerns itself with cheminformatics as the use of the Internet in chemistry. What is Genomics?Genomics is a field which existed before the completion of the sequences of genomes, but in the crudest of forms, for example the oft-re-referenced estimate of 100 000 genes in the human genome derived from a(n) (in)famous piece of "back of an envelope" genomics, guessing the weight of chromosomes and the density of the genes they bear. Genomics is any attempt to analyze or compare the entire genetic complement of a species or species (plural). It is, of course possible to compare genomes by comparing more-or-less representative subsets of genes within genomes. What is Mathematical Biology?Mathematical biology is easier to distinguish from bioinformatics than computational biology. Mathematical biology also tackles biological problems, but the methods it uses to tackle them need not be numerical and need not be implemented in software or hardware. Indeed, such methods need not "solve" anything; in mathematical biology it would be considered reasonable to publish a result which merely establishes that a biological problem belongs to a particular general class. The distinction between bioinformatics and mathematical biology was illuminated by an email I received from Alex Kasman at the College of Charleston. According to his working definition, he distinguished bioinformatics which (under the tight definition at least)... "...seems to focus almost exclusively on specific algorithms that can be applied to large molecular biological data sets..." ...from mathematical biology which... "...includes things of theoretical interest which are not necessarily algorithmic, not necessarily molecular in nature, and are not necessarily useful in analyzing collected data." What is Proteomics?A recent review on proteomics in the journal Nature defined the field this way: "The term proteome was first coined to describe the set of proteins encoded by the genome1. The study of the proteome, called proteomics, now evokes not only all the proteins in any given cell, but also the set of all protein isoforms and modifications, the interactions between them, the structural description of proteins and their higher-order complexes, and for that matter almost everything 'post-genomic'." Michael J.Dunn, the Editor-in-Chief of Proteomics defines the "proteome" as: "the PROTEin complement of the genOME" and proteomics to be concerned with: "qualitative and quantitative studies of gene expression at the level of the functional proteins themselves" that is: "an interface between protein biochemistry and molecular biology" Characterizing the many tens of thousands of proteins expressed in a given cell type at a given time---whether measuring their molecular weights or isoelectric points, identifying their ligands or determining their structures---involves the storage and comparison of vast numbers of data. Inevitably this requires bioinformatics. Here is a constructively skeptical review by Lukas Huber. What is Pharmacogenomics?Pharmacogenomics is the application of genomic approaches and technologies to the identification of drug targets. Examples include trawling entire genomes for potential receptors by bioinformatics means, or by investigating patterns of gene expression in both pathogens and hosts during infection, or by examining the characteristic expression patterns found in tumours or patients samples for diagnostic purposes (possibly in the pursuit of potential cancer therapy targets). The term "pharmacogenomics" is used for the more "trivial"---but arguably more useful---application of bioinformatics approaches to the cataloguing and processing of information relating to pharmacology and genetics, for example the accumulation of information in databases like this one. (Thanks to Ivanovi.) What is Pharmacogenetics?All individuals respond differently to drug treatments; some positively, others with little obvious change in their conditions and yet others with side effects or allergic reactions. Much of this variation is known to have a genetic basis. Pharmacogenetics is a subset of pharmacogenomics which uses genomic/bioinformatic methods to identify genomic correlates, for example SNPs (Single Nucleotide Polymorphisms), characteristic of particular patient response profiles and use those markers to inform the administration and development of therapies. Strikingly, such approaches have been used to "resurrect" drugs thought previously to be ineffective, but subsequently found to work with in subset of patients. They can also be used for optimizing the doses of chemotherapy for particular patients. Overview of most common bioinformatics programsEveryday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHATIF. Overview of most common bioinformatics technologyCurrently, a lot of bioinformatics work is concerned with the technology of databases (Thanks again to Ivanovi.) These databases include both "public" repositories of gene data like GenBank or the Protein DataBank (the PDB), and private databases, like those used by research groups involved in gene mapping projects or those held by biotech companies. Making such