NETTAB 2005

1. NETTAB 2005 Presentation of the NETTAB 2005 Workshop Paolo Romano1 & Angelo Facchiano2 1National Cancer Research Institute, Genova, Italy 2ISA/CNR, Avellino, Italy

2. The acronym NETwork Tools and Applications in Biology A series of workshops focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics

3. NETTAB Workshops 2001-2 “CORBA and XML: towards a bioinformatics integrated network environment” http://www.nettab.org/2001/ Genova, 17-19 May 2001 ----------------- “Agents in Bioinformatics” http://www.nettab.org/2002/ Bologna, 12-14 July 2002

4. NETTAB Workshops 2003-4 “Bioinformatics for the management, analysis and interpretation of microarray data” http://www.nettab.org/2003/ Casalecchio di Reno (BO), 17-19 November 2003 ----------------- “Models and metaphors from biology to bioinformatics tools” http://www.nettab.org/2004/ Camerino (MC), 5-7 September 2004

5. About bioinformatics Some aspects of bioinformatics: • Huge amount of data (not only sequences, increasing microarray data, coming soon metabolic pathways, interaction maps, gene networks,…) • Exponential increase of data ( > 10% every 3 months), soon not locally manageable • Largely distributed information and application softwares • Heterogeneous data structures, semantics and information systems • Research environment in continuous evolution and with user specific needs

6. About bioinformatics From human to machine orientation: • The huge amount of information makes its access un-exhaustive and inefficient and requires the development of complex searching and retrieval softwares. • Biologists connect to many web sites and switch among the sites to submit and retrieve preliminar and intermediate data. Final achievements are the result of a manual integration activity. • Softwares can be developed to perform the integration activity, provided that they are taught the “meaning” of the information, how to link data and how to pipe retrieval and analysis steps.

7. Workflows Abilities for coping with biological information overflow: • A workflow is a “Computerized facilitation or automation of a business process, in whole or part” (Workflow Management Coalition) • Its main goal is the implemention of data analysis processes in a standardized environment. • Its main advantages relates to: • effectiveness: fully automatic procedure, it frees the bioscientist from repetitive interactions with the web, it supports good practice, • reproducibility: analysis can be replicated over time, • reusability: intermediate results can be used, • traceability: the workflow is carried out in a transparent analysis environment.

8. Workflows in bioinformatics Machine orientation is improving: • Web services have been implemented by EBI/NCBI • Registries of biological web services (bioMOBY) Implementation of workflows already started: • Biopipe, as an add-on to bioperl • GPipe as an extension of Pise • Taverna, within MyGrid • Many others are coming

9. Workshop NETTAB 2005 (Preliminar title) Workflows management: new abilities for biological information overflow Second University of Naples, Naples, Italy, early October 2005 http://www.nettab.org/2005/ (soon)

10. Workshop formula NETTAB 2005 workshop intends to focus on the design and implementation of workflows by: • Introducing the basic knowledge in related technologies, in a non trivial way • Outlining the promising features of workflows in bioinformatics • Showing some valuable examples in bioinformatics • Allowing for as much discussion as possible (panel, contest) • Demonstrating “how it works” practically (tutorials)

11. See you in Naples! Programme Committee: Paolo Romano (chair), Angelo Facchiano, Pietro Leo, Emanuela Merelli, Matthew Pocock, many others to come Organizing Committee: Angelo Facchiano (chair), Assunta Manniello, Domenico Marra, many others to come This presentation will soon be available in the NETTAB web site: http://www.nettab.org/2005/