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Embnet.News Volume 5 Nr embnet.news Volume 5 Nr. 2 Page 1 embnet.news Volume 5 Nr2 (ISSN1023-4144) June 30, 1998 Two superlative "amateur" projects are this summer moving Editorial into the professional and commercial arenas. Both SwissProt and SRS were started through the vision, This year EMBnet celebrates its tenth anniversary. In the brilliance and high standards of single academic researchers, fast moving field of bioinformatics, you don't have to wait carried on for many years on something less than a 21 years to come of age. Indeed, after 21 years you are almost shoestring and suffered from a series of funding crises. The certainly obsolete. research community including amateur, academic, commercial and multinational came increasingly to Ten years ago, bioinformatics was, for many of us, an appreciate that these were essential tools for their trade. amateur occupation. Amateur, however, only in the sense that the cost of making significant contributions making Now, at least for commercial users, this long free lunch is the financial rewards, if any, very low. I well remember being set to end. There is a report on the development of SIB, told that "a simple FORTRAN program - It'll take you ten which incorporates the Swiss end of SwissProt in this issue. minutes" would provide the analytical tool necessary to crack In contrast to bioinformatics, sequencing has always had an unsolved evolutionary problem. much higher intrinsic costs. In recent years, partly because automation has brought the cost of each sequenced base The days when the whole EMBL DNA database could be down, mega-sequencing projects have become almost printed out on form-feed paper and scanned by eye were standard practice provided the funding was available. before my time, but in 1990 the datasets were still tiny and 'missing data' could be extremely frustrating. Now the Rumour had it that, before TIGR delivered the Haemophilus datasets are enormous: four Encyclopaedia Britannicas' influenzae genome into the public domain, this organism worth of bases in the current EMBL. had been sequenced at least twice, privately, by rival pharmaceutical companies. There is still a role for those simple FORTRAN programs, by now translated into C++ or perl scripts to feel sufficiently In this issue Peter Rice describes how the Wellcome Trust modern, but having available the complete genome sequence has committed substantially more than 100 Mecu to the of many organisms, you can address really big evolutionary Sanger Centre for its human genome sequencing project. questions. And with the complete genome sequence of an Let us hope that genome data is released as quickly as organism you no longer have to worry about any sampling possible to the public domain so that all of us can use it to bias. continue our research, be it applied academic or wholly theoretical. There have also been big changes as to rewards. All of us have friends and former colleagues who now have We have seen how commercial concerns depend upon pure uncountable salaries, horrific workloads and company cars. science in universities and research institutes. If the commercial world fails to nurture the academic community, Contents by making data available, indirectly through tax dollars or Editorial 1 by direct funding or collaboration then this resource will Sequencing UK 2 shrivel up and blow away on the winds of change. Node Focus: ANGIS in Australia 2 Software Development : EMBOSS 6 Software Development : TOPS 7 The embnet.news editorial board: Book Review : Biological Sequence Analysis 11 12 Database and Software Development : The Genome MOT Alan Bleasby Conferences 14 Rob Harper INTERviewNET : Christoph Sensen 15 Node Focus : Swiss Institute of Bioinformatics 16 Robert Herzog Web Wanderer : Real Servers 19 Andrew Lloyd Node News 20 Rodrigo Lopez The EMBnet Nodes 22 Peter Rice embnet.news information 24 embnet.news Volume 5 Nr. 2 Page 2 patent some of these sequences. This venture will not fulfil Press Release 13th May 1998 the aims of the international collaboration of the Human Genome Project, although it will provide complementary Wellcome Trust Announces Major Increase in information. Human Genome Sequencing The Wellcome Trust believes that the human genome should be sequenced, through an international collaboration, as The Wellcome Trust has announced a major increase in its speedily and accurately as possible, with the results being flagship investment in British science in the sequencing of placed immediately in the public domain. To this end, it is the human genome, the book of life. Previously committed to open discussion with existing members of the Human to funding the sequencing of one sixth of the human genome Genome Project with a view to an international agreement at the Sanger Centre, the Wellcome Trust has today decided whereby up to 50% of the genome could be sequenced in to double this to one third. This decision will make available the UK. an additional £110 million over seven years, bringing the total Trust