Nabble - Bio.net - Embl-db

EMBL-Bank Release 102 is ready

2009-12-15T06:22:54Z

Release 102 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

Please try to use these mirror sites for download.
Following sites are not ready at the moment but will be within next couple of days.

ftp://ftp.cbi.pku.edu.cn/pub/databases/embl/ (China)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 102 data at Thu, 26-NOV-2009 11:43:20.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 102 building process has started

2009-11-26T06:51:34Z

We have begun the process of building release EMBL Release 102 building
process has started of the EMBL Nucleotide Sequence Database on Thursday
26th Nov 2009.

Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 102 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r102u064.dat.gz
The subsequent update file will contain post-release 102 data and be named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r103u001.dat.gz as usual.

Cumulative update:
The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 102 is built and is
publicly available - we expect that to be around 15th Dec 2009.
see
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
European Nucleotide Archive team
EMBL-EBI

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EMBL-Bank Release 101 is ready

2009-09-10T05:15:41Z

Release 101 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://ftp.cbi.pku.edu.cn/pub/databases/embl/ (China)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)

Please try to use these mirror sites for download.
Note that crc_gz.txt file is updated on 10 Sep and will be mirrored
within next 24 hours.
Following site is not ready at the moment but will be within next day.

ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 101 data at Fri, 28-AUG-2009 07:23:18.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 101 building process has started

2009-08-28T05:26:23Z

We have begun the process of building release EMBL Release 101 building
process has started of the EMBL Nucleotide Sequence Database on Friday
28th Aug 2009.

Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 101 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r101u076.dat.gz
The subsequent update file will contain post-release 101 data and be named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r102u001.dat.gz as usual.

Cumulative update:
The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 101 is built and is
publicly available - we expect that to be around 15th Sep 2009.
see
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL Databank
EMBL-EBI

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CFP: SWAT4LS 2009 Semantic Web Applications and Tools for Life Sciences

2009-08-07T05:13:58Z

Apologies for possible multiple posts
-----------------------------------------------------

First CFP: SWAT4LS Semantic Web Applications and Tools for Life Sciences 2009

***Location and date
Amsterdam, Science Park, November 20th 2009
(http://www.swat4ls.org/2009/)

***Rationale

The adoption of semantic-enabled applications and
collaborative social environments is ever more
common in the Life Sciences. The Semantic Web
provides a set of technologies and standards that
are key to support semantic markup, ontology
development, distributed information resources
and collaborative social environemnts. Altogether
the adoption of the Semantic Web in the Life
Sciences has potential impact on the future of
publishing, biological research and medecine.
This workshop will provide a venue to present and
discuss benefits and limits of the adoption of
these technologies and tools in biomedical
informatics and computational biology. It will
showcase experiences, information resources,
tools development and applications. It will bring
together researchers, both developers and users,
from the various fields of Biology,
Bioinformatics and Computer Science, to discuss
goals, current limits and some real use cases for
Semantic Web technologies in Life Sciences.

***Topics

Topics of interest include, but are not limited to:

* Standards, Technologies, Tools for the Semantic Web
o Semantic Web standards and new proposals (RDF, OWL, SKOS,... )
o Biomedical Ontologies and related tools
o Formal approaches to large biomedical knowledge bases
* Systems for a Semantic Web for Bioinformatics
o RDF stores, Reasoners, query and
visualization systems for life sciences
o Semantic biomedical Web Services
o Semantics aware Biological Data Integration Systems
* Existing and prospective applications of the Semantic Web for Bioinformatics
o Semantics aware application tools
o Semantic collaborative research environments
o Case studies, use cases, and scenarios

***Scientific Committee (committed so far)

* Christopher J. O. Baker, Department of Computer
Science and Applied Statistics, University of New Brunswick, Saint John, Canada
* Pedro Barahona, Department of Informatics, New
University of Lisboa, Lisboa, Portugal
* Liliana Barrio-Alvers, Transinsight GmbH, Dresden, Germany
* Olivier Bodenreider, National Library of
Medicine, Bethesda, United States of America
* Matt-Mouley Bouamrane, School of Computer
Science, University of Manchester, Manchester, United Kingdom
* Werner Ceusters, NY CoE in Bioinformatics and
Life Sciences, University at Buffalo, Buffalo, United States of America
* Kei Cheung, Center for Medical Informatics,
Yale University School of Medicine, New Haven, United States of America
* Tim Clark, Center for Innovative Computing,
Harvard University, United States of America
* Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France
* Olivier Dameron, INSERM U936, University of Rennes 1, Rennes, France
* Michel Dumontier, Carleton University, Ottawa, Ontario, Canada
* Huajun Chen, Zhejiang University, Hangzhou, China
* Duncan Hull, School of Chemistry, University of
Manchester, Manchester, United Kingdom
* C. Maria Keet, Faculty of Computer Science,
Free University of Bozen-Bolzano, Bolzano, Italy
* Graham Kemp, Chalmers University of Technology, Sweden
* Jacob Tilman Koehler, Department of Molecular
Biotechnology, Institute of Medical Biology,
University of Tromsö, Tromsö, Norway
* Michael Krauthammer, Department of Pathology,
Yale University School of Medicine, United States of America
* Martin Kuiper, Department of Pathology, Systems
Biology group, Department of Biology, Norwegian
University of Science and Technology, Trondheim, Norway
* Patrick Lambrix, Department of Computer and
Information Science, Linköping University, Linköping, Sweden
* Phillip Lord, School of Computing Science,
Newcastle University, Newcastle-upon-Tyne, United Kingdom
* M. Scott Marshall, Leiden University Medical
Center / University of Amsterdam, Amsterdam, The Netherlands
* Chris Mungall, Lawrence Berkeley National
Laboratories, United States of America
* Stephan Philippi, Institute for Software
Technology, University of Koblenz-Landau, Koblenz, Germany
* Marco Roos, Instituut voor Informatica,
University of Amsterdam, Amsterdam, The Netherlands
* Alan Ruttenberg, Science Commons, Cambridge, United States of America
* Matthias Samwald, DERI, Galway, Ireland, and
Konrad Lorenz Institute for Evolution and
Cognition Research, Altenberg, Austria
* Nigam Shah, Center for Biomedical Informatics
Research, Stanford, United States of America
* Michael Schröder, Biotechnology Centre, TU Dresden, Dresden, Germany
* Robert Stevens, School of Computer Science,
University of Manchester, Manchester, United Kingdom
* Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama, Japan
* Mark D. Wilkinson, iCAPTURE Center, St. Paul Hospital, Vancouver, Canada

