BioASP Newsletter
Volume 2, Edition 3
February 23, 2004

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Research news

European Virtual Institute receives 12 million Eur
The Commission of the European Union has awarded 12 million Euro to 24 bioinformatics groups based in 14 countries throughout Europe. Intention is to create a pan-European BioSapiens Network of Excellence in bioinformatics. The network is creating a virtual research institute and organizing a European school for training in bioinformatics. The Centre of Molecular and Biomolecular Informatics (CMBI / KUN) is project partner in this consortium and will cooperate closely with the Netherlands Bioinformatics Centre (NBIC). As genome-sequencing efforts continue rapidly, biologists are literally drowning in a sea of data. Bioinformatics is trying to keep up and is also contributing to the information overload. The infrastructure between computational biologists and experimentalists needs to be improved. The Commission of the European Union has developed new instruments as part of its sixth Framework Programme (FP6). This Framework Programme is the EU`s main means of   funding research in Europe. One of these instruments, the "Network of Excellence" (NoE), is designed to tackle the fragmentation of European research by creating durable structures for future research in certain priority areas, including life sciences, genomics and biotechnology for health.
(Source: EMBL, 23-01-2004)
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Silico analysis of complete bacterial genomes
Scientists of the Erasmus Medical Center have developed a website, in silico, which runs a software program that performs three basic tasks in completely sequenced bacterial genomes by in silico analysis: AFLP-PCR, PCR amplification and endonuclease restriction. Theoretical AFLP-PCR analyzes similar parameters, and includes a suggestion tool providing a list of commercial restriction enzyme pairs yielding up to 50 amplicons in the selected genome. For PCR, after selection of the genome and introduction of primers, fragment size, DNA sequence and corresponding ORF identity of the resulting PCR product is computed. Plasmids of sequenced species may be included in the analysis. Endonuclease restriction calculates the number of restriction sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, PFGE image and restriction maps are illustrated. Other tools in this site are ORF search by name and DNA to protein translation as well as restriction digestion of user-defined DNA sequences. In this issue of Bioinformatics, Marijke van Baren and Peter Heutink (Dept. Clinical Genetics, Erasmus Medical Center) comment on the web application PCR suite. This is an extension of the primer design program Primer3. It allows the design of primer sets encompassing SNPs, all exons of a single gene, all open reading frames in a list of cDNAs or the creation of overlapping PCR products.
(Source: Bioinformatics, 29-01-2004)
(http://www.in-silico.com)
(http://www.eur.nl/fgg/kgen/primer)
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Biotechnology:Back to the Future?!
The congress is organized for the members of the Netherlands Biotechnological Society and those who are interested in biotechnology. It focuses on the latest developments and challenges in biotechnology. Besides that it aims to create a stimulating environment were science, business and society can meet. The program is divided into 4 parallel sessions and features three workshops. The sessions address major biotechnological business sectors, important developments and other emerging areas of general interest and importance. These include Bioinformatics & Database management, Downstream Processing, Biopharmaceuticals and Neutraceuticals, -'Omics', Fermentation Technology & Biocatalysis, Metabolic Engineering, Environmental & Sustainable Biotechnology and Agro/Food Biotechnology. The topics of the workshops are BIO-Starters, Public Aspects and Biotechnology in the 3rd World.
(Source: Chemisch Weekblad/NBV, 17-01-2004)
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Chemotherapy or no chemotherapy
Agendia plans to independently develop microarray-based tests for various diseases based on gene expression profiles. Such diagnostic tools could enable higher quality clinical management for cancer patients. Agendia was formed last year by researchers from the Netherlands Cancer Institute (NKI) in Amsterdam who co-authored a set of landmark studies reported last year in the New England Journal of Medicine and Nature. NKI, together with Rosetta Inpharmatics, a subsidiary of Merck & Co, conducted the original breast cancer research using custom microarrays from Agilent Technologies and archived tissue samples. They identified gene expression signature patterns that correlate to aggressive tumors and those tumors less likely to spread. While further research is necessary, the study concluded that gene expression information has the potential to assist physicians in determining which patients may benefit from follow-up chemotherapy and which patients could possibly forego it, thereby reducing the amount of unnecessary adjuvant chemotherapy. Agendia aims to become the leading global gene expression profiling service. Founders of Agendia think they need about 8 million Euro to get profitable. This is not much for a biotech start-up. It is probably the first start-up firm that was able to start a research practice-test within a few months after the foundation. Normally the climate is very difficult for start-ups. Rene Bernards, one of the founders, is dissatisfied with the level of support from the Dutch Government. "At first I was surprised by the amount of help for starters, but soon you lose yourselve in the terrible bureaucracy", says Bernards.
(Source: NRC Handelsblad, 31-01-2004)
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Professor Ritsert Jansen gets Vici-subsidy