databases accessible via open standards is very important. Consumers of bioinformatics data use a range of computer platforms: from the more powerful and forbidding UNIX boxes favoured by the developers and curators to the far friendlier Macs often found populating the labs of computer-wary biologists. Databases of existing sequencing data can be used to identify homologues of new molecules that have been amplified and sequenced in the lab. The property of sharing a common ancestor, homology, can be a very powerful indicator in bioinformatics (see below). Acquisition of sequence dataBioinformatics tools can be used to obtain sequences of genes or proteins of interest, either from material obtained, labelled, prepared and examined in electric fields by individual researchers/groups or from repositories of sequences from previously investigated material. Analysis of dataBoth types of sequence can then be analysed in many ways with bioinformatics tools. They can be assembled. Note that this is one of the occasions when the meaning of a biological term differs markedly from a computational one (see the amusing confusion over the issue at Web-based geek forum Slashdot). Computer scientists, banish from your mind any thought of assembly language. Sequencing can only be performed for relatively short stretches of a biomolecule and finished sequences are therefore prepared by arranging overlapping "reads" of monomers (single beads on a molecular chain) into a single continuous passage of "code". This is the bioinformatic sense of assembly. They can be mapped---that is, their sequences can be parsed to find sites where so-called "restriction enzymes" will cut them. They can be compared, usually by aligning corresponding segments and looking for matching and mismatching letters in their sequences. Genes or proteins that are sufficiently similar are likely to be related and are therefore said to be "homologous" to each other---the whole truth is rather more complicated than this. Such cousins are called "homologues". If a homologue (a related molecule) exists, then a newly discovered protein may be modelled---that is the three dimensional structure of the gene product can be predicted without doing laboratory experiments. Bioinformatics is used in primer design. Primers are short sequences needed to make many copies of (amplify) a piece of DNA as used in PCR (the Polymerase Chain Reaction). Bioinformatics is used to attempt to predict the function of actual gene products. Information about the similarity, and, by implication, the relatedness of proteins is used to trace the "family trees" of different molecules through evolutionary time. There are various other applications of computer analysis to sequence data, but, with so much raw data being generated by the Human Genome Project and other initiatives in biology, computers are presently essential for many biologists just to manage their day-to-day results Molecular modelling / structural biology is a growing field which can be considered part of bioinformatics. There are, for example, tools which allow you (often via the Net) to make pretty good predictions of the secondary structure of proteins arising from a given amino acid sequence, often based on known "solved" structures and other sequenced molecules acquired by structural biologists. Structural biologists use "bioinformatics" to handle the vast and complex data from X-ray crystallography, nuclear magnetic resonance (NMR) and electron microscopy investigations and create the 3-D models of molecules that seem to be everywhere in the media. noteUnfortunately the word "map" is used in several different ways in biology/genetics/bioinformatics. The definition given above is the one most frequently used in this context, but a gene can be said to be "mapped" when its parent chromosome has been identified, when its physical or genetic distance from other genes is established and---less frequently---when the structure and locations of its various coding components (its "exons") are established. What is Bioinformatics?---The Loose definitionThere are other fields---for example medical imaging / image analysis which might be considered part of bioinformatics. There is also a whole other discipline of biologically-inspired computation; genetic algorithms, AI, neural networks. Often these areas interact in strange ways. Neural networks, inspired by crude models of the functioning of nerve cells in the brain, are used in a program called PHD to predict, surprisingly accurately, the secondary structures of proteins from their primary sequences. What almost all bioinformatics has in common is the processing of large amounts of biologically-derived information, whether DNA sequences or breast X-rays. How old is the discipline?"How old is bioinformatics?" The answer to this one depends on which source you choose to read. From T K Attwood and D J Parry-Smith's "Introduction to Bioinformatics", Prentice-Hall 1999 [Longman Higher Education; ISBN 0582327881]:
From Mark S. Boguski's article in the "Trends Guide to Bioinformatics" Elsevier, Trends Supplement 1998 p1:
Books: Can you recommend any bioinformatics books?
