BioWikis - NETTAB 2010 Call for Contributions

Blatantly not sorry for cross-posting,

Dan.


---------- Forwarded message ----------
From:  <[email protected]>
Date: 30 June 2010 17:15
Subject: [Nettab-Announce] NETTAB 2010 Call for Contributions
To: [email protected]



NETTAB 2010 on "Biological Wikis"

November 29 - December 1, 2010, Naples, Italy
http://www.nettab.org/

CALL FOR PAPERS

See below for Topics, Contributions sought, Deadlines, Instructions
and Committees.

RATIONALE
It is now clear that wiki systems offer a variety of advantages for
the management of biological data and information.
Some of the specific aims of wikis for biology (bio-wikis) include:
=A0 =A0* Collaborative development and sharing of knowledge
=A0 =A0* Collaborative annotation of database contents
=A0 =A0* Collaborative creation of database contents

The collaborative development and sharing of documentation and
knowledge allows communities to promote, exploit, discuss and reach
consensus on procedures, data, experiences, news, and other varied
information. Indeed valuable expertise and interests in special topics
are usually distributed, and are rarely concentrated in a unique site
or research group.

The collaborative annotation of biological databases is increasingly
under consideration because extended and accurate curation of an ever
increasing volume of data is extremely costly and time consuming. Such
distributed networks can help to improve and extend databases curation
beyond that which is possible with, typically, limited numbers of
curation staff. It allows users to contribute their expertise and
observations =A0independently of database central organizations.
Although the contents of the database are collaboratively annotated,
the underlying databases themselves are left unchanged.

Furthermore, collaborative creation of community databases can capture
emerging structure in rapidly developing fields. These database-wikis
are indexes of biologically relevant data that emerge from focused and
rapidly developing communities. They form a stopgap between
unstructured discussion in fora and on mailing lists and the 'mature'
databases that emerge subsequently. Hence they can be useful for
discerning trends and promoting best practices, as well as =A0collect
unique and timely information.

In the future, collaborative 'wiki' updates of almost all database
contents can be envisaged. However several important issues need to be
addressed:
=A0 =A0* How reliable are user contributions?
=A0 =A0* What format should annotations take?
=A0 =A0* How is this information feed back into 'authoritative' databases?

Procedures should be implemented to support assessment of users'
contributions, extraction of structured data from annotations, uptake
of original data into reference databases. The authoritativeness of
contributions is essential: how can quality be assessed? How do we
deal with contributions from casual end users, since these are usually
not considered adequate when compared with professional annotation at
service centers. Can the open edition model of many wiki systems, e.g.
Wikipedia, be as successful in life sciences? =A0Alternatively, should
the usual criteria for assessing quality of research be applied,
including peer-evaluation of contributions and identification of
users? Crediting users for their contributions (e.g. authorship
assignment) may be necessary to stimulate =A0the broadest possible
participation. =A0Which further benefits may be imagined to acknowledge
user investment (subscriptions to services, journals, ...)?

Special features may be required to cater for the specificity of
biological data: textual information is only a small part of
biological data, how can the numerous and heterogeneous biological
data types be catered for, e.g. =A0images, plots, diagrams? An
adaptation of current wiki systems is needed. A survey of existing
systems as well as current development efforts will be useful, so that
possible synergies can be identified and supported, as well as ensure
a coherent set of interoperable biological wikis.

TOPICS
The following list is not meant to be exclusive of any further topics
as stated above.

Submitted contributions should address one or more of the following topics:
=A0 =A0* Wiki development tools
=A0 =A0 =A0 =A0 =A0o Wikimedia
=A0 =A0 =A0 =A0 =A0o Wikimedia extensions
=A0 =A0 =A0 =A0 =A0o Semantic Wikis
=A0 =A0 =A0 =A0 =A0o Wiki-coupled CMSs
=A0 =A0 =A0 =A0 =A0o Other wikis
=A0 =A0* Arising issues for the biomedical domain:
=A0 =A0 =A0 =A0 =A0o Authoritativeness of contributions and sites
=A0 =A0 =A0 =A0 =A0o Quality assessment
=A0 =A0 =A0 =A0 =A0o Users acknowledgement
=A0 =A0 =A0 =A0 =A0o Stimulatation of quality contributions
=A0 =A0 =A0 =A0 =A0o Authorships management and reward
=A0 =A0 =A0 =A0 =A0o 'Scientific production' value for contributions
=A0 =A0 =A0 =A0 =A0o Management of bioinformatics data types
=A0 =A0* Wikis and collaborative systems for:
=A0 =A0 =A0 =A0 =A0o Genomics, proteomics, metabolomics, any -omics
=A0 =A0 =A0 =A0 =A0o Proteins analysis and visualization
=A0 =A0 =A0 =A0 =A0o gene and proteins interactions
=A0 =A0 =A0 =A0 =A0o metabolic pathways
=A0 =A0 =A0 =A0 =A0o oncology research
=A0 =A0* Issues to be tackled by wiki and collaborative research for:
=A0 =A0 =A0 =A0 =A0o Genomics, proteomics, metabolomics, any -omics
=A0 =A0 =A0 =A0 =A0o Proteins analysis and visualization
=A0 =A0 =A0 =A0 =A0o gene and proteins interactions
=A0 =A0 =A0 =A0 =A0o metabolic pathways
=A0 =A0 =A0 =A0 =A0o oncology research

TYPE OF CONTRIBUTIONS

The following possible contributions are sought:
=A0 =A0* Oral communications
=A0 =A0* Posters
=A0 =A0* Software demos
All accepted contributions will be published in the proceedings of the work=
shop.