and the organizers

***Type of contributions

The following possible contributions are sought:

* Oral communications (regular papers)
* Posters
* Software demos

All accepted oral communications and posters will be published with
CEUR-WS.

***Deadlines

* Submission openinig: 1 September 2009
* Submission of oral communications: 28 September 2009
* Submission for posters and demos: 15 October 2009
* Communication of acceptance: 23 October 2009
* Camera ready: 6 November 2009

***Instructions

All papers and posters must be in English and
must be submitted through the EasyChair review
system at http://www.easychair.org/conferences/?conf=swat4ls-09 .
Please upload all submissions as PDF files in
LNCS format (see http://www.springer.de/comp/lncs/authors.html).
To ensure high quality, submitted papers will be
carefully peer-reviewed by at least three members of the Scientific Committee.

* Submissions for Oral communications should be between 10 and 15 pages.
* Posters submissions should be between 4 and 8 pages.
* Software demo proposals should also be between 4 and 8 pages.

***Proceedings

All accepted oral communications and posters will
be published with the CEUR-WS.org Workshop
Proceedings service (see http://ceur-ws.org/).
We are in the process of negotiating the
possibility to have a special issue of a major
bioinformatics journal related to the 2009
edition of swat4ls. To this end, a special Call
will be launched shortly after the workshop, for
extended and revised versions of contributions
submitted to the workshop and accepted either as oral communication or poster.

***Organization

* M. Scott Marshall, Leiden University Medical
Center / University of Amsterdam, The Netherlands
* Albert Burger, School of Mathematical and
Computer Sciences, Heriot-Watt University, and
Human Genetics Unit, Medical Research Council,
Edinburgh, Scotland, United Kingdom
* Adrian Paschke, Corporate Semantic Web, Freie Universitaet Berlin, Germany
* Paolo Romano, Bioinformatics, National Cancer
Research Institute, Genova, Italy
* Andrea Splendiani, Biomathematics and
Bioinformatics dept., Rothamsted Research, UK

-----------
For any further information or clarification,
please visit the website at
http://www.swat4ls.org/2009 or contact the
organization by email at info @ swat4ls.org

Paolo Romano (paolo.romano@...)
Bioinformatics
National Cancer Research Institute (IST)

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EMBL-Bank Release 100 is ready

2009-06-15T02:42:04Z

Release 100 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://ftp.cbi.pku.edu.cn/pub/databases/embl/ (China*)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)

Please try to use these mirror sites for download.
*: Note the chinese mirror site address has changed.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 100 data at Fri, 29-MAY-2009 07:58:42.

Thank you for your support for the EMBL Nucleotide Sequence Database,
aka EMBL-Bank, to see our 100th release.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL File Server News No. 4, March 21st 1991

2009-06-08T17:20:22Z

Dear Sir/Madam,

I need ClustalW 1.83 source code for my research and couldn't get it by the automatic email.

Could you please let me know how can I get the source code?

Thanks,

Elham,

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EMBL Release 100 building process has started

2009-05-29T04:45:28Z

We have begun the process of building release EMBL Release 100 building
process has started of the EMBL Nucleotide Sequence Database on Friday
29th May 2009.

Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 100 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r100u076.dat.gz
The subsequent update file will contain post-release 100 data and be named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r101u001.dat.gz as usual.

Cumulative update:
The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 100 is built and is
publicly available - we expect that to be around 15th June 2009.
see
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL Databank
EMBL-EBI

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Embl-db mailing list
Embl-db@...
http://www.bio.net/biomail/listinfo/embl-db

CFP NETTAB 2009: deadline approaching

2009-04-24T10:30:08Z

Dear colleagues,

I would like to inform you about next NETTAB 2009
workshop, whose focus topic could be of your interest.

The focus theme, indeed, is "Technologies, Tools
and Applications for Collaborative and Social
Bioinformatics Research and Development".
The workshop will be held in Catania, Sicily, on June 10-13, 2009.
I attach here below the Call for papers.

Please spread this announcement to your network.
Best regards. Stefania Parodi
on behalf of NETTAB 2009 Organizing Committee

===

Last Call for Papers

NETTAB 2009 Workshop on
"Technologies, Tools and Applications for
Collaborative and Social Bioinformatics Research and Development"
with a Special Session on:
"Methods and Tools for RNA Structure and Functional Analysis"

June 10-13, 2009
Department of Computer Science, University of Catania, Italy

http://www.nettab.org/2009/

Deadline approaching: April 28, 2009: Oral communication submission
Contributions must be short papers of around
THREE A4 pages or 12.000 characters long.
Submit through the EasyChair system at:
http://www.easychair.org/conferences/?conf=nettab2009 .
See web site for details.

