An 'executive summary' of BioinfoTools aims
Answers to frequently asked questions about BioinfoTools
Read Dr. Jacobs' occasional opinion piece
Learn what BioinfoTools is developing
Links, tutorials & free software
Getting in touch with BioinfoTools
Copyrights & liabilities
Quick jump to: BioinfoTools Home page
>> Resources (this page)
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.
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
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.
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
list. While comprehensive for its time, it is starting to show its
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
Let us know! Cythia Gibbs, the co-author of a
bioinformatics textbook with O'Reilly books has written some
("Computers + Biology = Bioinformatics")
for people wishing to get into bioformatics development and deployment. A
(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
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
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
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
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
New Zealand Biotechnology Association
web site includes a
of more than 145 New Zealand companies with interest in the biotechnology
sector in several formats including an
of Biotechnology companies in New Zealand. In addition some more general
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
cluster group, based in Christchurch
(see map), famous for their "high-tech
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.
University of Otago
Centre for Innovation fosters the commercialisation of research (see also
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
Celentis. As a large
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
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
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
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
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.
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.