Scientific Programme Overview

In the style of the other NETTAB workshops, NETTAB 2010 will include: keynote lectures given by leading experts in the field, oral communications from selected contributions, open discussion, selected software demonstrations and posters, as well as tutorials.

Monday, November 29, 2010 (Tutorial day)
Session type	Start	End	Title	Speaker	Duration
Tutorial	11:30	13:00	Mining biological pathways using WikiPathways web services and more...	Thomas Kelder, Department of Bioinformatics (BiGCaT), Maastricht University, the Netherlands	1:30
Break	13:00	14:00	Lunch break		1:00
Tutorial	14:00	15:30	Semantic MediaWiki: a community database and more.	Dan Bolser, College of Life Sciences, University of Dundee, Scotland, United Kingdom	1:30
Break	15:30	15:45	Coffee Break		0:15
Tutorial	15:45	17:15	Everything you wanted to know about Wikipedia but were too afraid to ask	Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom Andrew Su, Bioinformatics and Computational Biology, Genomics Institute of the Novartis Research Foundation (GNF), San Diego, USA	1:30
Tutorial	17:15	18:45	How to create your own collaborative publishing project with WikiGenes	Robert Hoffmann, Computational Biology Center, cBIO, Memorial Sloan-Kettering Cancer Center, MSKCC, New York, USA	1:30
Social	20:00	21:00	Social activity (TBD)		1:00
Tuesday, November 30, 2010 (NETTAB day)
Session type	Start	End	Title	Speaker	Duration
Scientific Session	9:00	10:40	Session 1: Chairperson: Alexander Pico		1:40
			The Pros and Cons of Wikipedia for Scientists (Invited lecture)	Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom	40
			SNPedia	Mike Cariaso, Keygene, The Netherlands	30
			TOPSAN: a collaborative annotation environment for structural genomics and beyond	Adam Godzik, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA	30
Break	10:40	11:00	Coffee break and NETTAB/BBCC common poster session		20
Scientific Session	11:00	13:00	Session 2: Chairperson: Paolo Romano		2:00
			Collaborative publishing with authorship tracking and reputation system - WikiGenes (Invited lecture)	Robert Hoffmann Computational Biology Center, cBIO, Memorial Sloan-Kettering Cancer Center, MSKCC, New York, USA	40
			The wiki-based Transcription Factor Encyclopedia and a model for robust community participation	Wyeth Wasserman, Department of Medical Genetics, University of British Columbia, Vancouver, Canada	30
			Extending Mediawiki for community annotation	Daniel Renfro, Department of Biochemistry & Biophysics, Texas A&M University, USA	30
			The Bioinformatics Italian Society (BITS)	Manuela Helmer Citterich, Molecolar Bioinformatics, Biology Department, University of Rome "Tor Vergata", Italy	20
Break	13:40	14:00	Lunch break		1:00
Scientific Session	14:00	16:10	Session 3: Chairperson: Dan Bolser		2:10
			WikiPathways, community-based curation for biological pathways (Invited lecture)	Alexander Pico Gladstone Institute of Cardiovascular Disease, San Francisco, USA	40
			Demonstration of a citation-enabled workflow using the ConceptWiki triple based approach	Christine Chichester, Netherlands Bioinformatics Centre, Nijmegen, The Netherlands	30
			Towards A General-Purpose Database Wiki for Biological Database Curation (Software demonstration))	James Cheney, School of Informatics, University of Edinburgh, Scotland, United Kiingdom	20
			PDBWiki: Success or failure? (Invited lecture)	Dan Bolser, College of Life Sciences, University of Dundee, Scotland, United Kingdom	40
Break	16:10	16:40	Coffee break and NETTAB/BBCC common poster session		30
Scientific Session	16:40	19:00	Session 4: Chairperson: Robert Hoffmann		2:20
			The Gene Wiki: Achieving critical mass and mining for novel annotations (Invited lecture)	Andrew Su, Bioinformatics and Computational Biology, Genomics Institute of the Novartis Research Foundation (GNF), San Diego, USA	40
			SBML2SMW: bridging System Biology with semantic web tech-nologies for biomedical knowledge acquisition and hypothesis elicitation (with Software demonstration)	Luca Toldo, Merck KGaA, Darmstadt, Germany	30
			The future of biological wikis	Panel discussion with all speakers	1:10
Social	20:00	22:30	Social dinner Restaurant "Il Transatlantico" (Via Luculliana, 15, Borgo Santa Lucia, very near to the Congress Center)		2:30
Wednesday, December 1, 2010 (BBCC day)
Session type	Start	End	Title	Speaker	Duration
Scientific Session	9:30	11:10	Session 5: Chairpersons: Claudia Angelini and Italia De Feis		1:40
			Repository for statistical analysis of mass spectrometry data	Federica Viti, Institute for Biomedical Technologies - Italian National Research Council, Milano, Italy	20
			Mathematical Models for Feature Selection and their Application to Bioinformatics	Giovanni Felici, Istituto di Analisi dei Sistemi ed Informatica - CNR, Rome, Italy	20
			Toward an Improved Combinatoric Biclustering Algorithm	Ekaterina Nosova, Department of Mathematics and Computer Sciences, University of Salerno, Fisciano (Salerno), Italy	20
			RNA-seq: from computational challenges to biological insights	Valerio Costa, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples, Italy	20
			Eliciting Fuzzy Knowledge from the PIMA Dataset	Antonio d'Acierno, Institute of Food Sciences - Italian National Research Council, Avellino, Italy	20
Break	11:10	11:30	Coffee break		20
Scientific Session	11:30	13:00	Session 6: Chairpersons: Angelo Facchiano and Paolo Romano		1:30
			Genome duplication and gene annotation: an example for a reference plant species	Alessandra Vigilante, Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples "Federico II", Italy	20
			Computational prediction and experimental analysis of RNA structures	Stefano Giacomelli, Institute of Protein Biochemistry, CNR, Naples, Italy	20
			Clinical bioinformatics: a research agenda to support health care transformation	Riccardo Bellazzi, University of Pavia, Italy	30
			First Announcement of NETTAB 2011	Riccardo Bellazzi, University of Pavia, Italy, and Paolo Romano, National Cancer Research Institute of Genova, Italy	20