In the field of bioinformatics Ritsert Jansen of the University of Groningen (RUG) received a Vici-subsidy of 1.25 million from NWO. The Netherlands Organisation for Scientific Research (NWO) has granted 26 excellent scientists a so called Vici-subsidy. Every scientist receives in total a maximum of 1,250,000 euro. With this he or she has to build up a research group. The Vici-subsidy is meant for very skilled and experienced scientists who successfully developed a new research program. They belong to the best 10% of their research field. Besides that they have proved to be able to coach young scientists. Jansen works together with researchers to think along during the entire stage, from the scheme of experiments to data-analysis. He is trying to bring together two separate worlds: classic genetics and genomics. Untill now genomics was often focusing on a few individuals because of the expensive techniques, however this is changing and it is now possible to map DNA activity of entire pedigrees.
(Source: Chemisch Weekblad/RUG/NWO, 31-01-2004)
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New subsidy scheme from Ministry of Ecomic Affairs
From January 1st 2004 there is a new subsidy scheme 'Innovatiesubsidie Samenwerkingsprojecten' which focuses on promoting cooperation in the field of research and development. Companies and public knowledge institutions are being stimulated and facilitated to cooperate on a national or international level. By using each others knowledge and skills companies are able to improve their position and stand up to competitors. The scheme has to contribute to a durable economic growth by consolidating the innovation power of the Dutch economy. In 2004 the budget of the subsidy scheme is about 80 million euro. For research and/or development projects applies a maximum subisy 2 million euro per project. The subsidy percentage for research is 50%, for development 25%. The new scheme replaces the existing ones: Technologische Samenwerking (TS), Technische Ontwikkelingsprojecten (TOP) and Economie, Ecologie & Technologie (EET). To raise the effectivity, these schemes are streamlined in the 'Innovatiesubsidie Samenwerkingsprojecten'. Projects are considerable in case of clear innovation, good economic perspectives, technological perspectives and contribution to durable economic growth. From March 1st technological innovative companies are able to appeal at Senter.
(Source: Senter/EZ, 31-01-2004)
(http://www.senter.nl/samenwerking)
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Research lab for informatics
The Technical University Eindhoven (TU/e) has started a research lab for informatics. The lab will bridge the gap between the need of quality software in the industry and the theoretically oriented research from universities. This so-called LaQuSO (Laboratory for Quality Software) has been placed at the Department of Mathematics and Computer Science of the TU/e. The lab will cooperate with the industry to convert academic knowledge into methods and tools for detecting errors in products of the industry rapidly. For universities this means that research will be extended with empirical studies. The lab mainly focuses on quality of software. When quality of the software is authorized, such products will receive a quality mark. Founders of the lab hope it will soon grow to one of the most leading academic institutions for quality software in Europe.
(Source: Onderzoek Nederland/TU Eindhoven, 30-01-2004)
(http://www.laquso.com)
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Galapagos receives grant for Alzheimer research
Galapagos Genomics has been awarded by the IWT (The Flemish Institute for the Promotion of Industrial Scientific-Technological Research) a Euro 1.4 million technology development grant in Belgium for Alzheimer`s Disease research. The IWT grant enables Galapagos to expand discovery activities in one of their core disease areas. They will build of Alzheimer`s Disease relevant assays using neuronal cells and will use these in combination with its adenoviral based target discovery platform. Functionally identified and validated targets will lead to drug discovery programs that ultimately will be partnered with pharmaceutical companies to develop new Alzheimer`s disease therapeutics. Alzheimer`s disease is a neurological disorder clinically characterized by the progressive loss of intellectual capacities leading to cognitive impairment and ultimately to full dementia. New insights into the underlying Alzheimer's disease processes as well as new treatments are urgently required to treat the disease. Galapagos Genomics is a discovery company focused on the rapid identification and validation of disease modifying drug targets by functional screening in human disease models. Galapagos was founded in 1999 by Crucell and Tibotec to exploit Crucell`s unique PER.C6TM technology for target discovery.
(Source: Stockwatch, 12-02-2004)
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Wageningen researcher head of CGIAR programme
Dr Theo van Hintum, who works for the Centre for Genetic Resources (the Wageningen genebank), will head an international research programme intended to make genebank material quickly available to developing countries. The programme is financed by CGIAR, the umbrella organisation consisting of a network of international agricultural research institutes that make scientific knowledge available to developing countries. Van Hintum will go in search of methods for identifying drought-resistant plant varieties. His search will take the form of a pilot project to develop techniques to help researchers locate starting material quickly in large genebanks for use in developing new varieties. The change from financing institutes to financing research programmes enables CGIAR to involve external universities and research institutes in the work it does. By strengthening relations with important centres of research CGIAR hopes to gain quicker access to recent scientific knowledge. The programme will have an annual budget of 16 million. Van Hintum will head one of the five sub-programmes in the project.
(Source: Wisp'r, 12-02-2004)
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BioASP news