Motivation
The most recent developments of collaborative
development tools are impressive. Researchers can
now collaboratively develop software (open source
systems), discuss and compare development
strategies (social networks), write documents
(google docs, wiki systems), build knowledge
bases. So, it may now be the time for presenting
current technologies, tools and applications for
collaborative work and for discussing
perspectives of their utilization in support of Bioinformatics.
For these reasons, NETTAB 2009 will be devoted to
"Technologies, Tools and Applications for
Collaborative and Social Bioinformatics Research and Development".
The RNA community is also taking advantage of
collaborative research tools such as Wikis and
other virtual environments. The RNA WikiProject
contains now over 600 articles describing
families of noncoding RNAs based on the Rfam
database, and invite the community to update,
edit, and correct those articles. Therefore, the
NETTAB 2009 special session will focus on
collaborative research project, computational
methods and tools for the analysis of RNA
structures and functions, with a special emphasis on ncRNAs.

Invited Speakers (more to be announced)
# Alex Bateman
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
# Tim Clark
Director of Informatics, MassGeneral Institute
for Neurodegenerative Disease Neurology Research
Department, Massachusetts General Hospital, Boston, USA
# Duncan Hull
School of Chemistry, University of Manchester, Manchester, UK
# Gabriel Valiente
Technical University of Catalonia, Department of Software, Barcelona, Spain
# Debora Marks
Systems Biology Department, Harvard Medical School, Boston, USA

Topics
- Collaborative Web sites (bioinformatics.org, biojava, bioperl, )
- Communities of Practices (CoPs)
Scientific practices in scientific communities
Automatic detection / gathering / modelling of scientific practices
Implementations of CoPs
- Social networking (myExperiment, Annotea, myScience)
Social Bookmarking
Semantic Document Markup
Relationships mining from literature
- Open Source development
Sharing of data models, libraries, interfaces
- Social software for collaborative documentation development
Wikis, blogs, google docs
Knowledge Wikis
Social-software-mediated collaborative scientific research
Social-software-mediated collaborative tools' development
Knowledge base collaborative development
Ontologies collaborative development
- Education and training tools
E-learning
Virtual environments

Methods and Tools for RNA Structure and Functional Analysis
- RNA structure prediction
- Collaborative studies of RNAs
- ncRNAs functional analysis and classification
- miRNAs and networks
- Genome-wide functional studies
- Identification of ncRNAs
- Databases of ncRNAs and miRNA targets
- miRNA targets prediction
- Synthetic miRNA and siRNA design
- Gene expression analysis
- Analysis of viral RNAs
- RNAi therapeutics
- Identification of ncRNAs biomarkers
- RNA-protein interaction prediction

Deadlines
Contributions for both oral communications and
posters must be short papers of around THREE A4
pages or 12.000 characters long.
They must be submitted through the EasyChair
system at: http://www.easychair.org/conferences/?conf=nettab2009 .

- April 28, 2009: Oral communication submission
Acceptation communication: May 12, 2009
- May 15, 2009: Posters submission
- May 17, 2009: Early registration
- June 10-13, 2009: Tutorials and Workshop

Calls for SPECIAL ISSUES
We plan to launch Calls for Special Issues on the
themes of the workshop in peer-review journals
with associated Impact factor around July for submission in September 2009.

Best regards. Paolo Romano
on behalf of NETTAB 2009 Chairs

Paolo Romano (paolo.romano@...)
Bioinformatics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288 Fax: +39-010-5737-295

NETTAB '09 - Ninth International Workshop on
Network Tools and Applications in Biology
10-13 June 2009, Catania, Italy
http://www.nettab.org/2009/ (soon available)

Paolo Romano (paolo.romano@...)
Bioinformatics
National Cancer Research Institute (IST)

Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA.
Come fare:
Nella prossima dichiarazione dei redditi metti la firma
nell'apposito riquadro del 5 per mille,
scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova :
c.f. 80 100 850 108
Istituto Nazionale per la Ricerca sul Cancro
L.go R. Benzi, 10 -16132 Genova
http://www.istge.it

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EMBL-Bank Release 99 is ready

2009-03-09T03:59:03Z

Release 99 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)

Please try to use these mirror sites for download.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 99 data at Thu, 26-FEB-2009 10:25:05.

The next release will be (unsurprisingly) release 100.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 99 building process has started

2009-02-26T06:42:51Z

We have begun the process of building release 99 of the EMBL Nucleotide
Sequence Database on Thursday 26th Feb 2009
Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 99 is placed:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r99u036.dat.gz
The subsequent update file will contain post-release 99 data and be
named:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r100u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 99 is built and is
publicly available - we expect that to be around 10th Mar 2009.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Thank you,
Mikyung Jang
EMBL-databank
EMBL-EBI

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Call for papers/Reviewers

2009-02-09T23:52:11Z

Journal of Veterinary Medicine and Animal Health

www.academicjournals.org/JVMAH

Dear colleague

Call for papers/Reviewers

Journal of Veterinary Medicine and Animal Health (JVMAH)’

Journal of Veterinary Medicine and Animal Health (JVMAH) publishes high-quality articles in English, in all areas of the subject. All papers published by JVMAH are peer reviewed. JVMAH is a very rapid response journal with an issue published every month. All articles published in JVMAH are peer-reviewed. The following types of papers are considered for publication:

· Original articles in basic and applied research.

