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WebST 2016: early registration deadline 19 January
by GRLMC 25 Dec '15

25 Dec '15

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ***************************************************************************** INTERNATIONAL SUMMER SCHOOL ON WEB SCIENCE AND TECHNOLOGY WEBST 2016 BILBAO, SPAIN JULY 18-22, 2016 Organized by: University of Deusto Rovira i VirgiliUniversity http://grammars.grlmc.com/webst2016/ ***************************************************************************** AIM: WebST 2016 is a research training event addressed to graduates and postgraduates in the first steps of their academic career. With a global scope, it aims at updating them about the most recent advances in the critical, multidisciplinary and fast developing area of web studies, which covers a large spectrum of current exciting research and industrial innovation from computing and technologies to social sciences and the humanities and has turned out to be the largest socio-technical infrastructure in human history. Renowned academics and industry pioneers will lecture and share their views with the audience. Most subareas of web science and technology will be displayed, namely: content analysis and information extraction, information networks, search, data and semantics, ontologies, user behavior and personalization, online communities, social networks, economic transactions, mobility, security and privacy, graph analysis, web mining and applications. Main challenges and opportunities will be identified through 4 keynote lectures, 20 six-hour courses, and 1 round table, which will tackle the most active and promising topics from various perspectives: philosophy, sociology, politics, digital humanities, economics, computer science, engineering and mathematics. The organizers believe outstanding speakers will attract the brightest and most motivated students. Interaction will be a main component of the event. Moreover, an open session will give participants the opportunity to present their own work in progress in 5 minutes. ADDRESSED TO: Graduates and postgraduates from around the world. There are no formal pre-requisites in terms of academic degrees. However, since there will be differences in the course levels, specific knowledge background may be assumed for some of them. WebST 2016 is also appropriate for more senior people who want to keep themselves updated on recent developments and future trends. All will surely find it fruitful to listen and discuss with major researchers, scholars, industry leaders and innovators. REGIME: In addition to keynotes, at least 2 courses will run in parallel during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another. VENUE: WebST 2016 will take place in Bilbao, the capital of the Basque Country region, famous for its gastronomy and the seat of the GuggenheimMuseum. The venue will be: DeustoTech, School of Engineering University of Deusto Avda. Universidades, 24 48014 Bilbao KEYNOTE SPEAKERS: (to be completed) Ricardo Baeza-Yates (Yahoo Labs), Big Data in the Web Jiawei Han (University of Illinois, Urbana-Champaign), From Data to Knowledge: A Data-to-Network-to-Knowledge (D2N2K) Paradigm Amit P. Sheth (WrightStateUniversity), Building Intelligent Systems: Semantic, Cognitive and Perceptual Computing to Exploit Physical-Cyber-Social Big Data PROFESSORS AND COURSES: (to be completed) Boualem Benatallah (University of New South Wales), [advanced] API Engineering and Management Vassilis Christophides (INRIA, Paris), [introductory/intermediate] Entity Resolution in the Web of Data Aldo Gangemi (Italian National Research Council, Rome), [intermediate/advanced] Open Knowledge Extraction: From Machine Reading to the Semantic Web Alon Halevy (Recruit Institute of Technology), [introductory] Structured Data on the Web Jiawei Han (University of Illinois, Urbana-Champaign), [intermediate] Construction and Mining of Text-Rich Heterogeneous Information Networks Andreas Hotho (University of Würzburg), [intermediate] Social Semantics in the Web Ravi Kumar (Google), tba Haewoon Kwak (Qatar Foundation), [introductory/intermediate] From Social Network Analysis to Social Media Analytics and beyond: Challenges and Opportunities Cathy Marshall (TexasA&MUniversity), [introductory] Qualitative Methods for Studying Users on the Web Mirco Musolesi (University College London), [introductory/intermediate] Mining Big (and Small) Mobile Data Bijan Parsia (University of Manchester), [introductory] The Semantic Web and Linked Data Prabhakar Raghavan (Google), tba Uli Sattler (University of Manchester), [introductory] OWL, Underlying Logics, and What This Reasoning Is All about Munindar P. Singh (North CarolinaStateUniversity), [introductory/intermediate] Web Applications as Sociotechnical Systems: A Basis for a Science of Security and Privacy Barry Smith (University at Buffalo), [introductory] Towards Ontological Foundations for Web Science Raphael Volz (Pforzheim University of Applied Science), [introductory] Improving Prediction Models with Open Data OPEN SESSION An open session will collect 5-minute presentations of work in progress by participants. They should submit a half-page abstract containing title, authors, and summary of the research to florentinalilica.voicu (at) urv.cat by July 15, 2016. ORGANIZING COMMITTEE: Carlos Martín-Vide (co-chair) Manuel Jesús Parra Royón Borja Sanz (co-chair) Florentina Lilica Voicu REGISTRATION: It has to be done at http://grammars.grlmc.com/webst2016/Registration.php The selection of up to 8 courses requested in the registration template is only tentative and non-binding. For the sake of organization, it will be helpful to have an approximation of the respective demand for each course. Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed and the on-line registration facility disabled when the capacity of the venue will be completed. It is much recommended to register prior to the event. FEES: Fees are a flat rate covering the attendance to all courses during the week. There are several early registration deadlines. Fees depend on the registration deadline. ACCOMMODATION: Suggestions of accommodation will be available on the webpage in due time. CERTIFICATE: Participants will be delivered a certificate of attendance. QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu (at) urv.cat ACKNOWLEDGEMENTS: University of Deusto Rovira i Virgili University

