[MOBY-l] CFP: NETTAB 2009 on Collaborative Bioinformatics Research and Development (open source, social networks, wikis, ...)

Fri Apr 3 15:43:19 UTC 2009

Apologies if you receive more copies.
===========================

Announce and Preliminary 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/

Submissions deadlines:
- April 28, 2009: Oral communication submission
- May 15, 2009: Posters submission
Submissions must be short papers of around 3 pages or 12.000 characters long.
Special Issues in peer-review journals on 
workshop's topics planned: post-workshop ad hoc Call for papers will be issued.

RATIONALE
Advent of Wide Area Networks (WAN) allowed the 
availability of distributed information and 
prompted the need for searching and retrieving 
this data (Network Information Retrieval tools, 
NIR), as well the development of unprecedented 
communications between users (Computer Mediated 
Communication tools, CMC). Initially, CMC was 
asynchronous and based on electronic mail and 
newsgroups. From email systems, mailing lists and 
newsletter were soon derived, while newsgroups 
generated, shortly after, electronic fora. 
Synchronous communication were introduced through 
the advent of chat services. On this line, 
current multimedia teleconference systems were 
then set up. Virtual reality was first introduced 
for educational purposes by means of MUD 
(Multi-users Domain) systems, and especially by 
means of MOO (MUD Object-oriented). This line 
produced current virtual reality environment, 
like the emerging Second Life system.
Life Sciences researchers largely took profit 
from CMC tools. The bionet newsgroups hierarchy 
remains one of the most famous and useful CMC 
system supporting life science research. Many 
mailing lists that were born in that context are 
still used. The development of open source 
software was largely made possible by the 
possibility of exchanging, in an effective way, 
knowledge, practices and skills among 
researchers. Web sites of communities of 
scientists were set up and often constituted the 
base for a real collaborative development and research.
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".

Moreover, there will be a special session on 
"Methods and Tools for RNA Structure and Functional Analysis".

The transcription of almost all genomes generates 
a great number of coding and non-coding RNAs 
(ncRNAs).  Although RNA is central to the 
synthesis of proteins, it is not only a messenger 
of genetic information: many cellular functions 
depend on ncRNAs, which exert their functions by 
their sequence and structure.  In particular, 
small silencing RNAs (miRNAs, siRNAs and piRNAs) 
play a crucial role in many physiological 
processes and their aberrant expression is a 
common feature of human diseases including 
cancer. Models and tools  able to increase our 
understanding of RNAs functions and their 
involvement in diseases may lead to the design of new RNA-based  therapeutics.
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.

KEYNOTE SPEAKER

# 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

# Michael Levitt
Stanford University, USA

# 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
Submissions for both oral communications and 
posters must be short papers of around THREE A4 
pages or 12.000 characters long.

- 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 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

AIUTACI AD AIUTARE: 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