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Semantic, Social, and Mobile Applications for Bioinformatics EMBnet.journal Volume 19 Supplement B October 2013 NETTAB 2013 Workshop on “Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories” 16-18 October 2013, Lido of Venice, Italy http://www.nettab.org/2013/ 2 EDITORIAL/CONTENT EMBnet.journal 19.B Editorial Contents Dear reader, welcome to a new supplement of Editorial ..............................................................2 EMBnet.journal, an international, open access, Preface - NETTAB 2013 ........................................3 peer-reviewed bioinformatics journal. Scientific Programme.........................................7 This supplement is dedicated to the NETTAB Keynote Lectures .............................................. 11 2013 workshop focused on Tutorials ............................................................ 15 “Semantic, Social and Mobile Applications Oral Communications .....................................20 for Bioinformatics and Biomedical Laboratories”, Posters ..............................................................63 held 16-18 October 2013 in Venice Lido, Italy. Node information ............................................88 NETTAB 2013 is the thirteenth in a series of international workshops on Network Tools and Applications in Biology. NETTAB workshops are aimed at presenting and discussing emerging ICT technologies whose adoption in support of biology could be of particular interest. EMBnet.journal is very pleased to publish the contributions to the workshop presented at this important event. For this special issue (19.B), the selection of articles was overseen by the Conference Scientific Committee, while the lay- out and logistics were organised by the EMBnet. journal Editorial Team. For future conferences, our Online Journal System (OJS) can also be used for receiving, ar- chiving and managing the full review process. In this series, we have also published the First Scientific Meeting of the COST Action, SeqAhead (issue 17.B), proceedings of the Bioinformatics EMBnet.journal Italian Society (BITS) 9th Annual Meeting, 2-4 May 2012 (issue 18.A), proceedings of the NETTAB Executive Editorial Board 2012 Workshop on “Integrated Bio-Search”, 14- Erik Bongcam-Rudloff, Department of Animal Breeding and 16 November 2012, Como, Italy (issue 18.B), Genetics, SLU, SE, [email protected] and the SeqAhead “The Next NGS Challenge Teresa K. Attwood, Faculty of Life Sciences and School of Conference: Data Processing and Integration”, Computer Sciences, University of Manchester, Manchester, UK, 14-16 May 2013, Valencia, Spain (issue 19.A). [email protected] We therefore continue to welcome contribu- Domenica D’Elia, Institute for Biomedical Technologies, CNR, tions from other Societies and Networks, and en- Bari, IT, courage interested parties to contact members [email protected] Andreas Gisel, Institute for Biomedical Technologies, CNR, Bari, IT, of the Editorial Board. [email protected] Laurent Falquet, University of Fribourg, Fribourg, CH EMBnet.journal Editorial Board [email protected] Pedro Fernandes, Instituto Gulbenkian. PT, [email protected] Lubos Klucar, Institute of Molecular Biology, SAS, Bratislava, SK, [email protected] Martin Norling, Swedish University of Agriculture, SLU, Uppsala, SE, [email protected] Vicky Schneider-Gricar, The Genome Analysis Centre (TGAC). Cover picture: Sunset on the Venice’s lagoon. Venice, Italy, Norwich, UK, 2008. [© Nicola Cannata] [email protected] EMBnet.journal 19.B EMBnet.journal 3 Preface NETTAB 2013 Workshop on “Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories” and Mobile Applications for Bioinformatics and Biomedical Laboratories”. Human beings are social animals and ICT have recently permeated human society of newer forms and ways of participation in social ac- tivities. In the Internet, the hype has shifted from Web2.0 to Social Media; in science too, this de- velopment is evident. Beside facilitating com- Nicola Cannata1, Paolo Romano2 munication and making easier the sharing of 1University of Camerino, Camerino (MC), Italy information, social platforms and technologies 2IRCCS AOU San Martino IST, Genoa, Italy are enhancing learning, problem solving and crowdsourcing. In biology, and especially in the Due to the distributed nature of biomedical in- “-omic” disciplines, we already rely on a wide dif- formation resources, and to their heterogeneity fusion of social tools and applications, e.g. for and size, it is now clear that bioinformatics plays distributed annotations, Wiki knowledge bases, an essential role in every domain of biomedical documentation and productivity. research, from experimental to clinical studies. On the other hand, access to the Internet is In this context, network