Learning Biocomputing on the Internet
David T. Croke 
Biocomputing in a Central Position
Here we are at the end of the second
VSNS Biocomputing Course and looking forward to a third! Many people
looking at this web site may wonder why anyone would want to learn or even
to do Biocomputing on the Internet. The reality is that this is the best
way to learn, to share expertise and to perform analyses of DNA or protein
sequences that may interest you.
In the last five years, Biocomputing (in the broadest sense of the term)
has moved into a central position in molecular biology research. Enormous improvements
in genetic mapping and sequencing technology have led to the accumulation
of vast amounts of biological information in the databases. Centres such
as the European BioInformatics Institute
(EBI) and ExPASy
help to manage these libraries of sequences and of other information. If
you are doing molecular biology it is now almost impossible to avoid the
need to compare and/or to analyse sequences. Analysing the base sequences
of DNA molecules or the amino-acid sequences of protein molecules can tell
us a lot about their structure and function. It can even be used to give
us insights into the process of evolution!
So, we all need to acquire these skills. The question is, how easy can
we make that learning process?
How to Analyse your Orphan Sequences without Having to Struggle with UNIX!
Classically, the analytical software to identify new DNA or protein sequences and to search for homology with known sequences runs on fast computers which often have complicated operating systems like UNIX. For a "wet biologist", interested more in the biology than in the computing, the effort required to gain a working knowledge of such operating systems and to run the programs is often too much. The Internet holds the answer to this problem!The most important tool which makes Biocomputing accessible to all is the World Wide Web (WWW); the Web is a system which allows us to access public information (text, pictures and a lot more) stored on computers around the world with a single easy-to-use browser program. Increasingly, the software needed to analyse sequences (such as the BLAST program for similarity/homology searching -- that is, for looking for DNA or protein sequences similar to one that you are interested in) can be accessed via the WWW using a form-based interface. Basically, all you need to do is to cut & paste your query sequence onto a query form and run the analysis. No need to struggle with obscure system commands or syntax! More and more of these facilities available on the WWW use this kind of "front-end" to make life easier for us; one of the best examples is the Search Launcher at Baylor College of Medicine.
Gaining Knowledge About the Inner Workings of Sequence Analysis Tools
The fact that it is getting easier to analyse sequences via the WWW doesn't substitute for knowing what is the right question to ask! Deciding what analyses to perform and in what order demands some knowledge of how the analytical programs work, their strengths and weaknesses. The Web is perfect for gaining this kind of knowledge! On the internet, you can read our HyperText Coursebook, participate in virtual tutorials (held in BioMOO), talk to the wide range of people involved in the area (including computer scientists, evolutionary biologists, etc.) and attend virtual lectures delivered by some of the leaders in the field. For example, during the last 12 months we have had several lectures from Bill Pearson, who has developed some of the most important software used in sequence analysis.So, here is an invitation to anyone interested in Biocomputing out there on the net. Have a look at the VSNS Biocomputing WWW site and read about our future plans! This will give you an idea of the range of people who have participated in the first two courses, how many disciplines and how many nationalities we come from. We have all learned a great deal and have had a lot of fun. At least our hypertext course book will stay accessible for years to come, even if no new courses ever materialise. But I really hope they do! :-)