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[bioinfo] NETTAB 2017
by Alexander Botzki 16 Mar '17

16 Mar '17

--------------------------------------------------------------------------------- NETTAB 2017 Methods, tools & platforms for Personalized Medicine in the Big Data Era 16-18 October 2017, Palermo, Italy http://www.igst.it/nettab/2017/ CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS AND POSTERS Keynote Speakers (confirmed only) - Winston Hide, Professor of Computational Biology, University of Sheffield, UK. - Anita Grigoriadis, Lecturer in Cancer Bioinformatics, King's College, London, UK. - Further Keynote speakers will be announced soon. TOPICS The special topic is "Methods, tools & platforms for Personalized Medicine in the Big Data Era", which includes: Data management: Biomedical Big Data Management, Standards for Clinical and Genetic Data, Data Privacy and Security, Omics Data Integration, Biobanks Data analysis: Omics Data analysis, Genetic Mutation Analysis, Biomarkers Discovery, NGS Data Analysis, Patient Information Analytics Tools and Services: Clinical Genomics Services, Models for Clinic and Genetic Data, Mobile tools and applications, Interoperability of Clinical and omic tools, Communication Technologies for Health-Care. Platforms: Integrated Data Warehouses, Integration of Applications and Data Services, Clinical Decision Support Systems, Healthcare Systems Traditional NETTAB topics also apply (see full list in the web site). DEADLINES Abstracts for oral communications: May 26, 2017 Abstracts for posters, software demo and late posters: TBA INSTRUCTIONS Submissions are sought for oral communications, posters and software demos. Abstracts must be submitted at http://www.easychair.org/conferences/?conf=nettab2017 See full instructions: http://www.igst.it/nettab/2017/submissions/instructions-for-authors/ CHAIRS Paolo Romano & Alfonso Urso & Alfonso Valencia CONTACTS Email: nettab.workshops(a)gmail.com Twitter: @NETTABWorkshops Announce list: https://groups.google.com/d/forum/nettab-announce LinkedIn: https://www.linkedin.com/groups/3209661 Paolo Romano IRCCS AOU San Martino IST Genova, Italy Skype: p.romano Email: paolo.romano(a)hsanmartino.it - paolo.dm.romano(a)gmail.com

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[Final Days for Registration] Lorentz Centre workshop Life Sciences with Industry 2017 in Leiden: April 3 – 7, 2017
by Ertaylan Gökhan (MACSBIO) 15 Mar '17

15 Mar '17

Dear All, This is a final reminder to register for the Lorentz Centre workshop Life Sciences with Industry 2017 before 19th of March 2017. There are only a few spots left. Best Regards, Gökhan Ertaylan, PhD Maastricht Centre for Systems Biology (MaCSBio) - Maastricht University http://macsbio.maastrichtuniversity.nl/ Universiteitssingel 60, 6229 ER Maastricht • +31 (0) 43 38 81123 [cid:AD5B6BCD-6229-45A4-9606-B735CFDC8172@wireless.unimaas.local] [cid:C5024CF8-88BC-4C23-8AB4-4EC19083DB86@wireless.unimaas.local] This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. ************************************************************************************* We invite researchers (especially PhD students and postdocs) from all branches of the life sciences to participate in the one-week Lorentz Centre workshop Life Sciences with Industry 2017 in Leiden: April 3 – 7, 2017. During the workshop, the about 24 participants will tackle in groups of eight, three scientifically challenging and commercially important problems formulated by the following three companies. Bejo Zaden B.V. Genomic selection, genome-wide selection or genomic prediction in vegetables BaseClear B.V. DNA data storage: reading and writing data in DNA in fast and cost-effective way Heineken Getting the taste of alcohol in alcohol-free drinks For a full description of these challenges see: https://www.lorentzcenter.nl/lc/web/2017/862/info.php3?wsid=862&venue=Snell… The workshop will take place in Leiden in the building of the Lorentz Center, an organisation that is specialised in organising scientific workshops (http://www.lorentzcenter.nl/) To create multi-disciplinary teams, participants will be selected based on their (i) specific background, (ii) motivation to participate, and (iii) date of registration (first come first served). Register on the workshop website:https://www.lorentzcenter.nl/lc/web/2017/862/registration.php3?wsid=862&venue=Snellius Deadline: Sunday March 19, 2017. Participation is free of charge, including hotel accommodation, lunches and two dinners during the workshop. The workshop is sponsored by the Lorentz Center, the Research School BioSB (http://biosb.nl/) NWO - Domain Applied and Engineering Sciences (http://www.stw.nl/) and the three companies involved. Need for more information? Contact (Gerda Filippo<mailto:filippo@lorentzcenter.nl>) at the Lorentz Center (phone +31 71 527 5401). We hope to welcome you on April 3rd 2017. the organisers: • Dr. Gökhan Ertaylan, MaCSBio, Maastricht University • Dr. Karen van Eunen, University of Groningen • Dr. Ellen Feddes, NWO-Domain Applied and Engineering Sciences, Utrecht • Prof. Dr. Bas Teusink, Vrije Universiteit Amsterdam • Prof. Dr. em. Roel van Driel, Universiteit van Amsterdam *************************************************************************************