It's notoriously difficult to find any books on bioinformatics itself that cater well for all of those coming from computing, from mathematics and from biology backgrounds. The few textbooks available in the field tend to be eyewateringly expensive as well. I've divided suggested reading into books of general interest, those best suited to people coming from a computational/mathematical background and books for biologists interested in bioinformatics. Where a book is also listed in Bioinformatics.Org's books section I have linked the title to the relevant entry there. Links to other lists of bioinformatics books follow this section of suggested reading. General introductionsMany people are curious about the Human Genome (Project). The completion of the first draft probably represents bioinformatics' coming of age as a discipline. The first couple of books are aimed at the intelligent layperson. A gossipy and insightful account of the race to sequence the genome can be found in "The Sequence" by Kevin Davies [Weidenfeld; ISBN 0297646982]. Matt Ridley's "Genome" [Fourth Estate; ISBN 185702835X] is both an interesting layperson's introduction to the issues raised by the bioinformatic revolution and an overview of its biology and enormous scope. If I remember rightly, Ridley's book received a slightly snooty review from Walter Bodmer. This is understandable, since his and Robin McKie's excellent "pre-genomic" guide to the Human Genome Mapping Project, "The Book of Life" [Oxford Paperbacks; ISBN 0195114876] was undeservedly in a remainders bin when I bought my copy a couple of years ago. If you are a non-biological scientist (or a non-scientist) and are hooked by these, why not go back to the "real beginning" of the race and read James Watson's entertaining and indiscreet memoir of his and Francis Crick's determination of the structure of DNA, "The Double Helix" [Penguin; ISBN 0140268774]---now updated with an introduction by media don Steve Jones. Nigel Barber at Peterborough Regional College in the UK recommends Gary Zweiger's "Transducing the Genome" [McGraw-Hill Professional Publishing: ISBN 0071369805]. The summary at Amazon makes it sound a tad pretentious, but all the reviews seem pretty positive so it might be worth a read. If you are a quantitative scientist and would like a deeper knowledge of contemporary (molecular) biology, but you want to acquire it as painlessly as possible you could try the following:
There are two classic competing texts in cell and molecular biology which Maximilian Haeussler reminds me to include: Alberts et al's Molecular Biology of the Cell [Garland Science: ISBN 0815340729] and Molecular Biology of the Gene [Benjamin Cummings: ISBN 0321248643]. Computational/Mathematical aspectsIf you are a hardcore maths/computing person Michael Waterman's "Introduction to Computational Biology" [Chapman & Hall/CRC Statistics and Mathematics; ISBN 0412993910] and Pavel Pevzner's "Computational Molecular Biology - An Algorithmic Approach" [The MIT Press (A Bradford Book); ISBN 0262161974] will give you all the discrete maths you can shake a stick at, but perfunctory introductions to the biology. Bioinformatics.Org's very own Jeff Bizzaro recommends Dan Gusfield's "Algorithms on Strings, Trees and Sequences" [Cambridge, 1997 ISBN 0-52158-519-8], Richard Durbin, S. Eddy, A. Krogh, G. Mitchison "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" [Cambridge, 1997 ISBN 0-52162-971-3] (which I think is one of the clearest and most comprehensive guides to alignment algorithms) and---for that full "computers-to-biology conversion"--- Geoffrey M. Cooper "The Cell: A Molecular Approach" [ASM Press, 1996 ISBN 0-87893-119-8]. Jeff Ames writes that a second edition of this book is now available [Sinauer Associates, Incorporated, 2000 ISBN 0-87893-106-6] and that this version---if you can find it in the shops---comes with a CD. Applying bioinformatics to biological researchOne outstanding general text for the biologist is David W. Mount's "Bioinformatics" [Cold Spring Harbor Press; ISBN 0879696087]. It's not cheap, but it's the best I've seen if you are studying bioinformatics itself. Bioinformatics has been dismissed by some as "the science of BLAST searches". The best collection of advice so far on doing BLAST searches is O'Reilly's BLAST book by Ian Korf, Mark Yandell and Joseph Bedell [O'Reilly ISBN 0-596-00299-8]. I reviewed it enthusiastically, but not uncritically, for the UK UNIX Users' Group magazine. I'd go as far as to say that all biologists thinking of using BLAST in their research should read the relevant sections before they even go near a computer. If you wish to use general bioinformatics tools, especially if you are a little wary of computers, my new "best" book is "Bioinformatics for Dummies" [John Wiley and Sons ISBN 0764516965]. It is (obviously) aimed at people who are beginners, who are happier using the Web rather than typing commands, and who are more interested in learning than in impressing people---the writing is friendly clear and unpretentious. However, like several of my other tips (below) it concentrates on Web-based resources so it will, inevitably, date. (This is partially compensated for by there being a companion Website.) Also, if you're coming to the subject as a computer user with a biological background, looking to exploit the many tools available, you might want to try Terry Attwood and David Parry-Smith's "Introduction to Bioinformatics" [Longman Higher Education; ISBN 0582327881], or Des Higgins and Willie Taylor's "Bioinformatics: Sequence Structure and Databanks" [Oxford University Press; ISBN 0199637903]. Another excellent practical introduction is Andreas Baxevanis and Francis Oulette's "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" [Wiley-Interscience; ISBN 0471383910], now in its new and improved second edition. Bax teaches bioinformatics all over Canada and the experience shows. Arthur Lesk has also produced an excellent teaching book particularly for protein bioinformatics in his Introduction to Bioinformatics Bioinformatics.Org also recommends Cynthia Gibas and Per Jambeck's "Developing Bioinformatics Skills" [O'Reilly, 2001 ISBN 1-56592-664-1]. Stuart Brown recommends his own book "Bioinformatics: A Biologist's Guide to Biocomputing and the Internet" [Eaton Pub Co; ISBN: 188129918X]. If he sends me a review copy I might recommend it too ;-) . Fiction books"Darwin's Radio" by Greg Bear [Ballantine Books, ISBN: 0345435249] is a wonderful hard SF thriller which stretches ideas derived from genome discoveries to their breaking point. It's gripping and humane. Leonard Crane, the author of Ninth Day of Creation kindly sent me a copy for review. So far it's an excellent read. I haven't finished it yet, not because it isn't a rattling good story, but because, like "Darwin's Radio", it is very long and because I am very busy. If you'd like to read a well-researched, but speculative, novel containing actual scenes of practising bioinformatics then try it. Ken Allen contributed the following reviews:
Further suggestions for this section are welcome. Other lists of bioinformatics booksSee also compbiology.org's list, Steve Brenner's list, and Aik Choon Tan's collection of books. Centres of Bioinformatics Activity: Where is bioinformatics done?The biggest and best source of bioinformatics links I have encountered is the Genome Web at the Rosalind Franklin Centre for Genomics Research at the Genome Campus near Cambridge, UK. Most of the links below come from that resource. My list is necessarily limited by comparison.
