CFP: NETTAB 2009 on Collaborative Bioinformatics Research and Development (social networks, wiki, ...)

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 lon=
g.
Special Issues in peer-review journals on =

workshop's topics planned: post-workshop ad hoc Call for papers will be iss=
ued.

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  therapeuti=
cs.
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, =85)
- 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 ([email protected])
Bioinformatics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295



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