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DILS 2017
by Venkata Pardhasaradhi SATAGOPAM 13 Mar '17

13 Mar '17

Dear all, Apologies if you receive this more than once ####################################################################### CALL FOR PAPERS (DILS'17) 12th International Conference on Data Integration in Life Science 2017 November 14-15, 2017, Luxembourg city, Luxembourg Conference Website: http://www.elisa-project.lu/en/dils-2017/ (FULL PAPER SUBMISSION DEADLINE: 2017/Jun/01) ####################################################################### The DILS conference aims to promote research and innovation in data and knowledge integration, sharing and exchange in the domain of life sciences. The notion of life sciences is expansive including the domains of biology and bioinformatics, biomedical data, medical data, environment data, and clinical and health information. Researchers, informaticians, students and entrepreneurs from biology, medicine, computer science and engineering, and clinical informatics are invited to share their knowledge and experience. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ TOPICS AND AREAS RESEARCH PAPERS ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ • Life Science Data Modelling o "Big Data" infrastructure o Data integration systems o Data models and standards o Ontology and its evolution o Architectures and data management techniques • Analysing, Indexing, and Querying Life Sciences Datasets o Linked Open Data o Machine Learning o Query formulation, processing and optimization • Annotating, Matching, and Sharing Life Sciences Datasets o Data annotation and maintenance o Ontology and Schema Matching • Privacy and Provenance of Life Sciences Datasets o Ethical, legal and social issues o Data owner sensitive data sharing o Privacy-preserving data integration and management o Sharing, updating and propagating data Industry papers, demos and application/experiences are also welcome to DILS'17. They will be selected according to industry-compliant assessment criteria. In all cases please refer to the submission procedure: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ PAPER SUBMISSION AND PUBLICATION ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Authors are invited to submit original contributions of technical rigor and practical relevance to DILS 2017. Three types of papers will be selected: Full research papers (up to 15 pages) Short research papers (8 pages) Industry/application/experience papers (8 pages). Papers are to be prepared using LNCS templates and submitted using the EasyChair site: https://easychair.org/conferences/?conf=dils2017 The proceedings of DILS will be published by Springer in the LNCS/LNAI/LNBI (Lecture Notes in Bioinformatics). ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ IMPORTANT DATES +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ June 1st , 2017: Paper submission deadline for research, industry, posters, demonstration, and application/experience papers August 25th , 2017: Notification of acceptance September 20th , 2017: Camera-ready copy due November 14-15, 2017: Conference days +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ORGANIZING COMMITTEE +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ General Chairs: • Marcos DA SILVEIRA • Cédric PRUSKI • Reinhard SCHNEIDER -- Venkata P. Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-6949 venkata.satagopam(a)uni.lu<mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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job opening
by Nicolaes G (BIOCH) 13 Mar '17