· Critical reviews, surveys, opinions, commentaries and essays.

Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue.

Instruction for authors and other details are available on our website www.academicjournals.org/JVMAH Prospective authors should send their manuscript(s) to JVMAH@...

Open Access

One key request of researchers across the world is unrestricted access to research publications. Journal of Veterinary Medicine and Animal Health (JVMAH) is fully committed Open Access Initiative by providing free access to all articles (both abstract and full PDF text) as soon as they are published. We ask you to support this initiative by publishing your papers in this journal.

Invitation to Review

JVMAH is seeking for qualified reviewers as members of the review board team. JVMAH serves as a great resource for researchers and students across the globe. We ask you to support this initiative by joining our reviewer’s team. If you are interested in serving as a reviewer, kindly send us your resume to JVMAH@...

Publication Alert

We will be glad to send you a publication alert showing the table of content with link to the various abstracts and full PDF text of articles published in each issue. Kindly send us an email if you will like to receive publication alert.

Best regards,

Michael Oruah

Editorial Assistant

Journal of Veterinary Medicine and Animal Health

E-mail: JVMAH@...

http://www.academicjournals.org/JVMAH

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[Cph-bioinformatics] Post Doc in Bioinformatics

2009-02-02T02:03:07Z

Dear all

Please pay attention to the 3-year Post Doc position in Bioinformatics at University of Copenhagen announced through this link: http://www.life.ku.dk/job.aspx (application deadline is 26th February)

Best regards

Miki

Anders Miki Bojesen, DVM, PhD
Department for Disease Biology
Faculty of Life Sciences
University of Copenhagen
Stigbøjlen 4, 2. floor
DK-1870 Frederiksberg C
Denmark
+45 35332671 (Phone)
+45 35332757 (Fax)
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CFP: 4th Special Track on Ontologies for Biomedical Systems

2009-02-01T07:38:52Z

CALL FOR PAPERS
----------
4th Special Track on Ontologies for Biomedical Systems
3-4 August 2009
Albuquerque, New Mexico

http://cbms09.biomap.org/

22nd IEEE International Symposium on Computer-Based Medical Systems

http://cvial.ee.ttu.edu/cbms2009/
----------

Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this track is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes:

* Biomedical Ontologies for Genetics, Proteomics, Diseases, Privacy etc
* Conceptual Models for Biological and Medical Data
* Semantics in Biological Data Modeling
* Use of semantics to manage Interoperation in Biomedical Databases
* Semantic Web technologies and formalisms for Biomedical Data
* Ontology representation and exchange languages for bioinformatics
* Biomedical Ontologies and OWL
* Biological Data Integration and Management using Ontologies
* Biomedical Data Engineering using Ontologies
* Application of Biomedical Ontologies for Heterogeneous Database Access
* Query Optimization Techniques for Biomedical Database using Ontologies
* Support of Ontologies for Biological Information Retrieval and Web Services
* Change Management in Biomedical Ontologies
* Tools for Development and Management of Biomedical Ontologies

PAPER SUBMISSION:

No hardcopy submissions are being accepted. Electronic submissions of original technical research papers will only be accepted in PDF format. Use a maximum of 6 pages IEEE two-column format, including figures and references. All submissions will be done electronically via the CBMS 2009 web submission system (http://www.easychair.org/conferences/?conf=ieeecbms2009). Select the track "Ontologies for Biomedical Systems", provide the information about the paper title, authors, keywords, and corresponding author's information (telephone, fax, mailing address, e-mail address). Please note that author names should not appear on the paper. Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2009 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. Selected papers from the track will be published in Special Issue of International Journal of Healthcare Information Systems and Informatics (IJHISI) in 2010.

IMPORTANT DATES:

April 1, 2009     Paper Submission Due
May 25, 2009     Notification of acceptance
June 21, 2009     Final camera-ready paper due
June 21, 2009     Pre-registration deadline

You must pre-register to have your paper published in the proceedings. If you only plan to attend and are not submitting a paper, pre-registration is still strongly encouraged.

TRACK CHAIRS:

Amandeep S. Sidhu
WA Centre for Comparative Genomics, Murdoch University, Perth, Australia

Matthew I. Bellgard
WA Centre for Comparative Genomics, Murdoch University, Perth, Australia

Jake Chen
Indiana University - Purdue University, Indianapolis, USA

For further questions, please contact technical program chair at: cbms@...
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EMBL-Bank Release 98 is ready

2009-01-26T02:49:18Z

Due to the flatfile error (lacking CDS cross reference), EMBL-bank decided
to produce release 98 earlier to fix the problem.
Release 98 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)

PLEASE try to use these mirror sites for download.

Due to the Chinese New Year holiday, Chinese site would be ready within next 1 week:

ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 98 data at Mon, 12-JAN-2009 08:03:10.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 98 building process has started

2009-01-12T05:47:34Z

Due to the immediate bug fix, we have begun the process of building
release 98 of the EMBL Nucleotide Sequence Database on Friday 9th Jan
2009.

Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 98 is placed:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r98u024.dat.gz
The subsequent update file will contain post-release 98 data and be named:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r99u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 98 is built and is
publicly available - we expect that to be around 26th Jan 2009.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more details.

