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BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information: Approaches using Linked Data and Semantics (5th edition)
by Femke Francissen 19 Dec '17

19 Dec '17

BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information:Approaches using Linked Data and Semantics (5th edition) With endorsements for FAIR* data stewardship ranging from Nature Genetics to the G7, and increasing pressure from funders for much stricter data management, FAIR data stewardship skills will be among the most wanted for the next decade. By following this course, you add these skills to your CV and learn cutting-edge semantic techniques to search and integrate health and life science data for efficient, reproducible data science. * FAIR: Findable, Accessible, Interoperable and Reusable for humans and computers Course coordinators: Marco Roos (LUMC), Katy Wolstencroft (LIACS, Leiden University) Date: 22-26 January 2018 Location: Amsterdam Science Park, The Netherlands Website link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Registration link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Target audience This course is for bioinformaticians who would like to learn about leading-edge data and knowledge integration solutions. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application (Semantic Web and Linked Data), (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how to publish your own data to make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD meetings <http://www.dtls.nl/fair-data/byod/> who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources. Description The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR <http://www.dtls.nl/fair-data/> (Findable, Accessible, Interoperable and Reusable). This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. After following this course students should be able to start creating their first applications based on these technologies or make more informed design decisions for their current application. In this course you will learn about: Linked Data and the Semantic Web technologies that underpin it How you can use Linked Data for data and knowledge integration in the Life Sciences Available Linked Data resources in the public domain and large-scale projects that use these resources How you can integrate your own data with Linked Data resources How you can combine data integration and analysis over distributed resources, using Web Services and workflows Confirmed lecturers: Frank van Harmelen (Vrije Universiteit Amsterdam), Andre Dekker (Maastricht University) Tentative programme: The program will include the following topics: Introduction to Semantic Interoperability and the Semantic Web; The Semantic Web in Use; The Semantic web in use – systems and guidelines; Data stewardship and making Data Understandable and Searchable (the FAIR principles); Using, Integrating and Analysing Data This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/>. Femke Francissen Community manager BioSB Research School

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ECCB 2018 Call for Tutorials, Workshops and SIGs
by Yves Moreau 18 Dec '17

18 Dec '17

> View this email in your browser <http://mailchi.mp/iscb/eccb-2018-call-for-tutorials-workshops-and-sigs?e=3f…> > > ECCB 2018 to be held in Athens, Greece, 8-12 September > The Hellenic Society for Computational Biology and Bioinformatics <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> will organize the seventeenth edition of the European Conference on Computational Biology in association with the ELIXIR. > > It is one of the main computational event in 2018 and will welcome scientists working in a variety of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. Participating in ECCB 2018 will be the perfect opportunity to keep pace with cutting edge research, and to network with members of ECCB community. > > Now Accepting Proposals for Workshops, Tutorials, and SIGs > The ECCB 2018 program commitee invites proposals for one or two day workshops or special interest group meetings (SIGs). > > Proposals are expected to provide participants with an informal setting to discuss technical issues, exchange research ideas, and to share practical experiences on a range of focused or emerging topics in bioinformatics. > > Each workshop/SIG should provide an interesting perspective on the cutting edge of a selected research field. Workshops may include any form of presentation such as talks or panel discussions. > > Call for Workshops/SIGs > <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> > Key Dates > <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> > Call for Tutorials > <https://iscb.us3.list-manage.com/track/click?u=4c0e7fa66594378a44ccd614e&id…> > ECCB 2018 > 17th European Conference on Computational Biology > September 8-12, 2018 > Athens, Greece - Stavros Niarchos Foundation Cultural Center > > > > > > > > This email was sent to yves.moreau(a)esat.kuleuven.be <mailto:yves.moreau@esat.kuleuven.be> > why did I get this? <https://iscb.us3.list-manage.com/about?u=4c0e7fa66594378a44ccd614e&id=04453…> unsubscribe from this list <https://iscb.us3.list-manage.com/unsubscribe?u=4c0e7fa66594378a44ccd614e&id…> update subscription preferences <https://iscb.us3.list-manage.com/profile?u=4c0e7fa66594378a44ccd614e&id=044…> > International Society for Computational Biology · 9650 Rockville Pike · Bethesda, MD 20814 · USA > >

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Tenure-track position in bioinformatics at UCLouvain
by Jean Baptiste Demoulin 11 Dec '17

