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European Virtual Institute receives 12
million Eur
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| 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
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| 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?!
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| 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.
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(Source: Chemisch Weekblad/RUG/NWO,
31-01-2004)
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New subsidy scheme from Ministry of Ecomic
Affairs
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| 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
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 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
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| 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
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| 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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Spotfire Course
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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. |
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(Source: BioASP)
(More
information?)
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Thesauri
and ontologies for genes and biomedical
topics
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| 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. |
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(Source: BioASP Interest Group
Textmining, 11-02-2004)
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Blast
the genome
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| 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. |
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(Source: BioASP)
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Protein
World Vibrations
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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. |
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(Source: BioASP)
(More information?)
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Users
Forum Calender
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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. |
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(Source: BioASP)
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Metabolic Pathways
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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! |
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(Source: BioASP)
(www.bioasp.nl)
(www.genmapp.org)
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ISMB/ECCB 2004 -
Glasgows
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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.
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(Source: BioASP)
(www.iscb.org/ismbeccb2004)
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New
discussions on the BioASP discussion
forum!
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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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