13 Mar '17

JOB OPENING Structural Bioinformatician (M/F) - PhD student position - 4 years 1. Description PhD student It is increasingly recognized that modulation of the immune system and inflammatory responses by immune checkpoint regulators, such as co-stimulatory molecules, control cellular functioning in health and disease. Our laboratory has a long history in the investigation of the role of co-stimulatory molecules in cardiovascular disease, including atherosclerosis and obesity. A recently obtained grant will further focus on the cell type specific regulation of immune checkpoint inhibitors, including CD40-CD40L interactions, and the signaling intermediates involved, in order to design and test novel therapeutics. TRAF signaling is an essential step in the co-stimulatory signaling process through the TNF-receptor in response to the presence of several known ligands. Functional CD40-TRAF signaling is known to have important contributions to development of a number of pathologies, including atherosclerosis and diabetes. You will use structural bioinformatics methods including virtual ligand screening to develop and optimize novel small-compound based therapeutic strategies. You will use rational methods to select potential ligands that target TRAF isoforms which may eventually be developed into novel orally available drugs to treat atherosclerosis. Based on the information collected in a previous project and based on functional studies of the same biological pathways also small compounds interfering with other targets in the same signaling pathway may be addressed. The compounds will be tested for their efficacy in in vitro assays as well as several relevant mouse models. Relevant papers - Zarzycka B, Seijkens T, Nabuurs SB, Ritschel T, Grommes J, Soehnlein O, Schrijver R, van Tiel CM, Hackeng TM, Weber C, Giehler F, Kieser A, Lutgens E, Vriend G, Nicolaes GA. Discovery of small molecule CD40-TRAF6 inhibitors.<http://www.ncbi.nlm.nih.gov/pubmed/25622654> J Chem Inf Model. 2015 23;55:294-307. - Chatzigeorgiou A, Seijkens T, Zarzycka B, ......Nicolaes G, Chavakis T, Lutgens E. Blocking CD40-TRAF6 signaling is a therapeutic target in obesity-associated insulin resistance.<http://www.ncbi.nlm.nih.gov/pubmed/24492375> Proc Natl Acad Sci U S A. 2014; 111:2686-91. 2. We ask For this four-year project (ERC Consolidator grant) we are searching for a PhD-student with a master degree in biomedical sciences, life sciences, medicinal chemistry or biochemistry. Especially candidates with experience in structural bioinformatics, drug design and programming in a LINUX environment are requested to apply. We search a PhD-student who is fascinated by scientific research and innovation, motivated and eager to learn, who can work methodically and accurately and who is a great team player and has great communication and presentation skills in English. The ideal candidate will combine in silico and in vitro experimentation. Considering a potential small teaching opportunity, the ability to speak Dutch would be considered an advantage. 3. Where... You will work in a multidisciplinary international team that focuses on the interplay between the vessel wall, plasma proteins and immune cells. This team is embedded in the Department of Medical Biochemistry of the Academic Medical Center Amsterdam (Amsterdam), and Maastricht University (Maastricht). The candidate will first be stationed at the Maastricht University, where you will work in the group of Dr. Gerry Nicolaes, expert in the development of small compounds. You will be trained in drug discovery, design and optimization under the direction of Dr. Gerry Nicolaes. Upon positive identification of novel biologically active compounds, you will be actively involved in the functional characterisation of molecules via in vitro and in vivo assays at the Amsterdam department of Medical Biochemistry, working under the direction of Prof. Esther Lutgens. 4. We offer You will be employed on the basis of a 36-hour week. Appointment is for four years. Your salary will depend on your qualifications and experience (according to UMC-CAO). 5. Contact details For more information please contact dr. G. Nicolaes (g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl>)

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open position PhD student/postdoc
by Vercoulen-2, Y. 08 Mar '17

08 Mar '17

Dear all, I have a position for a motivated PhD student or postdoc in bioinformatics & cancer research, starting in September. For details see: https://www.werkenbijumcutrecht.nl/vacatures/Paginas/postdoc-or--phd-studen… Interested candidates can contact me, or apply via the website. Best, Yvonne Yvonne Vercoulen, PhD Molecular Cancer Research Center for Molecular Medicine UMC Utrecht ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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PhD position "Analysis of genomic and epigenomic patterns in developmental disorders" (IB2, ULB, Brussels)
by Matthieu Defrance 08 Mar '17

