[Socbin] NETTAB 2010 on Biological Wikis: Call for Contributions

Paolo Romano paolo.romano at istge.it
Mon Jul 5 16:48:58 CEST 2010


I apologize for possible duplications.
==========================

NETTAB 2010 on "Biological Wikis"

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

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:
     * Collaborative development and sharing of knowledge
     * Collaborative annotation of database contents
     * 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  independently 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  collect 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:
     * How reliable are user contributions?
     * What format should annotations take?
     * 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?  Alternatively, 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  the broadest possible 
participation.  Which 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.  images, 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:
     * Wiki development tools
           o Wikimedia
           o Wikimedia extensions
           o Semantic Wikis
           o Wiki-coupled CMSs
           o Other wikis
     * Arising issues for the biomedical domain:
           o Authoritativeness of contributions and sites
           o Quality assessment
           o Users acknowledgement
           o Stimulatation of quality contributions
           o Authorships management and reward
           o 'Scientific production' value for contributions
           o Management of bioinformatics data types
     * Wikis and collaborative systems for:
           o Genomics, proteomics, metabolomics, any -omics
           o Proteins analysis and visualization
           o gene and proteins interactions
           o metabolic pathways
           o oncology research
     * Issues to be tackled by wiki and collaborative research for:
           o Genomics, proteomics, metabolomics, any -omics
           o Proteins analysis and visualization
           o gene and proteins interactions
           o metabolic pathways
           o oncology research

TYPE OF CONTRIBUTIONS

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

DEADLINES

*  September 24, 2010: Oral communications submission
           o Decisions announced: October 24, 2010
* October 17, 2010: Posters submission
           o 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=nettab2010.

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 info at nettab.org.

ORGANIZATION

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

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

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

Supporting Institutes, Scientific Societies and Projects
This list is still under definition.
    * National Research Council (CNR), Italy
    * National Cancer Research Institute (IST), Genoa, Italy
    * 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
   on behalf of the Scientific Committee


Paolo Romano (paolo.romano at istge.it)
Bioinformatics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295  Skype: p.romano
Web: http://www.nettab.org/promano/






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