Thank you,
Mikyung Jang
EMBL-databank
EMBL-EBI

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EMBL-Bank Release 97 is ready

2008-12-09T04:23:05Z

Release 97 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)

PLEASE try to use these mirror sites for download.

Following sites are not ready or accessible at the moment but will
be within next 24 hours:

ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 97 data at Fri, 28-NOV-2008
01:41:10.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 97 building process has started

2008-11-28T04:18:59Z

We have begun the process of building release 97 of the EMBL Nucleotide
Sequence Database on Friday 28th Nov 2008
Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 97 is placed:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r97u073.dat.gz
The subsequent update file will contain post-release 97 data and be
named:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r98u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 97 is built and is
publicly available - we expect that to be around 10th Dec 2008.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Thank you,
Mikyung Jang
EMBL-databank
EMBL-EBI

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EMBL-Bank Release 96 is ready

2008-09-09T04:29:29Z

Release 96 of the EMBL Nucleotide Sequence Database is available from the
EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

PLEASE try to use these mirror sites for download.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and updated
sequence data since the last full database release, please note that these
will be changed to include only post-release 96 data at Thu, 28-AUG-2008
11:05:31.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 96 building process has started

2008-08-28T08:20:09Z

We have begun the process of building release 96 of the EMBL Nucleotide
Sequence Database on Thursday 28th Aug 2008
Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 96 is placed:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r96u086.dat.gz
The subsequent update file will contain post-release 96 data and be
named:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r97u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 96 is built and is
publicly available - we expect that to be around 10th Sep 2008.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL-databank
EMBL-EBI

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REVISED DEADLINE - ECCB 2008 Workshop: Annotation, interpretation and management of Mutations (AIMM)- call for papers

2008-07-10T07:07:50Z

Dear Researcher,

Due to requests for an extension of the paper submission deadline for
the AIMM2008, we decided revise it to July 18th (start of SIG meetings at
the ISMB2008). Only minor extension can be granted thereafter.

In addition, we encourage the submission of short position papers on
topics that have not yet been published in research publications,
including proposals outlining how to address the representation
and integration of phenotypic information for the annotation of genotypic variability.

We look forward to seeing you in Sardinia

AIMM workshop @ ECCB 2008

===================================================================================================
ECCB 2008 Workshop: Annotation, interpretation and management of Mutations (AIMM) - call for papers
===================================================================================================

Preamble:

Genetic variability (SNPs, mutations) plays a key role in the analysis of genetic mechanisms and complex diseases. The effort in the gathering and understanding of the information regarding human variability is large, e.g. data collection from the 1000 genomes project. In step with such initiatives this workshop will focus on solutions in text mining, data warehousing and machine learning that allow better integration of mutation relevant information into a bioinformatics infrastructure. Altogether, the meeting participants will discuss the methods for the prediction of phenotypic effects induced by mutations, support to clinical decision processes involving mutations and the means that allow access and management of mutations with annotations from different data resources. Synergistic use of these technologies should facilitate inference of knowledge from sequence to structure to function and to phenotypes. The workshop brings together members of different disciplines to im!
prove know-how and technology transfer as well as better hypothesis generation for yet un-annotated mutations.

Keynote Speakers:

Catherine Worth
Leibniz-Institut f. Molekulare Pharmakologie, Berlin, DE
In Collaboration with Tom Blundell, Cambridge, UK

Kevin B. Cohen,
The Hunter Lab, Center for Computational Pharmacology
University of Colorado Health Sciences Center, Colorado, US

Intended audience:

This workshop reaches out to the following participants: data architects working on data modeling and knowledge representation, data warehouse curators seeking to address a backlog of un-curated mutations from the literature, designers of mining solutions and services for unstructured text, machine learning specialists developing classifiers for predictive analyses, structural biologists involved in protein engineering and physicians involved in genome scale population studies. The workshop includes keynote talks reporting on the management of SNP data and giving better insights on the importance of non-synonymous SNPs on diseases.

Submissions:

We invite both long (4000 words / 12 pages) and short papers (2000 words / 6 pages) on the topics listed below. Manuscript preparation and formatting instructions are available at the following website http://www.ebi.ac.uk/Rebholz-srv/aimm-instructions.html <https://owa.i2r.a-star.edu.sg/exchweb/bin/redir.asp?URL=http://www.ebi.ac.uk/Rebholz-srv/aimm-instructions.html>
We encourage proposals for workshop presentations that describe:

* Infrastructures and metadata to support archival and study of perturbations (mutations) and variations (SNPs) within biological systems.

* Integration of mutation-related data into systems level analysis of a biological sciences (disease, biomarkers, clinical, metabolomics).

* Novel techniques (information extraction, machine learning and others solutions) for the extraction of mutations and generation of annotations from the scientific literature.

* Tools and analyses predicting the impacts of mutations

* Hypothesis generation and reuse: building the derived insights of mutational studies into biological models

Submissions can be made through the EasyChair submission page:
http://www.easychair.org/conferences?conf=aimm2008 <https://owa.i2r.a-star.edu.sg/exchweb/bin/redir.asp?URL=http://www.easychair.org/conferences?conf=aimm2008>

All papers will be published in an online workshop proceedings with CEUR
http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/ <http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/>

Long papers may be invited to submit extended versions to a special issue of BMC Bioinformatics.

Organizers

Christopher J. O. Baker , PhD
Principal Investigator
Data Mining Department
Institute for Infocomm Research
21 Heng Mui Keng Terrace, Singapore 119613
Tel: +65 6874 3495
Email: cbaker@...

