Links

Below are a very limited number of links to useful internet sites for bioinformatics. This list is deliberately short: some of the more comprehensive lists are quite overwelming.

• The European Bioinformatics Institute near Cambridge, England, is an outstation of its German counterpart based at Heidelberg. Its site contains comprehensive and current links to the bioinformatics world.
• It is interesting to note the take up of bioinformatics in the commercial computer sector including those listed below. The quickest way to find material on these sites is to the use the quick search boxes, usually located near the top of the pages.
  • IBM
  • Compaq (now merged with Hewlett Packard)
  • Apple Computer
  • Sun Life Sciences section
  • Hewlett Packard
• A reasonable starting point for browsing the bioinformatics world is the Harvard BioLinks page. More comprehensive lists can be found, but the main sites can be quickly reached from this site.
• Another starting point is bioinformatics.org. This site contains a number of tutorials and an FAQ with useful links to newcomers. Those looking for free software, might check out the Projects page.
• A reasonably recently updated list of bioinformatics databases and tools maintained by Johan Robben may be a useful alternative starting point for some.
• A more comprehensive list (very comprehensive) is BioCatalog at the European Bioinformatics Institute. While comprehensive, the entries are in ASCII database format, which makes for difficult reading "by eye". At the time of writing this was last updated in July 2000.
• The Biocomputing Group of the Whitehead Institute maintains a well-designed site with links to many WWW-based tools. (These elaborate pages can try user's patience if they are opened on a slow connection or older computer however...)
• Historically "the" Bioinformatics research source list has been Pedro's list. While comprehensive for its time, it is starting to show its age.

Tutorials

Tutorials can be found by using the links listed above. If there is sufficient demand, direct links to a small number of tutorials will be placed here. Let us know! Cythia Gibbs, the co-author of a bioinformatics textbook with O'Reilly books has written some introductory comments ("Computers + Biology = Bioinformatics") for people wishing to get into bioformatics development and deployment. A related article (Why Biologists Want to Program Computers) by James Tisdall can be found on the same website.

Most of observations in these articles will be agreed to by most bioinformatics / computational biology researchers/developers, but be open-minded! These are personal observations and O'Reilly is a strong supporter of Open Source software (BioinfoTools has nothing any against either, but has a lot against lack of open-mindedness!). Others will have different ideas on a few of Cythia's points. James' article has a definite bias in favour of the Perl programming language (programmers can get rather zealous about their favourite programming language) and Cythia's article is ironically titled with one of the "myths" tackled in the first rumination column of this site (although I suspect she'd agree with what is written there). Some of the issues raised in these articles might be dealt with in a later Ruminations column.

A wide range of books on bioinformatics is now available, including at internet bookstore such as Amazon, Barnes and Noble, FatBrain, DA Direct and the like. If you are looking for course recommendations, you are welcome to send email queries to gjacobs@bioinfotools.com

Software

Free molecular biology software elsewhere on the internet

A large amount of free (or cheap) bioinformatics software is available via searching the WWW or using the links listed above. Commericial users should take care to note any restrictions on commercial use: many "academic" software packages now have license arrangments for commercial use. An appeal to sense: would academics please consider smaller players and independent scientists when making up these commercial-use licences - many seem to think the world is only made of vast multi-national firms.

A short list of useful free (or cheap) tools for bioinformatics on small Unix-based computers (ie. Mac OS X, Linux, etc.) may be listed here at a later date. These will be tools restricted those of interest to BioinfoTools.

Free software available from BioinfoTools

Some of the software Dr. Jacobs has developed in the past may be made available here at no cost or at an arbitrary price to cover distribution costs. In general, these products are not maintained as such (or at best whimsically), nor is support offered for them. They are to be used on a "as is" basis. Most of these tools are designed to run on Unix-based systems. Basic documentation will be supplied. Please do read the documentation before making any queries. In order to download these products you'll need to register first. Registration also enables you to optionally receive email advance notices about BioinfoTools products.

At present no software is available on-line. If you register, you will be informed when software is made available. To register, use the the inquiry form, setting the inquiry type to indicate that you wish to register for downloads, etc.

New Zealand biotechnology companies

Below are links to a few companies in the biotechnology area in New Zealand. To see a more complete list of companies, see the links in the first item below. The targets of companies' research range from human diseases and cancer to forestry and agriculture, reflecting traditional strengths in the New Zealand research industry. BioinfoTools is in direct contact with many of the companies listed below. As you can see, New Zealand has a quite active biotechnology sector!