List of poster abstracts

P1	Micronutrients In Wikipathways database Damariz Rivero Guedez, Jildau Bouwman, Suzan Wopereis, Ben van Ommen and Duccio Cavalieri
P2	Mirroring and Synchronization of Biological Wikis: lessons from the Gene Wiki Salvatore Loguercio, Benjamin Good and Andrew I. Su
P3	A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species Justin Preece, Pankaj Jaiswal and Justin Elser
P4	Free System Biology Collaborative Workbench: Design and implementation Abdul Mateen Rajput and Luca Toldo
P5	A Microfluidic Device for the Real-Time control of a Synthetic Gene Network Emanuele Orabona, Filippo Menolascina, Luca De Stefano and Diego di Bernardo
P6	Structural stability and dynamical properties of steric zipper polymorphs: implications for prion strains Francesca Stanzione, Alfonso De Simone, Luciana Esposito and Luigi Vitagliano
P7	Molecular Dynamics Simulations of Phenylalanine Hydroxylase Natural Mutants Leading to Hyperphenylalaninemia Franca Fraternali, Carla Carluccio, Arianna Fornili, Adriana Zagari and Francesco Salvatore
P8	Molecular modeling of the ligand binding domain of human Aryl hydrocarbon Receptor (AhR) and its interaction with 2,3,7,8-TCDD Maria Salzano, Anna Marabotti, and Angelo Facchiano
P9	Mutations at key pore-lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates Luisa Calvanese, Marialuisa Pellegrini-Calace, Romina Oliva
P10	CMPC: A Web Application to Visualize Residues-Residue Contacts at the Interface of Protein Complexes Anna Vangone, Romina Oliva, Luigi Cavallo
P11	Visual characterization of biomedical texts with word entropy Mirko Degli Esposti, Roxana Danger, Paolo Rosso and Sandra García Blasco
P12	REPAIRtoire . a database of DNA repair pathways Kaja Milanowska, Kristian Rother and Janusz Bujnicki
P13	A StateChart based representation for SBML descriptions Fabio Fioravanti, Manuela Helmer-Citterich and Enrico Nardelli
P14	Italian Network for Oncology Bioinformatics - RNBIO Paolo Romano
P15	An Integrated Microbial Wiki Kaushlesh Kumar Yadav, Satyendra kumar Singh and Anurag chaurasia
P16	Towards A General-Purpose Database Wiki for Biological Database Curation Heiko Mueller, Sam Lindley, Joanna Sharman, Tony Harmar, James Cheney and Peter Buneman

Presentations of invited lectures, oral communications, selected posters and tutorials will be available after the conclusion of the workshop.