NETTAB 2009 Workshop: Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development

Department of Computer Science, University of Catania, Italy

http://www.nettab.org/2009/

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

Gabriel Valiente
Technical University of Catalonia, Department of Software

Barcelona, Spain

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.

Contact:
Paolo Romano  Bioinformatics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy

Tel: +39-010-5737-288
Fax: +39-010-5737-295
e_mail: paolo.romano@istge.it