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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 ([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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