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Registration open: Course Essential skills in data-intensive research - enabling your life science research, 25-29 January 2016, Utrecht
by Celia.vanGelder＠radboudumc.nl 22 Dec '15

22 Dec '15

Course Essential skills in data-intensive research - enabling your life science research Date: 25-29 January 2016 Location: Surf<https://www.surf.nl/en/about-surf/contact/directions-to-surf-surfmarket-and…>, Utrecht Website including registration: https://www.surf.nl/en/agenda/2016/01/essential-skills-in-data-intensive-re… COURSE DESCRIPTION Successfully undertaking a PhD in the 21st century requires researchers, from all disciplines, to have basic training in software development and the management and stewardship of their data resources. However, for many scientists, the prospect of developing the skills needed to engage increasingly diverse and complex e-infrastructure is daunting. For this reason, NLeSC,<https://www.esciencecenter.nl/> and its partners SURFsara<http://www.surfsara.nl/>, DTL<http://www.dtls.nl/> and VU<http://www.vu.nl/en/> have set up a course that will provide PhD students in the life sciences, who are developing software or working with large data resources, the experience and knowledge to empower their use of data and development of research software. It will equip participants with essential skills required to optimise their research now and in the coming years.  Students completing this course will have the basic skills and knowledge required to manage large datasets, utilise databases, produce metadata and ensure the long-term stewardship of their data. The course will provide students with their first introductions to programming and will demonstrate that anyone can code. Participants will also understand the basic requirements of sustainable software development, including the use of coding environments and the need for version control and testing. Key aspects of software and data carpentry and data stewardship will be taught. Finally, the course will provide an introduction to e-infrastructure and show how this can be accessed and used to improve the speed and quality of research. For Life sciences the following essentials will be brought forward in the course: · Dealing with Data: Data Provenance & PID, FAIR Data Stewardship, From Excel to databases, SQL & Python practicals · Computation & Automation: Introductions to command line, programming (Python), Github, version control, unit testing, Debugging, Documentation. · e-Infrastructure: Introduction and examples moving from small local to big national compute and data storage services. Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31613375327 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Vacancy Scientist Biostatistics / Biotechnology @ DSM, Delft, The Netherlands
by Roubos, Hans 22 Dec '15

