September 2017 - BBClist - maillist.psb.ugent.be

Variant effect prediction course, 31th October - 3th November
by Sari van Heel - Vauhkala 04 Sep '17

04 Sep '17

Dear Members of BBClist, We would like to remind you about an upcoming international course that the Research Group Analysis Techniques in Life Science will organize in Breda (the Netherlands) in October-November 2017: Name course: Variant effect prediction Course date: 31 October – 3 November 2017 Registration fee: €900,- Website: http://www.alsavans.nl/uk%20site/Courses/avans-training-2542.html The digital registration form is available on our website. Should you have any questions, please do not hesitate to contact us by email at: si.vanheel-vauhkala(a)avans.nl<mailto:si.vanheel-vauhkala@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in Life Science Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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ELIXIR Belgium: Python for Data Processing course - 5-6 October 2017 in Leuven
by Alexander Botzki 04 Sep '17

04 Sep '17

Dear all, We would like to announce the following ELIXIR Belgium course which is organised together with Geert Jan Bex from KU Leuven/UHasselt. If you are interesting in intermediate Python programming please do not hesitate to register for this course at http://www.vib.be/en/training/research-training/courses/Pages/Python-for-Da… Python for Data Processing Use Python to solve real data transformation problems. Topics include regular expressions, parsing, data transformation, interaction with databases and external programs using libraries for scientific programming such as numpy, scipy, matplotlib, pandas, and biopython. Prerequisites Aimed for people with programming skills and basic knowledge of Python. If you have no knowledge of Python you should follow an introductory Python course first. Date: 5 and 6 October 2017 Location: ICTS Education Center KULeuven Trainer: Geert Jan Bex (KULeuven/UHasselt) More info and registration: http://www.vib.be/en/training/research-training/courses/Pages/Python-for-Da… Best regards, Alex Alexander Botzki – Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/>

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PhD / PD in Genetics / Bioinformatics at UMC Utrecht
by Jeroen de Ridder 04 Sep '17

04 Sep '17

Dear all, Open position for a PhD or Postdoc in my lab at the UMC Utrecht to work on the NWO-Vidi funded project: The 4D Genome Atlas - finding noncoding disease driver mutations using genome shape maps. We aim to develop novel methods to cancer-omics data integration using machine learning. The primary focus of the project is to integrate information on the noncoding genome, such as 3D conformation and epigenomic data, with cancer genomics data. We will follow a machine-learning approach to prioritize likely driving noncoding somatic variants. http://www.werkenbijumcutrecht.nl/vacatures/Paginas/phd-student-or-postdoc-… -- Jeroen de Ridder, PhD Associate professor / Principal Investigator | University Medical Center Utrecht - Center for Molecular Medicine | Address: Universiteitsweg 100<x-apple-data-detectors://8>, STR 1.305 | 3584 CG Utrecht, The Netherlands<x-apple-data-detectors://9> | Tel: +31 (0)88 7550406<tel:+31%2088%207550406> | Mob: +31 (0)6 24288813<tel:+31%206%2024288813> | Skype: j_de_ridder | Secretary: Monique van Schaik, M.A.H.vanSchaick(a)umcutrecht.nl<mailto:M.A.H.vanSchaick@umcutrecht.nl>, +31 (0)88 7568312<tel:+31%2088%207568312> ------------------------------------------------------------------------------ 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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Data Scientist Position at ONTOFORCE
by Bérénice Wulbrecht 01 Sep '17