11 Dec '17

Dear colleagues, The University of Louvain (UCL) invites applications for a professor position in bioinformatics, located on its Medical campus in Brussels (Woluwé-Saint-Lambert), Belgium. Thank you for forwarding this message to potential candidates. Best regards, Prof. Jean-Baptiste Demoulin De Duve Institute & Faculty of Pharmacy and Biomedical Sciences University of Louvain - UCL Avenue Hippocrate 75, box B1.74.05 BE-1200 Brussels, Belgium Phone : +32 2 764 6529 Mobile : +32 485 589321 Web : www.deduveinstitute.be/research

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Postdoc position at Institute for Systems Biology - Shmulevich Lab - Computational Cancer Biology
by Theo Knijnenburg 08 Dec '17

08 Dec '17

Please feel free to distribute this ad among potential candidates. ___ *Institute for Systems Biology* *Postdoctoral Fellow* *Computational Cancer Biology* The Shmulevich group is seeking a computationally-oriented Postdoctoral Fellow. The successful applicant will work with an interdisciplinary team of computational biologists, bioinformaticians, basic scientists and clinical researchers to: 1) Integrate and analyze genomic data from The Cancer Genome Atlas (TCGA) and the Genomic Data Analysis Network (GDAN) with a focus on miRNA expression and regulation, and/or 2) Leverage heterogeneous cancer genomics data for drug sensitivity prediction and development of human cancer therapeutics as part of the Cancer Target Discovery And Development (CTD2) consortium. See attached PDF for details. https://www.systemsbiology.org/about/careers/

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Submit your abstract for Applied Bioinformatics in Life Sciences (2nd) 8-9 March 2018
by Alexander Botzki 08 Dec '17

08 Dec '17

Your invitation for #ABLS18 No Images? Click here http://email.vibconferences.be/t/r-e-jrtrirlk-kdnlrgz-u/ Deadline for abstract submission is 11 January 2018 Dear colleague, The second edition of the two day event ‘Applied Bioinformatics in Life Sciences’ organized by the Flanders Institute for Biotechnology (VIB), will take place on 8-9 March, 2018 in Leuven, Belgium. After a sold-out first edition in March 2016, this second edition will feature recent developments in bioinformatics research, and highlight the power of computational biology in the fields of medical, agricultural, and biotechnology research. With this email we would like to invite you to submit your own research for presentation and to join us and our speakers at #ABLS18. Register early [http://vibconferences.be/event/applied-bioinformatics-in-life-sciences-2nd-…] Special rate for PhD students + poster award To support junior researchers, VIB offers PhD students a special rate when registering before 11 January 2018. Showcase your own research to the international research community during the poster sessions at the conference. The best abstracts will be selected for a presentation and the best poster will receive a poster prize! Submit your abstract [http://vibconferences.be/event/applied-bioinformatics-in-life-sciences-2nd-…] Final program available The full line-up is as follows: Stein Aerts - VIB-KU Leuven Center for Brain & Disease Research, BENaama Barkai - Weizmann Institute of Science, ILStephan Beck - UCL, UKYana Bromberg - Rutgers University, USAlbert Heck - Utrecht University, NLMichael MacCoss - University of Washington, USSteven Maere - VIB-UGent Center for Plant Systems biology, BEChristine Orengo - University College London, UKMarkus Ralser - The Francis Crick Institute, UKSeung Yon (Sue) Rhee - Carnegie Institution for Science, USFrederic Rousseau - VIB-KU Leuven Center for Brain & Disease Research, BERon Shamir - Tel Aviv University, ILOliver Stegle - EMBL-EBI, UKHenk Stunnenberg - Radboud Institute for Molecular Life Science, NLInes Thiele - University of Luxembourg, LUJanet Thornton - EMBL-EBI, UKMichele Vendruscolo - University of Cambridge, UKVicki Wysocki - Ohio State University, US Grab this opportunity to meet experts in the field and to network with hundreds of scientists coming from all around the globe. Visit the website [http://vibconferences.be/event/applied-bioinformatics-in-life-sciences-2nd-…] for more info Explore the historical university city of Leuven Leuven households the KU Leuven. One of the oldest universities of Western Europe. The city is also home to the Anheuser-Busch InBev company, one of the world's largest brewing groups producing the Leuven-based Stella-Artois beer as one of their flagship brands. We hope to have triggered your interest in our conference. In case you have questions or remarks, please feel free to contact us. We look forward to welcoming you in Leuven in March 2018! With kind regards, Alexander Botzki Organizing Committee: Alexander Botzki, VIB Bioinformatics Core Brigida Gallone, VIB-KU Leuven Center for Microbiology Diether Lambrechts, VIB-KU Leuven Center for Cancer Biology Joost Schymkowitz, VIB-KU Leuven Center for Brain & Disease Research Vanezza Vermeirssen, VIB-UGent Center for Plant Systems biology Paola Masuzzo, VIB-UGent Center for Medical Biotechnology Evy Vierstraete, VIB Science Events manager To stop receiveiving our invitations please click below. Tweet http://email.vibconferences.be/t/r-tw-jrtrirlk-kdnlrgz-o/ Share [http://email.vibconferences.be/t/r-li-jrtrirlk-kdnlrgz-a/] Unsubscribe http://email.vibconferences.be/t/r-u-jrtrirlk-kdnlrgz-p/