Research centres
Sequencing centres
[XXXX INSERT DETAILS OF MORE SEQUENCING CENTRES HERE] Standards centres[XXXX INSERT DETAILS OF STANDARDS CENTRES HERE] What virtual centres (for example consortia and communities) for bioinformatics activity are there?[XXXX INSERT MORE DETAILS OF VIRTUAL BIOINFORMATICS CENTRES HERE] Online Resources: What bioinformatics Websites are there?'BlogsThe front page of Bioinformatics.Org itself is a bioinformatics 'Blog. The Bio-Web links to resources online for molecular and cell biologists and covers current news in various biological/computational fields. Genehack is the first bioinformatics 'Blog I ever encountered. InformationThe Australian National Genomic Information Service (ANGIS) is operated by the Australian Genomic Information Centre (currently at The University of Sydney) to offer software, databases, documentation, training and support for biologists "The University of Maryland AgNIC gateway is a guide to quality agricultural biotechnology information on the Internet." DirectoriesChristy Hightower, Engineering Librarian at the Science and Engineering Library, University of California Santa Cruz has already done this better than me. Visit her excellent article about bioinformatics Net resources in Issues in Science and Technology Librarianship. SocietiesHumberto Ortiz Zuazaga kindly introduced me to The International Society for Computational Biology which he points out "has links to programs of study and online courses in computational biology and to job postings". Collections of ToolsYou can start right here at Bioinformatics.Org if you are looking for a bioinformatics toolbox. I cannot recommend strongly enough the Rosalind Franklin Centre's "GenomeWeb". Of historical interest only now, I guess, is the legendary " Pedro's Molecular Biology Search and Analysis Tools". PortalsBioinformatics.Org is an international organization which promotes freedom and openness in the field of bioinformatics and is the root domain of a damned fine Website :-) . CCP11 (Collaborative Computational Project 11) is another product of the UK's Genome Campus. To quote their Web site, it was... "...established to foster the broad bioinformatics community and the UK research community in particular. Its purpose is to facilitate the transfer of knowledge and expertise through conferences, workshops, a newsletter and the use of the world wide web. CCP11 is funded by the BBSRC and is hosted at the MRC Rosalind Franklin Centre for Genomics Research RFCGR located on the Wellcome Trust Genome Campus, Cambridge." Jennifer Steinbachs runs compbiology.org which is a general computational biology site as well as being a portal to her own work. BioPlanet is well worth visiting. It describes itself as "a not-for-profit site, funded with our resources, for [its users'] benefit" ColorBasePair is a densely packed portal with lots of bioinformatics links Nick Yates runs his own informative bioinformatics site, unsurprisingly called nick-yates.com. He doesn't aim to make money from it, but it may have paid-for ads. Check out the glossaries---they are better than mine. TutorialsA great place to start, whether you come from a biological, physical or computational background is at Martin Vingron's superb online bioinformatics tutorial. (Begin by choosing a section from the left-hand-side menu bar.) Tom Smith and Don Emmeluth have produced a nice little exploration of bioinformatics using NCBI resources and tools. I recently stumbled upon a promising set of online lecture notes currently under construction by B. Steipe at the Genzentrum (Gene Center) at the Ludwig-Maximilians-Universität München (University of Munich). Chemistry for allA defiantly frames-free chemistry tutorial site. Mathematics for biologistsFirst of all, an almost completely painless introduction to the horrors of the quadratic equation by Peter Whalen, James Walker, and Drew Marticorena. C. J. Schwarz of the Department of Statistics and Acturial Science, Simon Fraser University has produced a course in statistics which is accompanied by set of sound, online PDF handouts. Here is a great guide to a whole array of statistical learning/teaching resources prepared by Juha Puranen of the University of Helsinki (English). Computers for biologistsProgramming for biologistsGeneral introduction to biology for computer scientistsEstrella Mountain Community College in the States offers this excellent short introduction to biology (actually "The Nature of Science and Biology". It's a great place for keyboard jockeys to start their journey to enlightenment. Thanks to Alex O'Neill for pointing out the broken link. GeneticsThe Dolan DNA Learning Center at Cold Spring Harbor has an outstanding interactive tutorial introducing genetics. To take full advantage of the multimedia elements you should download the Flash and Real players. Molecular biology for computer