DEADLINES

* =A0September 24, 2010: Oral communications submission
=A0 =A0 =A0 =A0 =A0o Decisions announced: October 24, 2010
* October 17, 2010: Posters submission
=A0 =A0 =A0 =A0 =A0o Decisions announced: October 24, 2010
* October 29, 2010: Early registration ends
* November 29 - December 1, 2010: Workshop and Tutorials

INSTRUCTIONS
Kindly follow the instructions carefully when preparing your
contribution and submit your contribution through the EasyChair system
at http://www.easychair.org/conferences/?conf=3Dnettab2010.

All contributions should follow the same format, as specified here:
font type: Times New Roman, font size: 12 pti, page size: A4, left and
right margins: 2.0 cm, upper margin: 2.5 cm, lower margin: 2.0 cm.

The lenght of contributions for oral communications should be between
3 and 5 pages, including tables and figures.
They should include: Abstract, Introduction, Methods, Results and
Discussion, References.
All contributions for oral communications will be evaluated by at
least three referees.

The length of contributions for posters should be no more then 3
pages, including tables and figures.
They should include: Introduction, Methods, Results, References.
All posters will be evaluated on the basis of their relevance fot the
workshop's topics only.

For any further information or clarification, please contact the
organization by email at [email protected]

ORGANIZATION

Co-chairs
=A0 =A0* Angelo Facchiano, CNR-ISA, Avellino, Italy
=A0 =A0* Paolo Romano, National Cancer Research Institute, Genoa, Italy

Scientific Committee
=A0 =A0* Claudia Angelini, IAC, National Research Council, Napoli, Italy
=A0 =A0* Roland Barriot, Universit=E9 Paul Sabatier - CNRS, Toulouse, France
=A0 =A0* Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, United Kin=
gdom
=A0 =A0* Dan Bolser, University of Dundee, Scotland, United kingdom
=A0 =A0* Philip E. Bourne, University of California, San Diego UCSD, La Jol=
la, USA
=A0 =A0* Mike Carasio, Keygene N.V., Wageningen, The Netherlands
=A0 =A0* Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, =
Italy
=A0 =A0* Italia De Feis, IAC, National Research Council, Napoli, Italy
=A0 =A0* Angelo Facchiano, ISA, National Research Council, Avellino, Italy
=A0 =A0* Carl Herrmann, Universit=E9 de la M=E9diterran=E9e, Marseille, Fra=
nce
=A0 =A0* Pascal Hingamp, Universit=E9 de la M=E9diterran=E9e, Marseille, Fr=
ance
=A0 =A0* Eran Hodis, Weizmann Institute of Science, Rehovot, Israel
=A0 =A0* Robert Hoffmann, Computational Biology Center, Memorial
Sloan-Kettering Cancer Center, New York, USA
=A0 =A0* Thomas Kelder, BiGCaT Bioinformatics, University of Maastricht,
The Netherlands
=A0 =A0* Alexander Pico, The Gladstone Institutes, University of
California, San Francisco, USA
=A0 =A0* Jaime Prilusky, Bioinformatics, Weizmann Institute of Science,
Rehovot, Israel
=A0 =A0* Paolo Romano, Bioinformatics, National Cancer Research Institute, =
Italy
=A0 =A0* Andrew Su, Bioinformatics, Genomics Institute of the Novartis
Research Foundation, San Diego, USA
=A0 =A0* Joel Sussman, Weizmann Institute of Science, Rehovot, Israel
=A0 =A0* Tim Vickers, Department of Molecular Microbiology, Washington
University in St. Louis, St. Louis, USA
=A0 =A0* Wyeth Wasserman, Department of Medical Genetics, University of
British Columbia, Vancouver, Canada
=A0 =A0* and further members yet to be confirmed

Organizing Committee
=A0 =A0* Claudia Angelini, IAC, National Research Council, Napoli, Italy
=A0 =A0* Maria Luisa Chiusano, University of Napoli "Federico II", Napoli, =
Italy
=A0 =A0* Italia De Feis, IAC, National Research Council, Napoli, Italy
=A0 =A0* Angelo Facchiano, ISA, National Research Council, Avellino, Italy
=A0 =A0* Paolo Romano, Bioinformatics, National Cancer Research Institute,
Genoa, Italy

Supporting Institutes, Scientific Societies and Projects
This list is still under definition.
=A0 * National Research Council (CNR), Italy
=A0 * National Cancer Research Institute (IST), Genoa, Italy
=A0 * Italian Network for Oncology Bioinformatics (RNBIO)

Sponsors
Sponsorships are still under definition. You are welcome to email us
for further information if you are interested in sponsoring this
workshop.

We look forward to meeting you in Naples!

Paolo Romano and Angelo Facchiano
=A0on behalf of the Scientific Committee

Paolo Romano ([email protected])
Bioinformatics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288 =A0Fax: +39-010-5737-295 =A0Skype: p.romano
Web: http://www.nettab.org/promano/





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