Dietrich Rebholz-Schuhmann, MD, PhD
Research Group Leader
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB101SD,
United Kingdom
Tel: +44 (0)1223 492 594
Email: Rebholz@...

Important Deadlines:

Paper Submission: July 7th
Acceptance: August 4th
Final Manuscripts: August 18th
Workshop: Monday, September 22, 2008

Venue: ECCB2008 @ Cagliari, Sardinia - Italy

Session Topics:

Mutation Databases and Metadata: Design, Content, Accuracy.

===========================================================

Over 400 mutation databases can be found with a 'google' search. Many are no longer maintained and cover very specific data sets. These repositories have been designed to support a wide range of features from SNPs, point mutations, insertions, deletions, and observed phenotypes. Furthermore they incorporate a wide range of modified protein features and metrics in the accompanying annotations to the mutation descriptions. In the main these databases are manually curated however mutation annotations are frequently inaccurate e.g. in the PDB, inaccurate to the degree of 40 % of all PDB records.

Extraction of mutations and annotations from literature:

========================================================

AI techniques such as text mining and natural language processing have been used to enable . A number of systems have been developed generally showing that extraction mutations from texts can be achieved with high levels of precision and recall. These systems remain prototype scale their adoption to measure the accuracy, recreation and update of existing mutation databases as we as their incorporation into semi manual annotation pipelines is the next milestone. In addition there is continuing discussion over the appropriate metrics for individual tasks within these systems which requires community involvement. This emergent technology now needs standardization.

Predicting the impacts of Mutations:

====================================

The ability to predict the impact of a mutation or the consequence of a sequence variant is central to the diagnosis of genetic diseases. Non-synonymous mutations may impact translational regulation, mRNA stability, mRNA splicing and rates of translation. Proteins affected by nsSNPs may have altered; catalytic sites, stability, ability to aggregate, and or posttranslational modifications. Moving from SNP to sequence to structure and function has been addressed with varying degrees of accuracy with sequence and structure based (molecular mechanism, empirical energy function or machine learning) methods. The need to apply such techniques at a genome scale requires that robust approaches are identified, benchmarked with standard metrics in order to assign valid significance to ns mutations. Reuse of existing mutation databases for checking quality of predictions is pivotal.

Mutation Data Integration and Reuse: Panel Discussion

=====================================================

http://www.ebi.ac.uk/Rebholz-srv/aimm.html <https://owa.i2r.a-star.edu.sg/exchweb/bin/redir.asp?URL=http://www.ebi.ac.uk/Rebholz-srv/aimm.html>

********************** ANNOUNCEMENT ********************************
We are moving to Fusionopolis! With effect of Monday, 28 July 2008, our official
address will be: Institute for Infocomm Research, 1 Fusionopolis Way, #21-01
Connexis, Singapore 138632. Main line: +65 64082000. Please visit
http://www.fusionopolis.a-star.edu.sg/ for more information on Fusionopolis.
*******************************************************************

------------ Institute For Infocomm Research - Disclaimer -------------This email is
confidential and may be privileged. If you are not the intended recipient, please delete
it and notify us immediately. Please do not copy or use it for any purpose, or disclose
its contents to any other person. Thank you
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EMBL-Bank Release 95 is ready

2008-06-11T01:16:38Z

Release 95 of the EMBL Nucleotide Sequence Database is available from
the EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

PLEASE try to use these mirror sites for download.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and
updated
sequence data since the last full database release, please note that
these will be changed to include only post-release 95 data at Thu,
29-MAY-2008 15:37:48.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL-Bank Release 95 is ready

2008-06-10T13:22:13Z

Release 95 of the EMBL Nucleotide Sequence Database is available from
the EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release
(Australia)ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

PLEASE try to use these mirror sites for download.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and
updated
sequence data since the last full database release, please note that
these will be changed to include only post-release 95 data at Thu,
29-MAY-2008 15:37:48.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 95 building process has started

2008-05-29T09:20:01Z

We have begun the process of building release 95 of the EMBL Nucleotide
Sequence Database on Thursday 29th May 2008
Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 95 is placed:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r95u080.dat.gz
The subsequent update file will contain post-release 95 data and be
named:
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/r96u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk/pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 95 is built and is
publicly available - we expect that to be around 15th June 2008.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL-databank
EMBL-EBI

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EMBL-Bank Release 94 is ready

2008-03-17T06:19:34Z

Release 94 of the EMBL Nucleotide Sequence Database is available from
the EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://ftp-bips.u-strasbg.fr/pub/ebi/pub/databases/embl/release (France*)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

*: Welcome the addition of French mirror site.
PLEASE try to use these mirror sites for download.

Following two sites are not ready or accessible at the moment but will
be in near future.
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)
ftp://ftp.es.embnet.org/pub/databases/embl/release/ (Spain)

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and
updated
sequence data since the last full database release, please note that
these will be changed to include only post-release 94 data at Thu,
28-FEB-2008 14:58:37.

Mikyung Jang
EMBL-Bank
EMBL-EBI

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EMBL Release 94 building process has started

2008-02-28T08:57:20Z

We have begun the process of building release 94 of the EMBL Nucleotide
Sequence Database on Thursday 28th Feb 2007
Daily updates:
For those who work with daily updates from the EBI ftp server (or mirror
sites) the last update file for release 94 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r94u083.dat.gz
The subsequent update file will contain post-release 94 data and be
named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r95u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 94 is built and is
publicly available - we expect that to be around 15th March 2008.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL Sequence Database Group
EMBL-EBI

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EMBL-Bank Release 93 is ready

2007-12-17T08:47:38Z

Release 93 of the EMBL Nucleotide Sequence Database is available from
the EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)

PLEASE try to use these mirror sites for download.