scientistsThe Institute of Arable Crop Research Beginner's Guide to Molecular Biology Protein chemistry for computer scientistsUnilever Education Advanced Series tutorial on proteins. Cell biology for computer scientistsThe University of Arizona has made available a high-quality tutorial in cell biology. Not only does it cover the facts, but it also attempts to introduce some of the philosophy of the field---recommended. Even better, it's also available en Español and in Italiano. Once you've worked your way through that you might like to see some scanning electron microscope images of some of the structures you've read about taken by members of John Heuser's lab. Evolution for computer scientistsBob Patterson maintains his "Darwiniana" with amazing diligence. Practical bioinformaticsOther lists of bioinformatics tutorialsEducation: Where can I study Bioinformatics...jump straight to introduction to education section This section is not complete, but contributions to broaden its coverage are welcome. Please do not direct questions about eligibility, course quality or admissions policy to me, but to ask the individual institutions directly. Use the links to obtain contact details. If an institution doesn't provide telephone numbers/email addresses or snailmail details on its Web site it doesn't deserve your patronage. This resource focuses on complete, full-time degree programmes rather than on individual study modules. Curating a list of the latter would be a full-time job. You can go to other places, however, if you are looking for short courses. Thanks to various contributors, including Wentian Li who pointed me to this list at Rockefeller which is mirrored at various other sites. And to Humberto Ortiz Zuazaga for mailing me a link to the ICSB, where you can find this list. If you are interested in U.S. programmes, here's a list from Curtin and here's a list from Stanford. Thanks to Amelie Stein who also supplied some of the individual entries in this section. Those wanting to find programmes in the Asia Pacific region could have a look at this resource maintained by the Asia Pacific Bioinformatics Network APBioNet. Thanks to Sentausa. In the UK The Bioinformatics Resource (part of the BBSRC's CCP11 project) project maintains (among many other resources) lists of (mainly) British Masters and PhDs in bioinformatics. If you have any suggestions or updates please contact me with them. You can publicize your course and offer a public service at the same time. AfricaRhodes University, Grahamstown, South Africa offers an MSc. in Bioinformatics and Computational Molecular Biology. Thanks to Natalie Twine. Cathal Seoighe wrote a while back about the South African National Bioinformatics Institute (SANBI). Ruediger Braeuning has since written to point out that bioinformatics training in South Africa has been radically reorganized. He says:
South African National Bioinformatics Institute (SANBI) Honours Bioinformatics Course at the University of the Western Cape. Next year the same institute will be offering a Master's in bioinformatics---thanks to Cathal Seoighe. If you know of any other bioinformatics courses on the African continent please feel free to mail me about them. The AmericasCanadaThanks to Jordan Patterson for the information that the University of Alberta offers four-year Biology or Computer Science degrees with a specialization in bioinformatics. The Faculty of Computer Science there offers Master's and PhD training in bioinformatics. Benjamin Horsman wrote to tell me that Simon Fraser University and the University of British Columbia are collaborating on a new Bioinformatics training program with the British Columbia Cancer Agency. The program offers post-graduate diploma, Master's, and PhD training in Bioinformatics. Now Simon Fraser University also offers a joint major programme in Molecular Biology and Biochemistry (MBB) and Computer Science in Bioinformatics. Thanks to Brittany Nielsen for the info. Thanks to Olga Likhodi for the information that Seneca College, Toronto offers a post-graduate diploma in Bioinformatics. Peter Kublik informs me that from 2003/2004 the University of Calgary will offer a bioinformatics programme. He's part of the first intake. The University of Waterloo, Department of Computer Science offers undergraduate and graduate courses in bioinformatics. More information is here. CaliforniaThe Keck Graduate Institute claims that computational biology is a core element of the curriculum in its Master of Bioscience degree. Stanford University offers academic and professional (distance-learning) MSs in Biomedical Bioinformatics as well as its PhD programme. Thanks to Betty Cheng. Thanks to Momchil Georgiev for the information that the University of California at San Diego offers a Bioinformatics graduate programme and to Dana Brehm that there is now a new bachelor's program, to quote her: "[This