tools, platforms and ap- nowadays increasingly happening through mo- plications are one of the most relevant research bile devices. Mobile Internet access is expect- and development domain for bioinformatics, ed to soon overtake access from standard PCs because they may indeed allow an efficient and workstations. Moreover, mobile phones are and effective integration of information, that is expected to become the main personal com- the basis for any further data analysis. puting devices. Smartphones and tablets rep- Since 2001, a series of workshops has been de- resent the most practical computing devices in voted to this topic and held annually in Italy, un- biomedical laboratories and they actually are der the name of “Network Tools and Applications the ideal companions for “always on the move” in Biology” (NETTAB). These workshops have been scientists. While we can observe a widespread aimed at presenting and discussing some of the diffusion of health and lifestyle mobile applica- most innovative Information and Communication tions and a rapid adoption of mobile solutions Technologies (ICTs) and their application in the in medicine and healthcare we cannot say the biomedical domain. same for life sciences and bioinformatics. Each workshop has been focused on a different Semantic methodologies and technologies are topic. Since 2001, many different focus themes instead well established in “-omic” projects. It have been explored, including Standardization can even be proudly observed that the bioin- for data integration (Genoa, 2001), Multi Agent formatics community was an early adopter of Systems (Bologna, 2002), Scientific workflows Semantic Web technologies. (Naples, 2005), Grid and Web Services (Santa In the NETTAB 2013 workshop, mobile and/or so- Margherita di Pula, 2006), Semantic Web (Pisa, cial and/or semantic solutions for bioinformatics 2007), Collaborative research and development and laboratory informatics problems will be ex- (Catania, 2009), and Biological Wikis (Naples, plored. It is our opinion that a savvy combina- 2010). tion of these three technologies could greatly The NETTAB 2013 workshop, the thirteenth in the enhance the research outcome of life scientists series, is held in Lido of Venice, Italy, on October and markedly simplify the workflows in biomedi- 16-18, 2013. It is focused on “Semantic, Social, cal laboratories. 4 Volume 19.B EMBnet.journal The workshop is open to all aspects of the focus The Chairs of the NETTAB 2013 workshop hope theme, including issues, methods, algorithms, that this is a great meeting for all participants. and technologies for the design and develop- Ideas, and doubts, on the perspectives of the ment of tools and platforms able to provide widespread application of these new technolo- semantic, social, and mobile applications sup- gies will be discussed with outstanding scien- porting bioinformatics and the activities carried tists such as Antony Williams, Ross King, Barend out in a biomedical laboratory. Mons, Andrea Splendiani, Christine Chichester, The Call for abstracts was able to attract 20 qual- Dominique Hazaël-Massieux, and Alex Clark, ity submissions that are after peer review and re- who present invited keynotes and tutorials, and vision included in these proceedings, grouped many others who enthusiastically join the work- by submission type. Oral communication ab- shop and actively participate in it. stracts are listed according to the presentation We wish to thanks all participants, but also all in the programme, while poster abstracts are or- Supporting Institutes and companies that made dered by first author name. this workshop possible and successful. Speakers Keynote Speakers Oral presentations Antony Williams Christine Chichester Royal Society of Chemistry René Witte Ismael Navas-Delgado Ross D. King Fabio Rinaldi School of Computer Science, University of Rebecca Lawrence Manchester, Manchester, United Kingdom Tim P. Eyres Barend Mons Steffen Möller Leiden University Medical Center, Leiden, Stian Soiland-Reyes and Netherlands Bioinformatics Center, The Alejandra Gonzalez-Beltran Netherlands Martijn Devisscher Larisa N. Soldatova Tutorials Mario Cannataro Andrea Splendiani IntelLeaf, United Kingdom, and Digital Enterprise Research Institute, Ireland Christine Chichester Swiss Institute of Bioinformatics, CALIPHO group, Geneva, Switzerland Dominique Hazaël-Massieux W3C/ERCIM, Sophia Antipolis, Biot, France Alex Clark Molecular Materials Informatics, Inc EMBnet.journal 19.B EMBnet.journal 5 Editors Paolo Romano IRCCS AOU San Martino IST, Genoa, Italy Nicola Cannata University of Camerino, Camerino (MC), Italy Chairs and Conference Committees Chairs Nicola Cannata University of Camerino, Camerino (MC), Italy Barend
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