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Postdoc position VIB-Janssen collaboration single cell transcriptomics
by Joke Reumers 06 Dec '17

06 Dec '17

Dear all, Please find at this link the job description for a postdoc position at Janssen Belgium in collaboration with the VIB Center for Inflammation Research, focused on single cell RNA sequencing in Alzheimer disease animal models. https://jobs.jnj.com/jobs/1700214162W/Post-Doctoral+Scientist%2C+Single+Cel… <https://jobs.jnj.com/jobs/1700214162W/Post-Doctoral+Scientist,+Single+Cell+…> For more information, you can contact me at jreumers(a)its.jnj.com <mailto:jreumers@its.jnj.com> +32 14 60 3324 Please forward to other channels where possible, Thanks, Joke Reumers

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Bioinformatician/Software Engineer position at LCSB, University of Luxembourg.
by Venkata Satagopam (TeC) 06 Dec '17

06 Dec '17

Dear all We are looking for a "Bioinformatician/Software Engineer (Research Associate) for Clinical and Next Generation Sequencing data analysis (m/f)” Please refer the below URL for more details: http://emea3.mrted.ly/1ns10 Best regards, Venkata -- Venkata Satagopam Technical Coordinator ELIXIR-Luxembourg Node 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 +352-466-644-36421 venkata.satagopam(a)elixir-luxembourg.org<mailto:venkata.satagopam@elixir-luxembourg.org> https://www.elixir-europe.org/about/elixir-luxembourg ----- 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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Postdoc: position Computational Network Biology in Plants - VIB-UGent Center for Plant Systems Biology
by Klaas Vandepoele 28 Nov '17

28 Nov '17

The Comparative Network Biology lab (Klaas Vandepoele) of the VIB Center for Plant Systems Biology is looking for a Postdoc Computational Network Biology in Plants. Our mission Our objective is to extract and validate biological knowledge from large-scale experimental data sets using data integration, comparative sequence and expression analysis, and network analysis. In our lab, we combine computational methods with experimental data to generate new insights about gene function, gene regulation and comparative genome biology. In this project, our objective is to * *delineate high-quality biological networks*in different plant species * *develop new methods to accurately translate biological networks*between different species (model species & crops) with different levels of genome complexity Job description * Fully funded Postdoc position for 2 years (start date March 2018 or later). * You get the freedom to design and execute a personal research project addressing some of the objectives listed above. * Through (inter)national collaborations with wetlab scientists, computational results can be experimentally validated! * Perform co-supervision of research projects of PhD students in the lab. * Access to a diverse set of training programs at VIB (both scientific & soft skills) * Reporting of results through publications in peer-reviewed international journals. * Attending and presenting your results at international scientific events. Your profile * You have PhD degree in Bioinformatics, Computational Biology or related. * You are enthusiastic about scientific research and have a strong interest in studying plant biology using genomics and systems biology approaches. * Through international peer-reviewed publications, you have a track record in plant genomics or systems biology research (people_only_having publications describing experimental/wetlab work will not be retained). * You are fluent with Linux/Unix and have good knowledge of Python or another programming/scripting language. * You have good communication and writing skills. * You are proficient in English. How to apply? Motivated candidates are asked to apply online (https://vibvzw.jobsoid.com/j/10785/postdoc-computational-network-biology-in…) Please make sure your application includes a letter of motivation, a detailed CV and the contact information of 2 references (including e-mail addresses and phone numbers). Applications will be accepted until 31 January 2018. -- best regards, Klaas Vandepoele - Professor Comparative Integrative Genomics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 22 --------------------------------------------------------- Lab website: http://bioinformatics.psb.ugent.be/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information, 22-26 January 2018, Amsterdam
by Femke Francissen 28 Nov '17