08 Mar '17

Ph.D position "Analysis of genomic and epigenomic patterns in developmental disorders" (IB2, ULB, Brussels) A PhD position on the "Analysis of genomic and epigenomic patterns in developmental disorders" is available at the Interuniversity Institute of Bioinformatics in Brussels (IB2, Université Libre de Bruxelles, Belgium). The research goal is to contribute to the development of new bioinformatic methodologies in order to analyze both genetic and epigenetic alterations (e.g. genetic mutations, DNA methylation alterations) that are involved in developmental pathologies. Both fundamental and clinical aspects of alterations will be addressed by mixing high-throughput data generated locally with already available external data. The position will be funded for 4 years. Screening of applications begins immediately and will continue until an outstanding candidate has been selected. The deadline for the application is set to the 30th of April 2017. PhD is expected to start in October 2017. The candidate should hold a master degree in bioinformatics, engineering, statistics, or in computer sciences and demonstrate proficiency in algorithmics, statistics or machine learning and in software development (R, python). Experience with sequencing data, genome-wide data sets (e.g. ChIP-Seq, RNA-Seq) or massive datasets analysis would be a plus. The applicant should demonstrate interest for biology and interdisciplinary research. Applications should include a detailed CV, a motivation letter, and names of two referees and should be sent to Dr. Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be) and Dr. Guillaume Smits (guillaume.smits(a)huderf.be)

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ELIXIR-EXCELERATE HPC Train-the-Researcher Course - 6-7 April 2017, Malaga, Spain
by Celia van Gelder 08 Mar '17

08 Mar '17

Dear all, ELIXIR-Spain is organizing a HPC Train-the-researcher Course, intended for bioinformatics users and developers that aim at using HPC resources to extend their activity beyond the limitations of sequential applications on commodity hardware (Note that this course will not suit participants that are looking for entry-level concepts in HPC). The course is organised as a two-day mini-symposium, and aims at introducing the participants in the complexities of parallel programming with emphasis on genome-scale comparison algorithms. · The theoretical aspects of this course cover (a) the parallel programing background, with a quick overview in the architectures and programming models; and (b) the basis for genome-scale sequence comparison algorithms. · The practical aspects are organised to master the concepts of data distribution and balancing using a Map-Reduce strategy and internal coding with MPI. The information about the course is here: https://chirimoyo.ac.uma.es/bitlab/portfolio/hpc-excelerate/ . ELIXIR Spain will be able to host a few people from each of the ELIXIR countries, there will not be a fee for the actual participation. Please spread this information in your organization as you see fit, Thank you! Best Celia Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht

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Galaxy Community Conference (GCC2017), Montpellier, France, 26-30 June
by Dave Clements 08 Mar '17

08 Mar '17

*2017 Galaxy Community Conference (GCC2017)* 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ -- The 2017 Galaxy Community Conference <https://gcc2017.sciencesconf.org/> will bring together several hundred researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, come from around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and will feature two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, all about data-intensive biology and the tools that support it. GCC2017 also includes data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/page/location>, just 10km from the Mediterranean. Abstract submission <https://gcc2017.sciencesconf.org/page/submit> is now open. If you work in or support data intensive life science research then GCC2017 is an ideal opportunity to present your work. The deadline for oral presentations is Apr 15 (23:59 Paris local time), and posters and computer demonstration submission closes on May 27 (23:59 Paris local time). The Lightning talk submission deadline is June 23 (23:59 Paris time). Early registration <https://gcc2017.sciencesconf.org/page/registration> is also open and starts at less than 55€ / day for post-docs and students. You can also book low cost conference housing <https://gcc2017.sciencesconf.org/page/lodging> when you register. Travel fellowships <https://new.galaxyproject.org/news/2017-03-gcc2017-fellowships/> are being offered by the Galaxy Community Fund for early career researchers that are travelling from afar. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you this summer in Montpellier! Au revoir, The GCC2017 Organising Committee PS: Please redistribute this announcement to any interested groups. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Summer school on ecological network inference and analysis
by Karoline Faust 07 Mar '17