investment in the Human Genome Project to £205 For further information: million. Kate Davey/Noorece Ahmed/Catherine Nestor Wellcome Trust Press Office The Trust is concerned that commercial entities might file Tel: 0171 611 8612/8540/8846 opportunistic patents on DNA sequences. The Trust is Fax: 0171 611 8416 conducting an urgent review of the credibility and scope of E-mail: [email protected] patents based solely on DNA sequences. It is prepared to challenge such patents. The Wellcome Trust is the world's largest charity spending some £250 million annually on medical research. The The Wellcome Trust is the leading European funder of human Wellcome Trust supports more than 3000 researchers, at genome sequencing and has established the Wellcome Trust 300 locations, in 30 different countries - laying the Genome Campus to help achieve this. Its early entry into foundations for the healthcare advances of the next century this work has enabled Dr John Sulston, Director of the Sanger and helping to maintain the UK's reputation as one of the Centre, and his colleagues, to generate one third of all the world's leading scientific nations. As well as funding major sequences which have been produced to date. Todays initiatives in the public understanding of science, the announcement will ensure the maintenance of this position. Wellcome Trust is the country's leading supporter of research The Human Genome Project is one of the most significant into the history of medicine. projects being carried out in scientific research. The aim of the programme is to identify, to a high degree of accuracy, the complete sequence of the human genome and make this data immediately and freely available to the international ANGIS Node focus research community so as to increase the effectiveness of biomedical research at all levels. History & structure This work is vital to • future health ANGIS is Australia's EMBnet node and joined the • the understanding of biology association in 1996. ANGIS (the Australian National • the UK pharmaceutical industry Genomic Information Service; http://www.angis.org.au) is • support the strong UK biomedical science base run from AGIC, the Australian Genomic Information Centre at the University of Sydney. ANGIS was established in 1991 The Human Genome Project is an international project with when the Australian government called for the formation the most substantial funding contributions from the of a National Genomic Information Service. The service Wellcome Trust and the US government. The Sanger Centre has been run from Sydney ever since, although the service and Washington University at St Louis in US have led the is becoming increasingly international collaborative process and through specific decentralised with ANGIS Nodes being established around meetings co-ordinating the Human Genome Project, the country and wider regions. established the international policy of free release of data and putting it in the public domain. A Big Country This week a commercial venture announced its intention to Australia is a large and diverse country. With a surface area produce partial sequences of the human genome, to delay almost as large as the continental USA Australia has, release of this information and to have exclusive rights to however, a population density 14 times smaller. With strong embnet.news Volume 5 Nr. 2 Page 3 Figure 1 Angis Subscribers & Nodes historic, cultural and economic ties to Europe then Australia, significant task as the main server had evolved over 6 years however, sits comfortably as a member of EMBnet, even if and consequently the system was readily portable. ANGIS it is located almost directly opposite on the globe (explaining took this opportunity to re-engineer the entire system (user the bleary eyes Australians have as they travel for >24 hours discs, database organisation and updates, software across a dozen time zones to get to Europe!). Australia is, engineering practices, etc) to allow increasingly efficient however, also part of Asia, increasingly sharing cultural and operation. Further adding to the tasks of the ANGIS Team, economic links with the region. As a consequence, Australia the Node machines are all administered and maintained from is one of the founding members of the fledgling APBioNet a remote location (Sydney). The Melbourne Node was (http://apbionet.angis.org.au), which has broad goals similar launched in 1996 and the Brisbane Node in 1997. ANGIS to EMBnet. also has built a bioinformatics education facility in Melbourne in collaboration with the Howard Florey Institute ANGIS Services which is used for regular courses run in that city. Recently ANGIS has also developed and installed a number of intranet nodes. Distribution - ANGIS Nodes Internet In January 1996 ANGIS was in crisis: Internet traffic bottlenecks between Sydney and outlying regions were ANGIS, like all EMBnet nodes, offers a suite of databases preventing effective delivery of ANGIS's Internet services and software from public and commercial sources.
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