Spotfire Course
BioASP organises a hands-on training on Spotfire DecisionSite. Spotfire DecisionSite for Functional Genomics is a comprehensive data analysis and visualisation application for gene expression data. The course is meant for people who have a BioASP Spotfire licence and others who are interested in using this micro array analysis tool. A teacher from Spotfire will fly in to give this one-day training.

The course is organised on March 8 (from 11:00 till 18:00 hours) in Amsterdam for € 275,- per person. You can apply by sending a message to rauwerda@science.uva.nl with your name and contact information before 27th of February. The course has a maximum number of 12 participants, so please reply quickly when you are interested in this course.
(Source: BioASP)
(More information?)
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Thesauri and ontologies for genes and biomedical topics
On February 25 the BioASP Interest Group Textmining will organize a meeting about thesauri and ontologies at Erasmus MC, Rotterdam, Josephine Nefkens Institute. Focus of the meeting is on the inventory of thesauri and onthologies in use by other participants and the relevance of some. Besides that, building thesauri and onthologies, development issues and solutions will be discussed. At last the need and approach for future cooperation will be discussed. Participating organsiations in this meeting are: Universities of Maastricht, Rotterdam, Nijmegen and Amsterdam, TNO TPD, Organon, Collexis, Oracle, Language and Computing, Knowledge concepts etc.
(Source: BioASP Interest Group Textmining, 11-02-2004)
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Blast the genome
Another service was added to the BioASP service platform on January 23rd: Genome Blast. Compare your sequence to genomic sequences and their gene products, using our superfast dBlast. Both the flavors BlastN and TBlastN are available. On a familiar web interface, you can specify specific search parameters, and output options, and you can search -at the moment- genomes of the human, the mouse, and/or the rat. You cannot specify a single chromosome - using dBlast on the supercomputer, specifying a chromosome likely takes longer than Blast on the whole genome itself! If you want other genomes or builds just give us the word and if they are available, we will make them available for you.
(Source: BioASP)
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Protein World Vibrations

Good vibrations during a meeting last Wednesday February 11th at Organon in Oss with the first batch of Protein World users and representatives from Gene-IT and BioASP. According to project coordinators Peter Groenen and Jaap Nieuwenhuis, serious steps are now being taken towards establishing Protein World firmly among the Dutch research community.

Users from the Amsterdam, Leiden and Rotterdam Medical Centres and the Universities of Wageningen and Nijmegen indicated that they envisage serious angles for using the PW data in their research. Two concrete research projects involving PW were presented during the meeting.