07 Mar '17

Dear all, We are pleased to announce our summer school on ecological network inference and analysis, which will take place in Leuven from the 11-13th of September 2017. The school will focus on ecological network theory and its practical application to sequencing data. Lectures and practicals will be given by a number of experts, including Stefanie Widder, Tim Poisot, Katharine Coyte, Elisa Beninca, Didier Gonze, Gipsi Lima-Mendez, Sebastian Schmidt, Hugo Roume, Vasilis Dakos, Miguel Fortuna and Jing Tang. For more information and registration, please visit: http://tinyurl.com/econetschool Kind regards, Karoline Faust, on behalf of the organizers -- Karoline Faust --------------------------------------------------- Email: karoline.faust(a)kuleuven.be Web: http://tinyurl.com/MicrobialSysBio --------------------------------------------------- Room 7.A130, Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology and Immunology KU Leuven, Campus Gasthuisberg Herestraat 49, postbus 1028 3000 Leuven Belgium ---------------------------------------------------

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FW: [bioinfo] Conference 'Understanding Protein Interactions: from Molecules to Organisms', Lyon 24-26 April 2017
by Alexander Botzki 06 Mar '17

06 Mar '17

From: Juliette Martin [mailto:juliette.martin@ibcp.fr] Sent: 06 March 2017 15:17 To: bioinfo(a)sfbi.fr Subject: [bioinfo] Conference 'Understanding Protein Interactions: from Molecules to Organisms', Lyon 24-26 April 2017 It is still time to register to the international meeting 'Understanding Protein Interactions: from Molecules to Organisms' that will take place in Lyon 24-26 April 2017: https://mapping2017.sciencesconf.org Registration is free but mandatory. Participants will have the opportunity to present their work via selected short talks or during the special ‘Laptop Session’, an interactive and lively alternative to the traditional poster session, where participants come with their laptop and present a short slide-show (2-3 slides) and eventually a linked demonstration of their work The preliminary program is now available: 24th of April Alexandre Bonvin, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands "High-resolution, integrative modelling of biomolecular complexes from fuzzy data" Ozlem Keskin, Koç University, Computational Systems Biology Lab, Turkey "Protein-protein interfaces: amino acid variations and hot spot residues" Yanay Ofran, Bar-Ian University, Systems Biology and Functional Genomics, Israel "All models are wrong, some are useful": Predicting and designing interactions based on multiple wrong models Contributed talk 1 25th of April Ilya Vakser, University of Kansas, Center for Computational Biology, USA "Comparative vs. Free Docking in Modeling of Interactome" Franca Fraternali, King's College London, Bioinformatics and Computational Biology, UK TBA Peter Uetz, Virginia Commonwealth University, Center for the Study of Biological Complexity, USA "Protein complexes and protein interaction networks in bacteria" Contributed talk 2 Contributed talk 3 ** Laptop Session ** Emmanuel Levy, Weizmann Institute of Science, Cell architecture lab, Israel "Proteins evolve on the edge of supramolecular self-assembly" Julia Shifman, Hebrew University of Jerusalem, Protein-Protein Interactions, Israel "Cold spots in Protein Binding" Elisa Fadda, Maynooth University, Computational Biophysics, Ireland "Are structure-less protein regions really so structure-less? An atomistic view of the architecture of disorder and its functions in protein-protein interactions" Rob Russel, University of Heidelberg, Protein Evolution Germany TBA Contributed talk 4 26th of April Raphael Guerois, Institute of Integrative Biology of the Cell, CEA, Unit of Bioenergetics, Structural Biology and Mechanisms, France "Structural modeling and design of protein interactions using evolution" Monika Fuxreiter, University of Debrecen, Laboratory of Protein Dynamics, Hungary "Dynamic interactions and fuzziness in protein complexes and higher-order assemblies" Patrick Aloy, Institute for Research in Biomedicine, Barcelona, Spain "A network biology approach to novel therapeutic strategies" Contributed talk 5

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