is an] undergraduate, interdisciplinary program for undergraduates leading to a B.S. degree. The new Bioinformatics major is offered by the Division of Biology, and the departments of Chemistry/Biochemistry, Computer Science and Engineering, and Bioengineering. A student may choose to major in Bioinformatics in any one of the four departments or division. The Division of Biology currently offers two Bioinformatics courses, and with the advent of the cross-disicplinary major, even more courses are going to be taught 2002-03 and 2003-04.". University of California, Irvine Informatics in Biology and Medicine David Delong wrote to me to point out that the College of Natural and Agricultural Sciences at the University of California, Riverside is developing a "Center in Genomics and Bioinformatics" which will offer a PhD curriculum in genomics and bioinformatics from academic year 2001-2002 onwards. Catherine Velazquez says that The University of California, Santa Cruz offers a new undergraduate BS course in bioinformatics. They have a Frequently Asked Questions. Now they also offer an MS/PhD in Bioinformatics. Thanks to Kevin Karplus for the update. ConnecticutJavier Rojas Balderrama emailed me to point out thatYale University offers a Bioinformatics and Computational Biology track as part of its combined Biological and Biomedical Sciences graduate programme. GeorgiaGeorgia Institute of Technology Masters of Science in Bioinformatics According to Eric VanWieren Georgia State University offers a Master's and PhD in Computer Science with a focus on bioinformatics. The university's Bachelor of Science in Computer Science also offers a "Fundamentals of Bioinformatics" course. IllinoisThe University of Illinois at Chicago offers graduate programmes covering Bioengineering Bioinformatics through its Bioengineering department as well as an undergraduate course track. Thanks to Amit Sabnis. IndianaIUPUI offers an MS programme in Bioinformatics. Indiana University also offers an MS programme in Bioinformatics. IowaIowa State University offers an Interdisciplinary Ph.D. Program in Bioinformatics and Computational Biology (BCB). MaineThe Jackson Lab, a World centre of mouse genome informatics offers a graduate training program. MarylandTim Young wrote to say that Johns Hopkins University in Maryland offers an MS in Bioinformatics through the Zanvyl Krieger School of Arts and Sciences Advanced Academic Programs and Whiting School of Engineering Engineering and Applied Science Programs for Professionals. They are also offering a Bioinfomatics concentration with their MS in Biotechnology program. MassachusettsBoston University offers a graduate programme and so does its partner North Eastern University. North Eastern also offers a Graduate Certificate in the subject. Brandeis University offers both a Master of Science in Bioinformatics and a Graduate Certificate in Bioinformatics. Thanks to Matt Foster. The Department of Computer Science at UMass Lowell offers various degrees from Bachelor's through to PhD. level in Computer Science with Bioinformatics options. MexicoAt the National Autonomous University of Mexico a doctoral program in biomedical sciences is available. Their Computational Molecular Biology Group is here. MinnesotaThe University of Minnesota offers a graduate programme in bioinformatics. Thanks to Anu Haniharan for drawing my attention to mixing up the Minnesota and New Jersey paragraphs. NebraskaThe University of Nebraska Lincoln offers an Interdisciplinary Bioinformatics Specialization. The Graduate Program of the Pathology-Microbiology Department at the University of Nebraska Medical Center (University of Nebraska at Omaha) offers a specialty track in bioinformatics. NewJerseyRama Penta wrote to say that Stevens Institute of Technology offers a Master's programme in Bioinformatics. The message also states that the University of Medicine and Dentistry New Jersey (UMDNJ) offers a programme in biomedical informatics. Thanks to Anu Haniharan for drawing my attention to mixing up the Minnesota and New Jersey paragraphs. Moustafa wrote to say that Ramapo College in New Jersey is the only school in New Jersey offering a Bachelor's degree in bioinformatics. New York StateThe University at Buffalo has been involved in establishing a "Center of Excellence in Bioinformatics". It used to a range of courses in bioinformatics and related subjects, but all the course links seem to be dead now. Thanks to Jeff Ligas for the original notification. Canisius College---also in Buffalo, NY---has had a state-approved B.S. in Bioinformatics since 2001. Thanks to Deb Burhans. Cornell and Rockefeller Universities, together with the Sloan-Kettering Research Institute offer a "Tri-institutional program in Computational Biology and Medicine". Thanks to Brant Inman. Rensselaer Polytechnic Institute offers both undergraduate and graduate programmes