Tackling Big Data in the Life Sciences
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Number 104 January 2016 ERCIM NEWS www.ercim.eu Special theme Tackling Big Data in the Life Sciences Also in this issue: Research and Society: “Women in ICT Research and Education” Editorial Information Contents JoINT ERCIM ACTIoNS ERCIM News is the magazine of ERCIM. Published quarterly, it reports on joint actions of the ERCIM partners, and aims to 4 International Workshop on Computational Intelligence reflect the contribution made by ERCIM to the European for Multimedia Understanding Community in Information Technology and Applied by Davide Moroni, Maria Trocan and Ales Prochazka Mathematics. Through short articles and news items, it pro - vides a forum for the exchange of information between the insti - CIM Working Group “Dependable tutes and also with the wider scientific community. This issue 5 Activities of the ER has a circulation of about 6,000 printed copies and is also Embedded Software-Intensive Systems” available online. by Erwin Schoitsch ERCIM News is published by ERCIM EEIG BP 93, F-06902 Sophia Antipolis Cedex, France RESEARCh AND SoCIETy Tel: +33 4 9238 5010, E-mail: [email protected] Director: Jérôme Chailloux This section “Women in ICT Research and Education” has ISSN 0926-4981 been coordinated by Lynda Hardman, CWI Editorial Board: 6 “Because it’s 2016” – Introduction Central editor: by Lynda Hardman Peter Kunz, ERCIM office ([email protected]) Local Editors: 7 Women in Informatics Research and Education Austria: Erwin Schoitsch ([email protected]) by Jane Hillston Belgium:Benoît Michel ([email protected]) Cyprus: Ioannis Krikidis ([email protected]) 8 Reflections from a Leadership Program for Women Czech Republic:Michal Haindl ([email protected]) in Scientific Positions France: Steve Kremer ([email protected]) by Katja Abrahamsson, Letizia Jaccheri and Harald Øverby Germany: Michael Krapp ([email protected]) Greece: Eleni Orphanoudakis ([email protected]), 10 The Girl Project Ada: A Successful Project for Artemios Voyiatzis ([email protected]) Recruiting Female Students to the ICT-Studies at NTNU Hungary: Erzsébet Csuhaj-Varjú ([email protected]) by Line Berg Italy: Carol Peters ([email protected]) Luxembourg: Thomas Tamisier ([email protected]) 12 Inspire, Network, Encourage – womENcourage 2015 Norway: Poul Heegaard ([email protected]) by Reyyan Ayfer and Bev Bachmayer Poland: Hung Son Nguyen ([email protected]) Portugal: Joaquim Jorge ([email protected]) 13 Integrating Gender in Research Institutions in Greece Spain: Silvia Abrahão ([email protected]) by Pavlos Hatzopoulos, Nelli Kambouri and Kathy Kikis- Sweden: Kersti Hedman ([email protected]) Papadakis Switzerland: Harry Rudin ([email protected]) The Netherlands: Annette Kik ([email protected]) 14 Women in IT Security Research: The Case of SBA W3C: Marie-Claire Forgue ([email protected]) Research by Veronika Nowak Contributions Contributions should be submitted to the local editor of your country SPECIAL ThEME Copyright notice The special theme section “Tackling Big Data in the Life All authors, as identified in each article, retain copyright of their Sciences” has been coordinated by Roeland Merks, CWI work and Marie-France Sagot, Inria. Advertising Introduction to the Special Theme For current advertising rates and conditions, see 16 Tackling Big Data in the Life Sciences http://ercim-news.ercim.eu/ or contact [email protected] by Roeland Merks and Marie-France Sagot ERCIM News online edition 17 Networks to the Rescue – From Big “Omics” Data to The online edition is published at Targeted Hypotheses http://ercim-news.ercim.eu/ by Gunnar Klau Subscription 18 Interactive Pay-As-You-Go-Integration of Life Science Subscribe to ERCIM News by sending an email to Data: The HUMIT Approach [email protected] or by filling out the form at the by Christoph Quix, Thomas Berlage and Matthias Jarke ERCIM News website: http://ercim-news.ercim.eu/ 20 Eliminating Blind Spots in Genetic Variant Discovery Next issue by Alexander Schönhuth and Tobias Marschall April 2016, Special theme: Planning and Logistics ERCIM NEWS 104 Janaury 2016 RESEARCh AND INNoVATIoN 21 Computational Estimation of Chromosome Structure by Claudia Caudai and Emanuele Salerno This section features news about research activities and innovative developments from European 22 Modelling Approaches to Inform the Control and research institutes Management of Invasive Seaweeds by James T. Murphy, Mark Johnson and Frédérique Viard 44 Secure and Privacy-Preserving Identity Management in the Cloud 24 Kbdock – Searching and Organising the Structural by Bernd Zwattendorfer, Stephan Krenn and Space of Protein-Protein Interactions Thomas Lorünser by Marie-Dominique Devignes, Malika Smaïl-Tabbone and David Ritchie 