Protein World (PW) is a BioASP research activity building on the results from the Grand Challenge computation performed in 2002 at SARA. The project has resulted in a service that provides a wide range of Life Sciences researchers access to both the raw data from this computation, and the advanced analyses drawn from these data.

(Source: BioASP)
(More information?)
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Users Forum Calender

BioASP values your opinion on our services. The Users Forum meetings are held every month and organised along some thematic lines, like micro array, textmining, comparative genomics and others, in such a way that every line has quarterly meetings. Aim of the Users Forum meetings is to provide a large user group with relevant information about (upcoming) services and learn from user experiences, and - more important - gather feedback about the (potential) use of our services, in order to improve our service package. The users forum is an open initiative and welcomes everybody who is interested in the use of our bioinformatics services. Please join the Users Forum and participate in one of the upcoming events:

February 2004
Text mining: "Thesauri & Ontologies"

March 2004
Training Rosetta

April 2004
Text mining for Micro Array experiments
Rosetta experiences: users for users

May 2004
Proteomics or Pathways (dep. on input)

June 2004
Micro array and  Biostatistics (dep. on input)

Section BioASP news gives the exact date and Programme of these meetings.

(Source: BioASP)
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Metabolic Pathways
BioASP service platform allows you to search through pathway databases (pathway, lenzyme, lcompound) with the application SRS. These pathway-databases are part of KEGG (Kyoto Encyclopedia of Genes and Genomes). Do you use these databases? And are they sufficient for your research? What other tools or databases do you (want to) use for your research? Are you familiar with GenMAPP (Gene Micro Array Pathway Profiler)? What is your opinion about this tool?
A lot of questions we could discuss during a users forum meeting. A meeting for people who are interested in pathway visualisation and analysis. Would you be interested in such a meeting? Please join the online discussion on www.bioasp.nl to let us know!
(Source: BioASP)
(www.bioasp.nl)
(www.genmapp.org)
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ISMB/ECCB 2004 - Glasgows
In 2004 - for the first time ever - Intelligent Systems for Molecular Biology (ISMB) will be held jointly with the European Conference on Computational Biology (ECCB). Glasgow is between July 31 and August 4 the place to be when you want to hear the latest news about bioinformatics and to extend your international network. The emphasis of the conference will be on biological and biomedical applications of bioinformatics.
BioASP will participate in this international bioinformatics event and demonstrate the Dutch bioinformatics application service provider. We consider organising a special event for Dutch guests of the conference in Glasgow. Therefore we need to know how many people are planning to visit the ISMB/ECCB 2004. If you have not yet replied to our e-mail about this topic, please send an e-mail to info@bioasp.nl with subject "ISMB/ECCB 2004" to let us know if your will visit the conference.
(Source: BioASP)
(www.iscb.org/ismbeccb2004)
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New discussions on the BioASP discussion forum!

Biomedical researchers were used to studies with a few endpoints and several replicates. Now, with microarrays, they conduct studies with thousands of endpoints - but no replicates. So they have to turn to new methods in statistics - but are good statistical methods available? In the present 'publish or perish' culture, can they afford to spend time, getting acquainted with the statistical theories that apply in the new situation? Can they evaluate - and use - the new statistical tools that are necessary, and being developed? And, not only 'can they', but: do they? Biological and biomedical researchers tended to regard statistics as a necessary evil, boring and dull, and statisticians were people to be avoided, mostly boring you with figures that in their opinion explained why your study was incorrect. A cordial collaboration between biomedical researchers and staticticians has never been realised, but should exist in this time of microarrays. Are there enough statisticians involved in bioinformatics? Also, is research on the application of statistics on microarrays sufficiently respected that statisticians can 'publish', and not 'perish'? Or are we in peril that, in the rush to publish, there is no time for analysis, because 'analyse and be penalized'?

Give your optinion, join the discussion on www.bioasp.nl > Tab Community > Enter the forum as a registered user.
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(Source: BioASP)
(www.bioasp.nl)
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This email-service is a monthly news service from Stichting BioASP aiming to inform participants and other interested parties about national and international developments in bioinformatics, genomics and related topics. For all your requests concerning this news service, please do not hesitate to contact us. Your feedback is always welcome and appreciated.
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