in bioinformatics Rochester Institute of Technology offers BS MS and BS/MS programmes in Bioinformatics. Thanks to Brandon H. According to Maureen Downey, the College of Staten Island, part of the City University of New York also offers a challenging program in bioinformatics. If you know of any other bioinformatics courses on the American continent please feel free to mail me about them. North CarolinaDuke University's Center for Bioinformatics and Computational Biology offers various bioinformatics programmes. The North Carolina State University Statistical Genetics and Bioinformatics Program offers Master's Bioinformatics and PhDs in bioinformatics. The University of North Carolina at Chapel Hill offers a programme in Bioinformatics and Computational Biology (BCB). OhioAndrew Johnson writes: "There is a relatively new Biomedical Informatics program in Ohio. (I'm entering the program in a few months). Though the department stands alone, it is in the College of Medicine at the Ohio State Medical Center. Entrance is offered through a new Integrated Biomedical Sciences Graduate Program.". PennysylvaniaThe University of Pennsylvania offers some of the best known and longest established bioinformatics programmes at Batchelor's, Master's and PhD levels. Thanks to Louis Licamele for pointing out my oversight (I just assumed I'd already listed them!) He also points out that Georgetown University is planning bioinformatics courses too. TexasTom Andrews, a student on the course, has written to me to tell me that Texas A&M University at Corpus Christi is currently offering a BS computer science degree in bioinformatics. Jeremy Read told me that St. Edward's University in Austin offers a B.S. in Bioinformatics. The Keck Center for Computational Biology---a joint venture of Baylor College of Medicine; University of Houston; Rice University; University of Texas Health Science Center, Houston; M.D. Anderson Cancer Center; and University of Texas Medical Branch, Galveston---offers undergraduate (not 2003) and graduate level training in Computational Biology. The University of Texas, El Paso offers a Master's in Bioinformatics. VirginiaGeorge Mason University offers both M.S. and PhD. programmes in Bioinformatics. The Virginia Polytechnic Institute and State University's Bioinformatics Institute offers graduate options in Bioinformatics. Thanks to William S. Preissner for correcting this entry. AsiaHong KongRaymond Lau drew my attention to the Bachelor of Science degree in bioinformatics at the University of Hong Kong. IndiaNiranjan Swaroop Sharma wrote to tell me about the Bioinformatics Institute of India which is offering a whole range of bioinformatics programmes and qualifications in both regular and distance learning formats. I would have reported on this earlier, but have not been able to view the site in Mozilla. I finally viewed the site using Konqueror today (24Jul03). Perhaps some tinkering with the ASP code is needed there... Vaibhav Sinha wrote to tell me that the Institute of Bioinformatics and Applied Biotechnology (IBAB) in Bangalore is offering bioinformatics courses. Thanks to Surjeet Singh for drawing my attention to the Indian Institute of Information Technology-Allahabd which runs a Master of Technology (M. Tech Bioinformatics) degree. According to Rahul Agrawal, the Indian Institute of Technology Delhi, New Delhi provides courses in Biochemical Engineering and Biotechnology. He adds that another branch of the Institute, IIT Kharagpur also provides various courses in this area. There is an Advanced (Graduate) Diploma in Bioinformatics in the Bioinformatics Centre at the Jawaharlal Nehru University. Madurai Kamaraj University in Madurai, India claims to have been the first in the country to initiate a bioinformatics programme and advanced diploma in bioinformatics at its School of Biotechnology Risabh Bhandari writes to say: "The recently rechristened CBT (Center for Biochemical Technology) [link dead 13Nov02] which is a CSIR Lab [in New] Delhi has started a PG Diploma in Bioinformatics in association with Informatics institute. The course covers a large area in the field with [its] primary focus on computational and programming concepts. The course is 6 months in duration, [and] conducted at the national Head office of [the] Informatics institute." The University of Pune, Maharashtra offers its MSc. in Bioinformatics and Advanced Diploma in Bioinformatics at the Bioinformatics Centre, India. Uma Paresmeswaran wrote to say that SASTRA, which is based near Trichy, Tamil Nadu, will be offering a B.Tech.Programme in Bioinformatics from 2003/2004, the first institute in India offering this course at the undergraduate level? There is, according to Aditi Arur, an MSc distance education program in Bioinformatics, offered by Sikkim Manipal University India. MalaysiaDr Amir Feisal Merican wrote to say that the Institute