01 Sep '17

Are you passionate about the endless potential of data and how this could be opened up to everyone? Then join us. We are ONTOFORCE, a Belgian company and global leader in the development of groundbreaking semantic search technologies. Our user-friendly search platform DISQOVER makes unique links between data sources, enabling everyone to be a data scientist. We’re now looking for a talented and highly motivated Data Scientist to join our data team. Our working environment In the data team, we handle the semantic integration of data and the management of open, public as well as private data sources. Because more data means more and better insights. And that’s what you, along with us, can make possible. At ONTOFORCE, we adhere to an agile development environment, giving every co-worker a high degree of freedom, room for initiative and the possibility to take up responsibility. The Data Scientist’s job description - As Data Scientist, you implement the ETL and semantic integration of new data sources in DISQOVER using semantic web technologies like RDF (Resource Description Framework), bash and python scripting and more. In other words, you extract, transform, load, link and map all types of public and private data. - You are able to interact with customers and translate their requirements into custom data integrations - Your knowledge helps us to continuously optimize the ONTOFORCE integration ontology by developing new methodologies for knowledge extraction, data integration and mapping. - You collaborate closely with the software architects, other team members and customers to ensure up-to-date technical knowledge for yourself and the team. You manage the automated data update pipeline. - As we work in a global setting with customers all over the world, you’re also prepared to travel occasionally. The Data Scientist’s profile You hold… - A PhD or a Master’s degree in computer science/informatics, engineering, bio informatics (or equivalent) Profound experience with scripting (e.g. Python) - At least 5 years of relevant experience - Profound experience with scripting (in e.g. Python) - Experience with Linux OS - Proficiency with distributed version control software (e.g. git) - Excellent oral and written communication skills in English A distinct plus would be knowledge of or experience with… - RDF, relational and graph based database technologies (SQL, SPARQL, etc.) - Machine learning and text mining technologies - Life sciences related data - Linked data and semantic web technologies People we love to work with are… - Passionate - Fast learners - Result and solution driven - Team players - Quality-driven Apply now! Do you have outstanding technical skills and a thorough understanding of the systems used in the context of Big Data integration? Are you a quality-driven communicator who’s interested in tackling big challenges? Then apply now! Want to know more? Visit our ONTOFORCE website <http://www.ontoforce.com/> or blog <http://www.ontoforce.com/blog/>. Or discover DISQOVER <https://www.disqover.com/#start> for yourself through our free license <https://www.disqover.com/#signup>. -- [image: logo ONTOFORCE] <http://www.ontoforce.com/> Berenice Wulbrecht DIRECTOR DATA SCIENCE berenice(a)ontoforce.com www.ontoforce.com Meetdistrict, Ottergemsesteenweg-Zuid 808, 9000 Gent, Belgium CIC, One Broadway, MA 02142 Cambridge, United States

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Fwd: Position available at Novo Nordisk : Principal Scientist in Computational Protein Design and Data Modelling
by Wim VRANKEN 01 Sep '17

01 Sep '17

Dear all, Please find below an advertisement for a position in structural bioinformatics in Denmark. Best regards, Wim Begin forwarded message: From: "LEDM (Leonardo De Maria)" <ledm(a)novonordisk.com<mailto:ledm@novonordisk.com>> Subject: Position available at Novo Nordisk : Principal Scientist in Computational Protein Design and Data Modelling Date: 1 September 2017 at 13:54:51 CEST To: "LEDM (Leonardo De Maria)" <ledm(a)novonordisk.com<mailto:ledm@novonordisk.com>> Cc: "LEDM (Leonardo De Maria)" <ledm(a)novonordisk.com<mailto:ledm@novonordisk.com>> Dear All A “Principal Scientist in Computational Protein Design and Data Modelling” position is available at Novo Nordisk in the Copenhagen metropolitan area https://www.novonordisk.com/careers/working-at-novo-nordisk/job-ad-display.… Please be so kind to share to your network. Thanks in advance. BR Leonardo _____________________ Leonardo De Maria Principal Scientist Global Research Novo Nordisk A/S Novo Nordisk Park DK-2760 Måløv Denmark +45 4444 8888 (phone) +45 3075 5071 (mobile) LeDM(a)novonordisk.com<mailto:LeDM@novonordisk.com> Facebook<http://www.facebook.com/novonordisk> | Twitter<http://www.twitter.com/novonordisk> | LinkedIn<http://www.linkedin.com/company/novo-nordisk> | Youtube<http://www.youtube.com/novonordisk> | Pinterest<http://www.pinterest.com/novonordisk> Driving change since 1923 Did you know that Novo Nordisk has been driving change to defeat diabetes for more than 90 years? Find out more here<http://www.novonordisk.com/content/Denmark/HQ/www-novonordisk-com/en_gb/hom…> This e-mail (including any attachments) is intended for the addressee(s) stated above only and may contain confidential information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information contained herein is strictly prohibited and may violate rights to proprietary information. If you are not an intended recipient, please return this e-mail to the sender and delete it immediately hereafter. Thank you. --------------------------------------------------------------------------------------- Prof. Dr. Wim Vranken wvranken(a)vub.ac.be<mailto:wvranken@vub.ac.be> Tel: +32 (0)2 6291996 (VUB) +32 (0)2 6505943 (IB^2) Building E, 5th Floor, E5.03, Pleinlaan 2 1050 Brussels, Belgium VUB - Structural Biology Brussels ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Director, http://ibsquare.be/ ---------------------------------------------------------------------------------------

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Fwd: Postdoc position on AgroPortal, GACS and ontology alignment in Montpellier, France
by Frederik Coppens 01 Sep '17