22 Dec '15

Dear colleagues, We have an open position for a: Scientist Biostatistics Research & Development | Netherlands, Delft Job ID: NUTR01669 | Close date: 2016-01-18 The Challenge Within the DSM Biotechnology Center there is a vacancy for the position of Scientist Biostatistics Located at Delft, The Netherlands The Position * As a Scientist Biostatistics, you will be located at the DSM Biotechnology Center in Delft, supporting business-driven R&D projects with design of experiments, data processing and statistically analysis for end-applications in food, pharma and/or bio-based chemicals and fuels. * Being part of the bioinformatics & modeling group, you will participate in multidisciplinary teams in which you will be the statistical expert across the different disciplines. * Projects may range from medium to high-throughput screenings for enzyme and strain development, applied biochemistry and analytical data, to QA/QC support for manufacturing, depending on your background and interest. * Your challenge will be to develop, implement and apply state-of-the-art statistical tools and workflows. The Ideal * Ph.D. in chemometrics, statistics, metabolic modeling, computational methods, bioinformatics, or a related discipline. Additional training or degree in biochemistry, molecular biology, food or biotechnology is considered to be an advantage. * Preferably 2-5 year experience, preferably in statistical data processing of biological data or fermentation data * Experience in setting up and applying statistical tools for quality control is an advantage. * Expert in R, Matlab, Spotfire, SAS, Minitab, Statgraphics or other statistical software packages * Experience using optimal experimental design techniques is a plus * Strong desire and proven ability to work collaboratively in multi-disciplinary project teams * Multidisciplinary team player, who takes initiative * Personal skills like problem analysis, creativity and being a strong communicator characterize your identity. DSM's wide diversity of disciplines makes it possible to offer employees a great variety of roles throughout their career. For instance, you may start your career in an area related to your education or qualifications, but your future is what you make of it. At DSM we stimulate people to determine their own career path and we encourage international careers. We strive to be an Employer of Choice and ensure that our employees are nurtured and given the opportunity to develop their talents. To learn more about DSM's HR vision and policy, please visit our website at www.dsm.com/career. The Procedure and Contact The DSM Recruitment and Selection Process is in line with the general procedure outlined elsewhere on our Career World. Please apply on-line and send your CV & cover letter and include information on your current remuneration. Please submit your application before deadline:10th of August Reference check procedures are part of the DSM Recruitment & Selection Process. You will be contacted when these references checks are required. http://www.dsm.com/corporate/careers/vacancies/dsmvacancies.html #LI-HN1 Kind regards, Hans Roubos | Principal Scientist Bioinformatics & Modeling | DSM Food Specialties B.V. | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | T +31 (0)15 2792147 | Trade Register Number 27235314 | Stay connected: [http://static.dsm.com/content/dam/dsm/images/twitter.png] <https://twitter.com/DSM> [http://static.dsm.com/content/dam/dsm/images/linkedin.png] <https://www.linkedin.com/company/3108> [http://static.dsm.com/content/dam/dsm/images/youtube.png] <https://www.youtube.com/user/dsmcompany> [http://static.dsm.com/content/dam/dsm/images/googleplus.png] <https://plus.google.com/117689312065000346895#117689312065000346895/posts> [http://static.dsm.com/content/dam/dsm/images/facebook.png] <https://www.facebook.com/DSMcompany> [http://static.dsm.com/content/dam/dsm/images/DSM_Email_EN.jpg] ________________________________ DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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ALPHY 2016
by Denis BAURAIN 22 Dec '15