Clusters

• The New Zealand Biotechnology Association web site includes a directory of more than 145 New Zealand companies with interest in the biotechnology sector in several formats including an alphabetic list of Biotechnology companies in New Zealand. In addition some more general biotechnology-related links are also provided.
• BioinfoTools is a member of the local biotechnology cluster, bioSouth. A directory of local biotechnology companies is available as a PDF file from this site, as is a brochure about the bioSouth cluster.
• Another nation-wide biotechnology portal is bioTENZ, bringing together leading New Zealand providers of biotechnology, natural products, pharmaceutical and biological products and services.
• BioinfoTools is also a member of the highly pro-active Canterbury Software cluster group, based in Christchurch (see map), famous for their "high-tech barbeques"!

Companies

• Pacific Edge Biotechnology Ltd., founded in 2001, is based in Dunedin (the location of BioinfoTools) at the University of Otago's Center for Innovation. This company has arisen from Professor Tony Reeve, Drs. Parry Guildford and Dr. Ian Morison and colleagues at the Cancer Genetic Centre at the University of Otago, of which Dr. Jacobs (founder of of BioinfoTools) was a member. Their work includes bioinformatics.
• The University of Otago Centre for Innovation fosters the commercialisation of research (see also press release)
• Global Technologies Ltd. is a private company with a range of biotechnology interests, in particular those related to meat by-products.
• AgResearch is a Crown Research Institute based at several locations in New Zealand, including Mosgiel, twenty minutes from BioinfoTools by road. AgResearch also has a commercial arm, Celentis. As a large company their biotechnology interests are diverse with an agricultural focus. Broad aims include the animal feed, human food and animal and human pharmaceutical interests. Work includes cattle and sheep genomics. Their national bioinformatics facilities are based at the local centre and BioinfoTools is in contact with their staff.
• Ovita is a consortium formed from AgResearch, Meat New Zealand and the New Zealand Wool Board which funds research with an agricultural focus.
• Genesis Research and Development Ltd. is a major public company based in Auckland and a pioneer for biotechnology in New Zealand. Founded a decade ago under the helm of Jim Watson, the company has grown to include a range of in-house research programmes including psoriasis (yielding a drug, PVAC, currently in in phase III clinical trials with international partners), genomics, sequence tag analysis and bioinformatics. Genesis has strong links with other companies in the biotechnology sector in New Zealand and overseas.
• Two more recently-founded Auckland-based companies are Via Lactia Biosciences and Neuronz. Neuronz's research is reflected in its name, being issues related to nerve cell death and the central nervous system. ViaLactia Biosciences is based on the dairy industry. Its programmes include genomics of cattle, their pastural food and their ruminant bacteria. An in-house bioinformatics program supports this work.
• The genomics genetics and bioinformatics of trees used in the timber and paper industries are among the projects tackled by Forest Research. This work is in collaboration with Signagen, whose focus is molecular breeding solutions for a wide range of forestry and agricultural species.
• Black Albatross is a high-end consulting firm based at the University of Otago, who have been reviewed on the Apple web site.

Selected bioinformatics conferences in the Asia/Pacific region

Below are listed some of the up-coming conferences in the region that may be of interest to readers. This is not a comprehensive list. Meeting organisers are welcome to recommend meetings to place on this page via the the inquiry form.

• Recently held was theBioinformatics 2002, conference at Merchant Court Hotel, Sydney, 21-22 October 2002. (Search for 'bioinformatics' once you have the conference organiser's home page open.)
• On the North Pacific rim at San Diego is is O'Reilly books second Bioinformatics Technology Conference on February 3-6th. Well-supported, but intended participants should note its slant towards the technology used in bioinformatics rather than perhaps the science behind it. (See the first ruminations column.)
• Pacific Symposium on Biocomputing 2003. PSB will be held on the Island of Kauai, Hawaii, on January 3-7th, 2003. This meeting has been run since (at least) 1996.
• The First Asia-Pacific Bioinformatics Conference, February 4-7th, 2003. Pass through New Zealand and take in the NZ conference and scenery while you're in this part of the world! (See next meeting listed.) This meeting is part of a related collection of meetings including the The Fourteenth Australasian Database Conference. All are held in Adelaide.
• NZ Bioinformatics Conference, Te Papa, Wellington. February 13-14 2002.