Following two sites are not ready at the moment but will be in near future.
ftp://ftp.es.embnet.org/pub/databases/embl/release/ (Spain)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and
updated
sequence data since the last full database release, please note that
these will be changed to include only post-release 93 data at Thu,
29-NOV-2007 13:26:18.

Mikyung Jang
EMBL-Bank

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EMBL Release 93 building process has started

2007-11-29T09:09:41Z

We have begun the process of building release 93 of the EMBL Nucleotide
Sequence Database on Thursday 29th Nov 2007
Daily updates:
For those who work with daily updates from the EBI ftp server (or
mirror
sites) the last update file for release 93 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r93u075.dat.gz
The subsequent update file will contain post-release 93 data and be
named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r94u001.dat.gz

The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 93 is built and is
publicly available - we expect that to be around 15th December 2007.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL Sequence Database Group
EMBL-EBI

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Mitochondrial DNA Concordance - Version 2.0

2007-10-10T14:31:17Z

Cannot access the site on //shelob.bioanth.cam.ac.uk/mtdna. It times out. Any clues?

Ian Davies

www.karisgarden.com/lusty/pnr2.htm

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EMBL-Bank Release 92 is ready

2007-09-12T09:43:31Z

Release 92 of the EMBL Nucleotide Sequence Database is available from
the EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)

PLEASE try to use these mirror sites for download.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and
updated
sequence data since the last full database release, please note that
these will be changed to include only post-release 92 data at Thu,
Aug 23 14:12:49 GST 2007

Mikyung Jang
EMBL-Bank

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EMBL Release 92 building process has started

2007-08-24T02:38:40Z

We have begun the process of building release 92 of the EMBL Nucleotide
Sequence Database on Thursday 23rd Aug 2007
Daily updates:
For those who work with daily updates from the EBI ftp server (or
mirror
sites) the last update file for release 92 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r92u072.dat.gz
The subsequent update file will contain post-release 91 data and be
named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r93u001.dat.gz as usual
Cumulative update [file:
]
The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and cum_*
files)
will continue to grow with new data until release 92 is built and is
publicly available - we expect that to be around 15th September 2007.

See
http://www.ebi.ac.uk/embl/Documentation/changesdetails.html for more
details.

Regards,
Mikyung Jang
EMBL Sequence Database Group
EMBL-EBI

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CFP: 3rd Int. WS on Scalable SW Knowledge Bases (SSWS '07)

2007-07-12T01:59:00Z

*********************************************************************
We apologize if you received multiple copies of this Call for Papers
Please feel free to distribute it to those who might be interested
*********************************************************************

LAST CALL FOR PAPERS (WITH DEADLINE EXTENSION)

THIRD INTERNATIONAL WORKSHOP ON
SCALABLE SEMANTIC WEB KNOWLEDGE BASE SYSTEMS (SSWS '07)

http://www.cs.rmit.edu.au/fedconf/index.html?page=ssws2007cfp

ON THE MOVE FEDERATED CONFERENCES 2007 (OTM'07)
http://www.cs.rmit.edu.au/fedconf

Vilamoura, Algarve, Portugal, Nov 25 - 30, 2007
Proceedings will be published by Springer Verlag

*********************************************************************

WORKSHOP DESCRIPTION

This workshop aims at creating a forum for discussing a critical issue for the
Semantic Web, that is, scalability. As the Semantic Web evolves, scalability becomes
increasingly important. This workshop will focus on addressing of the scalability
issue with respect to the development and deployment of knowledge base systems on the
Semantic Web. Typically, such systems deal with information described in Semantic Web
languages like OWL and RDF(S), and provide services such as storing, reasoning,
querying and debugging. There are two basic requirements for these systems. First,
they have to satisfy the application's semantic requirements by providing sufficient
reasoning support. Second, they must scale well in order to be of practical use.
Given the sheer size and distributed nature of the Semantic Web, these requirements
impose additional challenges beyond those addressed by earlier knowledge base
systems. This has been well recognized by the community. We expect that the above
issue is going to challenge the Semantic Web for a long time of period and
significant effort is needed in order to tackle the problem.

This workshop seeks to bring together researchers and practitioners to share their
recent ideas and progresses towards building scalable knowledge base systems for the
Semantic Web. The workshop will be centered on the discussion of three major aspects:

1. foundations, methods and technologies for pushing forward the state-of-the-art;
2. performance evaluation and related principles, methodologies and tools;
3. identification of important issues and future research directions.

WORKSHOP TOPICS

TOPICS OF INTERESTS for the workshop include, but are not limited to:

* Reasoning mechanisms, techniques and systems
* Query evaluation and optimization
* Performance evaluation and benchmarks
* Large Semantic Web repositories
* Distributed and concurrent knowledge base systems and P2P systems
* Large scale knowledge base management
* Semantic Web-based information integration

In addition, the workshop will include a working session on benchmarking and other
relevant topics solicited beforehand to participants. In order to be able to evaluate
scalability, the existence of agreed benchmarking datasets is of crucial
importance. In many related domains such as databases and theorem proving, standard
benchmarks exist and are ready to guide research on optimization techniques. In the
Semantic Web area, such benchmarking shave only just started to emerge and there is
no commonly agreed benchmark dataset for RDF and OWL reasoning and querying. The
workshop will address this issue in a special working session on benchmarking. In
this session, existing benchmarking initiatives will be presented and discussed by
organizers and participants of the workshop. The aim is to agree on a classification
of the existing datasets and requirements for additional datasets.