22 Dec '15

Apologies for cross-posting :-) __________________________________________________ ALPHY 2016: French-Belgian meeting on Bioinformatics and Evolutionary Genomics March 17-18 2016, Lille (France) Important date: Deadline for abstract submission, travel grant application and registration: January 15 2016 ALPHY is an annual meeting, organized in France since 1995, dedicated to the field of Bioinformatics and Comparative Genomics (ALPHY = ALignments and PHYlogeny). The main goal of this meeting is to promote informal communication in this highly multidisciplinary field, and to encourage young scientists to present their work. This year, ALPHY is co-organized by Belgian and French scientists in Lille, with the hope of enhancing scientific exchanges between research groups of these two countries. There will be two invited speakers (Karine Van Doninck and Christian Parisod), and the program will be open for around 20 contributions of 20' talks. ALPHY is funded by the GdR BiM (working group in Molecular Bioinformatics). Registration to the meeting is free, but mandatory. Please use the link below to register. If you wish to present your work, please submit an abstract in the registration form. Some budget will be available for supporting the travel expenses of young speakers. Please indicate whether you are asking for such a travel grant when registering. Tot straks ! A bientôt ! See you in Lille ! Alphy 2016 web site: http://lbbe.univ-lyon1.fr/alphy/ Contact: celine.poux(a)univ-lille1.fr The organizing committee: Denis Baurain Céline Brochier-Armanet Laurent Duret Nicolas Galtier Philippe Lemey Céline Poux Xavier Vekemans __________________________________________________

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New permanent position: drug discovery data scientist, Janssen
by Ceulemans, Hugo [JRDBE] 21 Dec '15

21 Dec '15

Drug discovery data scientist Key words: data sciences, computational biology, bioinformatics, drug discovery Permanent position at Janssen in Beerse Context Within the Discovery Sciences group, which provides advanced technology support to drug discovery projects in Janssen, the Computational Sciences department is responsible for comprehensive analyses of high-dimensional datasets. The position will be opened on the Beerse campus, which is the largest R&D center for small molecules within the entire Janssen group, investing over 1 billion euros each year in R&D. Activities cover the integration of information from the broadest possible spectrum of datasources (chemical structure, microscopy images and omics, ...) to comprehensively infer biological activities of millions of chemical compounds, and to apply these predictions to inform projects. In addition, the team designs and supports the execution of the generation of high-dimensional datasets (from cytometry or various sequencing approaches) from patient-derived material. The team is also responsible for the use of these data for the identification of potential mechanisms of disease and targets of intervention and the subpopulations of patients these mechanisms apply to. Job description In the context of the latter task, the department is opening a permanent position for a drug discovery data scientist, who will focus on the analysis and interpretation of high-dimensional datasets to identify interventional strategies for neurological, cardiovascular and metabolic, infectious, immunological or oncological diseases. The candidate will be responsible for * the translation of questions of disease experts in the therapeutic areas and wet lab colleagues, to a quantitative analysis formulation * the design and execution of targeted analysis approaches to link processed molecular and cellular data at scale to pathophysiological processes or clinical outcome, to produce actionable conclusions and to inform decision making * the development and internalization of rigorous state-of-the-art approaches for integrative data analysis, and build-out and leveraging of collaborations with leading academic and industrial scientific teams in life, computational and data sciences * work with informatics and statistics colleagues to offer the resulting analysis and visualization solutions to the project teams * contributing to the scientific weight of the department by authoring peer-reviewed papers and presenting at relevant conferences Qualifications and skills * PhD in Computational Biology or any related quantitative field with direct exposure to multidisciplinary biology or clinical context with ideally a few years of post-doctoral experience in an academic or industrial setting * demonstrated experience with linking high-dimensional molecular data, to phenotypic or clinical outcomes in constellations that led to hypothesis driven experimental or clinical follow-up * advanced programming and scripting skills that enable the development of functional prototypes * excellent communication, reporting and team interaction skills, self-motivation, proactivity and the ability to work independently If you are interested, please reply with the appropriate documentation to hceulema - at - its - dot - jnj - dot - com.