46 PRISMACLOUD – Privacy and Security Maintaining Services in the Cloud 25 The Source of the Data Flood: Sequencing Technologies by Daniel Slamanig, Agi Karyda and Thomas by Alberto Magi, Nadia Pisanti and Lorenzo Tattini Lorünser 27 Big Data in Support of the Digital Cancer Patient 47 TREDISEC: Towards Realizing a Truly Secure by Haridimos Kondylakis, Lefteris Koumakis, Manolis and Trustworthy Cloud Tsiknakis, Kostas Marias and Stephan Kiefer by Beatriz Gallego-Nicasio Crespo, Melek Önen and Ghassan Karame 28 Towards an On-board Personal Data Mining Framework For P4 Medicine 48 Smart Devices for the Home of the Future: A by Mohamed Boukhebouze, Stéphane Mouton and Jimmy New Model for Collaboration Nsenga by Daniele Spoladore, Gianfranco Modoni and Marco Sacco 30 Can Data-driven Self-Management Reduce Low Back Pain? 50 FOODWEB – Studying Food Consumption and by Kerstin Bach, Paul Jarle Mork and Agnar Aamodt Production Patterns on the Web by Christoph Trattner, Tomasz Kuśmierczyk and 31 Twitter can Help to Find Adverse Drug Reactions Kjetil Nørvåg by Mark Cieliebak, Dominic Egger and Fatih Uzdilli 51 Robots Learn Actions and Cooperative Tasks by 32 Trust for the “Doctor in the Loop” Imitation by Peter Kieseberg, Edgar Weippl and Andreas Holzinger by Maria Koskinopoulou and Panos Trahanias 34 Big Data Takes on Prostate Cancer 52 Unlocking the Secrets of the Dynamics of by Erwan Zerhouni, Bogdan Prisacari, Qing Zhong, Peter Earth’s Interior Wild and Maria Gabrani by Costas Bekas 35 Mining Electronic Health Records to Validate Knowledge in Pharmacogenomics EVENTS, IN BRIEf by Adrien Coulet and Malika Smaïl-Tabbone Announcement 36 Modelling the Growth of Blood Vessels in Health and 54 EMC² Summit in conjunction with the CPS Disease Week 2016 by Elisabeth G. Rens, Sonja E. M. Boas and Roeland M.H. Merks 54 More on IFIP TC6’s Open Digital Library 38 Modelling? Using Standards Can Help You Book by Brett G. Olivier and Bas Teusink 54 Online Social Networks: Human Cognitive Constraints in Facebook and Twitter Personal 39 Understanding Metadata to Exploit Life Sciences Open Graphs Data Datasets by Paulo Carvalho, Patrik Hitzelberger and Gilles Venturini In Brief 55 Lynda Hardman President Informatics Europe 40 Management of Big and Open Data in the Life Cycle Assessment of Ecosystem Services 55 QuSoft Research Center for Quantum Software by Benedetto Rugani, Paulo Carvalho and Benoit Othoniel Launched 42 WITDOM: Empowering Privacy and Security in Non- 55 ERCIM “Alain Bensoussan” Fellowship trusted Environments Programme by Juan Ramón Troncoso-Pastoriza and Elsa Prieto Pérez ERCIM NEWS 104 Janaury 2016 3 Joint ERCIM Actions Workshop lecture hall inside the Strahov Monastery in Prague and Dr. Joan Lasenby, invited speaker from the Engineering Department of the University of Cambridge, UK (photos taken by VIC CVUT). • Prof. Jonathan Chambers, Newcastle University, UK: Dig - International Workshop ital Signal Processing and Assistive Technologies. on Computational 41 papers were accepted for oral presentation by the pro - gramme chairs, Prof. Jonathan Chambers, Prof. Enis Cetin Intelligence for and Dr. Oldrich Vysata and the workshop featured a set of sessions focussing on current hot topics. A Data Fusion in Multimedia Understanding Biomedicine session stressed the role of computational intel - ligence in putting together data from different biosensors in by Davide Moroni, Maria Trocan and Ales Prochazka the diagnosis of disorders, treatment monitoring, rehabilita - tion and analysis of sport activities. A session was dedicated Over 80 researchers from academia and industry to Ambient Assisted Living (AAL) and Intelligent Tools for attended a workshop on Computational Intelligence for Disabled and Elderly People, where the focus was on how Multimedia Understanding organized by the ERCIM computational intelligence can be used to provide personal - MUSCLE Working Group in Prague, 29-30 October 2015. ized guidance that can empower people and foster a healthier lifestyle. Classical biological data and signal processing was The workshop was held in close collaboration with the the main theme of the BIODAT session, which featured sev - University of Chemistry and Technology and the Czech eral talks on EEG processing, including microsleep and spin - Technical University in Prague. Prof. Vladimir Marik and dles analysis. Finally, a session on Big and Linked Data was Dr. Davide Moroni were honorary chairs. included in which aspects related to smart cities, social media analytics and semantic data stream processing were Among the topics addressed by the MUSCLE working addressed. group, this year it was decided to give special emphasis to biomedical applications. Biological signals and images pose The workshop was held in the historical halls