of Biological Sciences, Faculty of Sciences, University of Malaya, Kuala Lumpur, is offering a BSc (Bioinformatics) undergraduate degree programme. Yam confirmed this that this degree has been taught for 3 years. Kebangsaan University, Malaysia (UKM) will start to offer a Bachelor's Degree in Bioinformatics to its next intake, in July, 2003. PakistanThanks to Abdul Hameed for pointing out that two universities in Pakistan---COMSATS Institute of Technology and the Mohammad Ali Jinnah University---will be offer four-year Bachelor of Sciences degrees in bioinformatics from September 2003. SingaporeThe Bioinformatics Centre of the National University of Singapore offers Undergraduate and PhD programmes in conjunction with the life sciences departments and research institutions at NUS. Lam Ah Wah wrote to tell me that the Nanyang Technological University (NTU) starts a BioInformatics undergraduate and part-time post-graduate MSc course in Jul 2002. Be warned: their Web site has hideous frame/window based "portal" which breaks half a dozen rules of good interface design. Chua Hian Koon managed to find a better link, and I browsed from there to the syllabus here. If you know of any other bioinformatics courses is Asia please feel free to mail me about them. AustralasiaAustraliaThe Research School of Biological Sciences, at the Australian National University in Canberra offers PhD., MSc. and Honours programs in Bioinformatics. You can obtain a Graduate Certificate in Bioinformatics from Curtin University of Technology in Western Australia. As of 2001 Flinders University in Adelaide offers a Bachelor's of Science in Bioinformatics. The Biochemistry Department of La Trobe University in Victoria also offers an undergraduate course in Bioinformatics. The University of Melbourne offers undergraduate study in Bioinformatics. Thanks to Gad. There are (according to H L View) PhD, MPhil and Honours programmes in bioinformatics (plus a bioinformatics minor) available at Murdoch University's Centre for Bioinformatics and Biological Computing. Rachel Oh said that is possible to study a near-bioinformatics programme at QUT (Queensland University of Technology): the B. Sci (biotech maj.) & IT (in software engineering & data comms) IF29. A copy of the course is available by searching their Website. The University of New South Wales in Sydney offers a Bachelor of Engineering in Bioinformatics. According to Jonathan Watts, "Queensland University of Technology in Brisbane QLD offers a Bachelor of Applied Science Innovation, with a major in Bioinformatics" from 2004. Sydney University in New South Wales offers a Bachelor's of Science and a postgraduate, Master of Applied Science degree in Bioinformatics. Thanks to Dominic Lau and Sebastien Gerega or the update. If you know of any other bioinformatics courses is Australasia please feel free to mail me about them. New ZealandThanks to Danushka for the information that the University of Auckland, New Zealand has a BSc (Hons) in bioinformatics. EuropeAustriaA bioinformatics option is offered as part of degree courses at the Graz University of Technology (Technische Universität Graz) in Graz, Austria. BelgiumA consortium including nearly all the French-speaking universities of Belgium (Bruxelles, Liège, Louvain, Mons, Namur and Gembloux) is offering the "Inter-University DEA/DES (Master) in Bioinformatics". The Department of Engineering at the Katholieke Universitiet of Leuvan offers a Master of Bioinformatics degree. DenmarkThe Bioinformatics Centre at The University of Copenhagen offers a two-year masters program in bioinformatics. Thanks to Thomas Litman.The Technical University of Denmark, Center for Biological Sequence Analysis offers a two-year International MSc. in bioinformatics. Syddansk Universitet (The University of Southern Denmark) offers both BSc- and MSc- level Bioinformatik / Experimental Bioinformatics. Thanks to Fiona Nielsen for the updated link---"Center for Experimental Bioinformatics". FinlandThe Finnish Graduate School in Computational Biology, Bioinformatics, and Biometry or "ComBi" is a joint venture of the University of Helsinki (English), the University of Turku (English) and the University of Tampere (English). FranceFabio Pardi writes that the Université Paris VII offers a DEA en Analyse de Génomes et Modélisation Moléculaire. Thanks to Brant Inman again for this link to the course. Isabelle da Piedade kindly provided this list of Master's and PhD programmes in France:
GermanyThanks to Amelie Stein for several of these entries. The Technische Fachhochschule Berlin (University of Applied Science) offers an MSc in Bioinformatics and the Freie Universität Berlin (Free University) offers both an MSc. and a BSc. in Bioinformatics. Thank you to Sebastian Kurscheid for this information. Alexandra Reitelmann wrote to say that Bonn-Aachen International Center for Information Tec |