28 Nov '17

BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information:Approaches using Linked Data and Semantics (5th edition) Course coordinators: Marco Roos (LUMC), Katy Wolstencroft (LIACS, Leiden University) Date: 22-26 January 2018 Location: Amsterdam Science Park, The Netherlands Website link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Registration link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Target audience This course is for bioinformaticians who would like to learn about leading-edge data and knowledge integration solutions. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application (Semantic Web and Linked Data), (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how to publish your own data to make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD meetings <http://www.dtls.nl/fair-data/byod/> who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources. Description The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR <http://www.dtls.nl/fair-data/> (Findable, Accessible, Interoperable and Reusable). This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. After following this course students should be able to start creating their first applications based on these technologies or make more informed design decisions for their current application. In this course you will learn about: Linked Data and the Semantic Web technologies that underpin it How you can use Linked Data for data and knowledge integration in the Life Sciences Available Linked Data resources in the public domain and large-scale projects that use these resources How you can integrate your own data with Linked Data resources How you can combine data integration and analysis over distributed resources, using Web Services and workflows Confirmed lecturers: Frank van Harmelen (Vrije Universiteit Amsterdam), Andre Dekker (Maastricht University) Tentative programme: The program will include the following topics: Introduction to Semantic Interoperability and the Semantic Web; The Semantic Web in Use; The Semantic web in use – systems and guidelines; Data stewardship and making Data Understandable and Searchable (the FAIR principles); Using, Integrating and Analysing Data This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/>. Femke Francissen Community manager BioSB Research School Visiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address (as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl <mailto:femke.francissen@biosb.nl> Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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Permanent position IT/biologist ULB-Neuroscience Institute
by Matthieu Defrance 28 Nov '17

28 Nov '17

The laboratory of Neurophysiology at the Université libre de Bruxelles (ULB, Brussels), member of the ULB-Neuroscience Institute (https://uni.ulb.ac.be) is recruiting a full time IT manager for a permanent position (http://www.ulb.ac.be/drh/emploi/index.html Référence 2017/41) The functions include: - Computer support for the various activities of the laboratory of Neurophysiology (http://neurophy.ulb.ac.be & http://celegans.ulb.ac.be/wordpress/) which includes both the processing of in vivo and in vitro electrophysiology data, imaging and behavioural analysis; as well as the Microscopy Facilitator Facility (LiMiF http://limif.ulb.ac.be) - Management of the local network and massive data flows (Tbs/year, continuous increase), in vitro and in vivo electrophysiology and imaging, server configuration and maintenance, data security, backup, archiving, etc . ; - IT support and support for the analysis of electrophysiological signals and image analysis to researchers; - Support for the implementation and maintenance of data acquisition systems for electrophysiology (patch clamp and imaging) in vitro and in vivo (Neuralinx) (optogenetics, behaviour, electrophysiology in vivo and calcium imaging by micro-endoscopy (Inscopix ) Development of software and script for coupling electrophysiological recordings or in vivo imaging and behavior (Matlab); - Support for simple analysis of imaging data (generic analyses for most users eg segmentation, counts) by open source software (eg ImageJ / Fiji) or commercial eg (LiMiF) ZEN, Huygens, Imaris, including support for local development of these softwares (macro / plugins). Some specific projects that require further development in image analysis will have to rely on dedicated resources (e.g. Master students in engineering / computer science, post- doc project, etc.); - Management of existing online booking software and their development according to the implementation of new equipments. Profile: Master in Computer Science or Civil Engineer in Computer science or other degrees of Civil Engineer. Experience in a similar function is an obvious but not mandatory asset. A motivated young graduate with a solid background may be suitable for the position. Knowledge and skills required: - Knowledge of computer science (PC, Mac and servers), programming (Matlab, Python, ImageJ, etc.), experience in signal analysis (electrophysiology) and / or in image processing (microscopy and / or video tracking); - Proficiency in written and spoken English is mandatory Desired Qualities: - Ability to work as a team player - while having a capacity for initiative and proactive action; - Sense of service and listening ability to capture the needs of biologists to efficiently translate them into hardware and / or software solutions; - Communication skills in English and, optionally, in French; - Stress resilience; - Adaptability to the various needs of users, often "in the emergency" (deadlines, etc.). To postulate: http://www.ulb.ac.be/drh/emploi/index.html Référence 2017/41 and fulfill the online document

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