01 Sep '17

Dear all Below a urgent call for a post-doc position in France related to ontologies. cheers Frederik > >> >> Dear collaborators, >> >> We NEED you to help us found a candidate postdoc for this position. Recently the position has been extended to 18 months (rather than 12) but we need a candidate from outside France by beginning of November or the funding will be lost. >> >> Please, transfer this email and send me recommendations. This is crucial for AgroPortal and shall be very good for GACS project. >> >> Clement >> >> De : jonquet=lirmm.fr(a)rda-groups.org <mailto:jonquet=lirmm.fr@rda-groups.org> [mailto:jonquet=lirmm.fr@rda-groups.org <mailto:jonquet=lirmm.fr@rda-groups.org>] De la part de jonquet >> Envoyé : vendredi 21 juillet 2017 14:40 >> À : 'Agricultural Data IG (IGAD)' <rda-agrdatainterop-ig(a)rda-groups.org <mailto:rda-agrdatainterop-ig@rda-groups.org>>; rda-agrisemantics-wg(a)rda-groups.org <mailto:rda-agrisemantics-wg@rda-groups.org>; gacs-wg(a)googlegroups.com <mailto:gacs-wg@googlegroups.com>; agroportal-users(a)lirmm.fr <mailto:agroportal-users@lirmm.fr>; support(a)bioontology.org <mailto:support@bioontology.org>; 'Vocabulary Services Interest Group' <vocabulary_services(a)rda-groups.org <mailto:vocabulary_services@rda-groups.org>> >> Objet : [rda-agrdatainterop-ig][vocabulary_services][rda-agrisemantics-wg] TR: Postdoc position on AgroPortal, GACS and ontology alignment in Montpellier, France >> >> Hello all, >> Just a quick email to ask you to share the postdoc offer we have in Montpellier to work on AgriSemantics related stuff : AgroPortal, ontology mapping and GACS ! >> It still open. A candidate from this community will be perfect! >> >> Bye >> Happy summer. >> Clement >> ----------------------------------------------------------- >> The NUMEV Labex (http://www.lirmm.fr/numev <http://www.lirmm.fr/numev>) and AgroPortal project (http://agroportal.lirmm.fr <http://agroportal.lirmm.fr/>) which builds an ontology repository for agronomy are offering a 1-year postdoc position for 2017-2018 in Montpellier, to work on agronomical ontologies and their alignments as well as take part in the international GACS initiative (http://www.agrisemantics.org/gacs/ <http://www.agrisemantics.org/gacs/>). >> >> Abstract: >> Standards vocabularies and ontologies are key elements to achieve data interoperability. The AgroPortal project (http://agroportal.lirmm.fr <http://agroportal.lirmm.fr/>) develops and supports a reference ontology repository for agronomy, plant sciences, biodiversity and nutrition. We have already designed and implemented an advanced prototype offering ontology-based services that hosts 64 ontologies or vocabularies including some reference resources in the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. One of the challenges when dealing with multiple ontologies is to determine their overlap and align them. >> We are offering a postdoc position to develop ontology mapping capabilities to align AgroPortal ontologies and participate into the international Global Agricultural Concept Scheme (GACS) project. With the experience and technology developed with the YAM++ application (LIRMM’s ontology alignment matcher), we will make AgroPortal a state-of-the-art platform for mapping extraction, generation, validation, evaluation, storage and retrieval by adopting a complete semantic web and linked open data approach and engaging the community for curation. We will first focus on the ontologies of the Montpellier community (agronomy, food, biodiversity) and then join the GACS project (integration of Agrovoc, NALt & CABt) in partnership with RDA AgriSemantics working group. >> >> More detail here: >> http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.pdf <http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.pdf> >> or >> http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.html <http://www.lirmm.fr/sifr/positions/2017_NUMEV-Lingua_postdoc_position.html> >> >> Please, consider transferring the job description in your labs and networks. >> >> Best regards >> Clement >> >> Dr. Clement JONQUET - PhD in Informatics - Assistant Professor >> University of Montpellier >> Coordinator of the SIFR <http://www.lirmm.fr/sifr/> and AgroPortal <http://agroportal.lirmm.fr/> projects >> Visiting scholar, Stanford University (EU Marie Curie fellow) >> >> jonquet(a)lirmm.fr <mailto:jonquet@lirmm.fr> >> http://www.lirmm.fr/~jonquet <http://www.lirmm.fr/~jonquet> >> >> @Montpellier : +33/4 67 14 97 43 >> @Stanford : +1 650 723 6725 >> >> Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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Open position Data steward biobank
by Patrick Kemmeren 01 Sep '17

01 Sep '17

Dear all, As part of our efforts in setting up the biggest pediatric oncology biobank in Europe, we are looking for a data steward biobank. For more details see: http://www.werkenbijprinsesmaximacentrum.nl/vacaturetekst-engels/data-manag… -- Patrick Kemmeren, PhD Principal Investigator T +31 (0)88 972 55 05 | M +31 (0)6 53 11 25 53 Princess Maxima Center * * *Princess Máxima Center for Pediatric Oncology* *Location Hubrecht institute*| Uppsalalaan 8 | 3584 CT Utrecht | T +31 (0)88 972 90 00 |***> Website* <http://prinsesmaximacentrum.com/>

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