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bioinformatics Post-doc position for 2 years
by Stephane Rombauts 19 Dec '15

19 Dec '15

Dear. > Comme vous le savez nous sommes toujours à la recherche d’un(e) candidat(e) pour un postDoc en bio-analyse . > Si la personne est étrangère et n’a pas séjourné en France nous pouvons lui proposer un contrat plus long >grace a un financement régional que nous avons obtenu sur le projet . in attachment position in France Roscoff (Bretagne) for a bioinformatics position for 2years if the candidate is currently not living in France. Deadline end of 2015!!! Best regards

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Computational Cancer Biology with GSK
by Lodewyk Wessels 18 Dec '15

18 Dec '15

Computational cancer biology for precision medicine Project outline For an ambitious joint project between the Netherlands Cancer Institute (NKI, Amsterdam, The Netherlands) and Glaxo Smith Kline (Philadelphia, USA) we invite excellent and ambitious postdocs with expertise in computational biology to apply. It is the goal of this international team to study BET and EZH2 inhibitors. More specifically, we will explore the molecular responses to these inhibitors, identify and understand additional mechanisms of acquired and intrinsic resistance and identify markers of sensitivity and resistance to these inhibitors. We will employ public and proprietary data derived from model systems as well as patient data. In addition to chemical profiling data, these data include gene expression, copy number and ChIP-sequencing profiles as well as mutation data. The expected duration of the initial phase of the project is 2 years. The computational biologists will collaborate closely with experimentalists, and there will be ample opportunity to validate hypotheses generated through computational analyses. Requirements Degree in bioinformatics, physics, engineering, computer science or mathematics A strong cancer biology interest and/or background Proficiency in programming languages such as R, Python, Perl. Contact details Please contact Lodewyk Wessels (phone +31 20 512 7987, e-mail: l.wessels(a)nki.nl <mailto:l.wessels@nki.nl>) or Mike McCabe (e-mail: michael.t.mccabe(a)gsk.com <mailto:michael.t.mccabe@gsk.com>). When applying, please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached as references. Also see http://ccb.nki.nl/open-positions/ <http://ccb.nki.nl/open-positions/> for further information. Closing date 15 February 2016

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Systems Biology post-doctoral position available: European Institute for Systems Biology and Medicine, Lyon France
by Bertrand 18 Dec '15

18 Dec '15

Dear all, We open a post-doctoral researcher position in Systems Biology and Medicine at CNRS-EISBM in Lyon, France, in relation to the IMI-eTRIKS consortium. The subject is '*Module-based development of disease-specific network reconstructions for data interpretation, disease stratification and biomarker discovery*'. We are looking for highly motivated candidates with a PhD in computational biology, systems biology, bioinfrmatics or equivalent. Experience in pathway reconstruction and familiarity with Systems Biology standards (SBGN, BioPAX, SBML) is desirable. Experience in programming (Java, Python) would also be desirable. The position requires good communication skills in English and involves working in collaboration with eTRIKS partners on translational medicine projects across Europe. More details can be found in the atached document. Please send your CV, application letter and the name of two references to Dr Charles Auffray: jobs(a)eisbm.org, mentionning the reference 'EISBM-12-15-AM'. Don't hesitate to circulate this offer to anyone interested! Best regards, Bertrand De Meulder -- EISBM logo <http://www.eisbm.org> *Bertrand De Meulder Researcher * European Institute for Systems Biology and Medicine Campus Charles Mérieux - Université de Lyon CNRS - UCBL - ENS *E-mail:*bdemeulder@eisbm.org <mailto:bdemeulder@eisbm.org> *Office:* +33(0)4 37 28 74 41 *Office* Université Claude Bernard 3^e étage plot 2 50 Avenue Tony Garnier 69366 Lyon cedex 07 France *Laboratory* LyonBioPôle - Centre d'Infectiologie 2^e étage Bât. Domilyon 321 Avenue Jean Jaurès 69007 Lyon France Follow us : EISBM eisbm.org <http://www.eisbm.org> | Facebook Facebook <http://www.facebook.com/EISBM> | Twitter Twitter <http://twitter.com/EISBM_EU> --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Bioinformatics post-doctoral position available: European Institute for Systems Biologi and Medicine, Lyon France
by Bertrand 18 Dec '15