IMPORTANT DATES

Abstract Submission Deadline July 20, 2007 (EXTENDED)
Paper Submission Deadline July 26, 2007
Acceptance Notification September 1, 2007
Camera Ready Due September 10, 2007
Registration Due September 10, 2007
OTM Conferences November 25 - 30, 2007

SUBMISSION GUIDELINES

All submitted papers will be carefully evaluated based on originality, significance,
technical soundness, clarity of expression, and relevance to SSWS. All submissions
must be in English, and will be refereed by a program committee comprising members of
the Working Group. Research submissions must not exceed 10 pages following the
Springer format. Submissions should be made in PDF format. Detailed formatting
instructions can be found at: http://www.springer.de/comp/lncs/authors.html

The final proceedings will be published by Springer Verlag as LNCS. Failure to commit
to presentation at the conference automatically excludes a paper from the
proceedings.
The paper submission site is located at
http://www.cs.rmit.edu.au/fedconf/ssws/2007/papers/

ORGANISATION COMMITTEE

Achille Fokoue
IBM T.J. Watson Research Center, NY, USA (Contact Person)
(http://domino.research.ibm.com/comm/research_people.nsf/pages/achille.index.html,
achille@...)

Yuanbo Guo
Microsoft Corp
(http://www.lehigh.edu/~yug2, yug2@...)

Thorsten Liebig
Ulm University, Germany
(http://www.informatik.uni-ulm.de/ki/liebig.html, thorsten.liebig@...)

Bijan Parsia
University of Manchester, UK
(http://www.cs.man.ac.uk/~bparsia/, bparsia@...)

Program Committee Members

Pascal Hitzler - University of Karlsruhe, Germany
York Sure - University of Karlsruhe, Germany
Kavitha Srinivas - IBM T.J. Watson Research Center, USA
Takahira Yamaguchi - Keio University, Japan
Raúl García Castro - Universidad Politecnica de Madrid, Spain
Aditya Kalyanpur - IBM T.J. Watson Research Center, USA
Oscar Corcho - University of Manchester, UK
Jeff Heflin - Lehigh University, USA
Ralf Möller - Hamburg University of Technology, Germany
Ian Horrocks - University of Manchester, UK
Boris Motik - University of Manchester, UK
Pierre-Antoine Champin - Lyon 1 University, France
Ying Ding - University of Innsbruck, Austria
Marko Luther - DoCoMo Eurolabs Munich, Germany
Timo Weithöner - Ulm University, Germany
Andy Seaborne - Hewlett-Packard, UK
Ulrike Sattler - University of Manchester, UK
Jan Wielemaker - University of Amsterdam, The Netherlands
Volker Haarslev - Condordia University, Canada

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EMBL-Bank Release 91 in XML formats

2007-07-03T06:09:37Z

>From this release 91, the EMBL Nucleotide Sequence Database starts
to support EMBL and newly introduced INSD XML format. Each format
of release files are available from

ftp://ftp.ebi.ac.uk/pub/databases/embl/emblxml/release
ftp://ftp.ebi.ac.uk/pub/databases/embl/insdxml/release

The availability of xml files at mirror sites is yet to be decided.

Mikyung Jang
EMBL-Bank
EBI

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EMBL-Bank Release 91 is ready

2007-06-21T08:38:52Z

Release 91 of the EMBL Nucleotide Sequence Database is available from
the EBI ftp servers and other verified mirror sites as follows:

ftp://ftp.ebi.ac.uk/pub/databases/embl/release (UK)
ftp://ftp.funet.fi/pub/sci/molbio/embl_release (Finland)
ftp://bio-mirror.net/biomirror/embl/release (USA)
ftp://biomirror.aarnet.edu.au/biomirror/embl/release (Australia)
ftp://bio-mirror.jp.apan.net/pub/biomirror/embl/release (Japan)
ftp://ftp.cbi.pku.edu.cn./pub/databases/embl/release/ (China)

PLEASE try to use these mirror sites for download.

Full release notes are available at:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.txt
http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.txt

For those who mirror our cumulative update files containing new and
updated
sequence data since the last full database release, please note that
these will be changed to include only post-release 91 data at Thu,
May 31 10:56:11 GMT 2007

Mikyung Jang
EMBL-Bank

_______________________________________________
Embl-db mailing list
Embl-db@...
http://www.bio.net/biomail/listinfo/embl-db

EMBL Release 91 building process has started

2007-06-01T04:55:59Z

We have begun the process of building release 91 of the EMBL
Nucleotide Sequence Database on Thursday 31st May 2007

Daily updates:
For those who work with daily updates from the EBI ftp server (or
mirror sites) the last update file for release 91 is placed:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r91u056.dat.gz

The subsequent update file will contain post-release 91 data and be
named:
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/r92u001.dat.gz as usual

The cumulative update file in
ftp://ftp.ebi.ac.uk:pub/databases/embl/new/cumulative.dat.gz (and
cum_* files) will continue to grow with new data until release 91 is
built and is
publicly available - we expect that to be around 15th June 2007.

EMBL will start to make INSD xml release from this release. It will be
available short after usual EMBL flat file release is published.

Regards,
Mikyung Jang
EMBL Sequence Database Group
EMBL-EBI

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Embl-db mailing list
Embl-db@...
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