18 Dec '15

Dear all, We open a post-doctoral researcher position in Bioinformatics at CNRS-EISBM in Lyon, France, in relation to the IMI-eTRIKS consortium. The subject is ' *Disease and target-specific knowledge enrichment using disease network models* '. We are looking for highly motivated candidates with a PhD in computational biology, bioinformatics, computer sciences, mathematics, physics or engineering, with a strong basis in programming (Python, Matlab, C/C++, Java, R or similar). Experience of analysis of biological networks is desirable. The position requires good communication skills in English and involves working in collaboration with eTRIKS partners on translational medicine projects across Europe. More details can be found in the atached document. Please send your CV, application letter and the name of two references to Dr Charles Auffray: jobs(a)eisbm.org, mentionning the reference 'EISBM-12-15-MS'. Don't hesitate to circulate this offer to anyone interested! Best regards, Bertrand De Meulder -- EISBM logo <http://www.eisbm.org> *Bertrand De Meulder Researcher * European Institute for Systems Biology and Medicine Campus Charles Mérieux - Université de Lyon CNRS - UCBL - ENS *E-mail:*bdemeulder@eisbm.org <mailto:bdemeulder@eisbm.org> *Office:* +33(0)4 37 28 74 41 *Office* Université Claude Bernard 3^e étage plot 2 50 Avenue Tony Garnier 69366 Lyon cedex 07 France *Laboratory* LyonBioPôle - Centre d'Infectiologie 2^e étage Bât. Domilyon 321 Avenue Jean Jaurès 69007 Lyon France Follow us : EISBM eisbm.org <http://www.eisbm.org> | Facebook Facebook <http://www.facebook.com/EISBM> | Twitter Twitter <http://twitter.com/EISBM_EU> --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Computational Biology post-doctoral position available: European Institute for Systems Biology and Medicine, Lyon France
by Bertrand 18 Dec '15

18 Dec '15

Dear all, We open a post-doctoral researcher position in Computational Biology at CNRS-EISBM in Lyon, France, in relation to the IMI-eTRIKS consortium. The subject is 'Contribution to the development of eTRIKS Galaxy tools and workflows for disease stratification and biomarker discovery from single and multiple omics datasets'. We are looking for highly motivated candidates with a PhD in sciences, computational biology, bioinformatics, computer sciences or equivalent, with a strong basis in programming (R and python), experience in omics analysis and excellent IT skills. Good communication skills in English are required, and experience with Big Data computing in a plus. More details can be found in the atached document. Please send your CV, application letter and the name of two references to Dr Charles Auffray: jobs(a)eisbm.org, mentionning the reference 'EISBM-12-15-BDM'. Don't hesitate to circulate this offer to anyone interested! Best regards, Bertrand De Meulder -- EISBM logo <http://www.eisbm.org> *Bertrand De Meulder Researcher * European Institute for Systems Biology and Medicine Campus Charles Mérieux - Université de Lyon CNRS - UCBL - ENS *E-mail:*bdemeulder@eisbm.org <mailto:bdemeulder@eisbm.org> *Office:* +33(0)4 37 28 74 41 *Office* Université Claude Bernard 3^e étage plot 2 50 Avenue Tony Garnier 69366 Lyon cedex 07 France *Laboratory* LyonBioPôle - Centre d'Infectiologie 2^e étage Bât. Domilyon 321 Avenue Jean Jaurès 69007 Lyon France Follow us : EISBM eisbm.org <http://www.eisbm.org> | Facebook Facebook <http://www.facebook.com/EISBM> | Twitter Twitter <http://twitter.com/EISBM_EU> --- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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