- BBClist - maillist.psb.ugent.be

ISMB 2020 CompMS – Save the date & call for proposals
by Wout Bittremieux 27 Feb '20

27 Feb '20

— ISMB 2020 CompMS – Save the date & call for proposals — Dear colleagues, Please join us during the ISMB 2020 conference for the Computational Mass Spectrometry (CompMS)COSI session on July 15, 2020inMontreal, Canada. The ISMB conferenceis the world's largest bioinformatics/computational biology conference. Every year it brings together scientists from computer science, molecular biology, mathematics, statistics, and related fields and provides an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. The conference fosters fresh dialogues, collaboration and learning opportunities, and is a gathering which shapes the future of the field. At the heart of the scientific program are ISCB’s Communities of Special Interest (COSIs), enabling community involvement and bolstering ISMB’s reputation as the leading conference in the field. The CompMS COSIpromotes the efficient, high quality analysis of mass spectrometrydata through dissemination and training in existing approaches and discussion of new, innovative approaches. The CompMS initiative aims to exploit synergies between different application domains, in particular proteomicsand metabolomics. A strong scientific and technical program showcases the best international developments in bioinformatics and computational biology, making ISMB 2020 a must attend event. Date: July 15, 2020 (CompMS COSI) / July 12–16, 2020 (ISMB) Venue: Palais des congrès de Montréal, Montreal, Canada Website: https://www.iscb.org/ismb2020 Key dates April 2, 2020: Abstract submission deadline April 30, 2020: Talk/poster acceptance notifications May 14, 2020: Late poster submission deadline May 21, 2020: Late poster acceptance notifications July 12–15, 2020: ISMB conference in Montreal Call for proposals Abstract submission for ISMB 2020 is now open! Submit your abstract to ISMB to present your work at the leading bioinformatics/computational biology conference. Attend the CompMS session to learn about the latest algorithmic advances in mass spectrometry-based proteomics and metabolomics. Please remember to select the CompMS COSI as your session of interest upon submitting your abstract. Call for abstracts: https://www.iscb.org/ismb2020-submit/abstracts We look forward to seeing you in Montreal! The CompMS organizing committee. Wout Bittremieux Oliver Kohlbacher William Stafford Noble Timo Sachsenberg Olga Vitek

1 0

vacancy for PhD student in bioinformatics available
by Ruigrok, Y.M. 26 Feb '20

26 Feb '20

We have a vacancy for a PhD student in bioinformatics available! We are looking for a highly motivated and skilled candidate with an MSc degree in exact sciences (mathematics, physics, computer science, statistics), biomedical technology or technical medicine and affinity with clinical research and data analysis. In this research project it will be your job to analyze a large and complex database of data of 2 million general practitioner patients. You will contribute to the development of technical methods through machine learning to predict the presence of intracranial aneurysms. An intracranial aneurysm is a bulging, weakened area in the wall of an artery in the brain. An aneurysm can rupture causing a brain hemorrhage (a so-called subarachnoid hemorrhage (SAH)), a type of stroke with devastating effects. This research is a collaboration between the Neurology department of the division Brain from the University Medical Center Utrecht (UMCU) and the Public Health & Primary Care Medicine department from the Leiden University Medical Center (LUMC). For more information please also see the vacancy (in Dutch) at: https://www.werkenbijumcutrecht.nl/vacatures/Paginas/oio-machine-learning-i… If you have any questions about this vacancy, please contact me at ij.m.ruigrok(a)umcutrecht.nl<mailto:ij.m.ruigrok@umcutrecht.nl>. With kind regards, Ynte Ruigrok [Universitair Medisch Centrum Utrecht] Neurologist, associate professor | Division Neurosciences, Neurology University Medical Center Utrecht | Room number G03.228 | Internal mail no G03.228 | P.O. Box 85500 | 3508 GA UTRECHT ________________________________ 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. P Please think of the environment before printing this email. ------------------------------------------------------------------------------ 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.

1 0

Data Driven Innovation in the Agritech Sector - 24/25 March 2020, Lyon
by Kim DE RUYCK 26 Feb '20

26 Feb '20

[ https://elixir-europe.org/events/sme-2020-lyon | ] Join this event to discuss how phenotyping, bioinformatics and datascience is contributing to the future of agriculture! You will be immersed in a world of data-driven innovation, with a mix of high-level keynote presentations and hands-on sessions to discuss and interact with other companies, academics and ELIXIR partners. [ https://elixir-europe.org/events/sme-2020-lyon | PROGRAM and REGISTRATION ]

1 0

PhD or post-doc position in the Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven)
by Guy Baele 25 Feb '20

25 Feb '20

The Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven) is looking for a motivated PhD student or postdoctoral researcher with a background in bioinformatics/computer science to perform research in a multidisciplinary team. The candidate for this position should have a strong quantitative background, and preferably hold a master's degree (with distinction/cum laude) and/or PhD in computer science / (bio-)informatics (or equivalent through experience). The candidate hence is preferably experienced in an object-oriented programming language such as Java, although KU Leuven offers courses in object-oriented programming (among others) which the candidates can take if necessary. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel. Full description at KU Leuven's job site: https://www.kuleuven.be/personeel/jobsite/jobs/55574468?hl=en&lang=en Apply here: http://www.kuleuven.be/eapplyingforjobs/light/55574468 Project description This project focuses on new developments in a popular Bayesian phylogenetic and phylodynamic inference framework (BEAST: https://github.com/beast-dev/beast-mcmc) and its applications to important evolutionary problems, with a particular focus on infectious diseases. BEAST is mostly written in Java, with its high-performance computational library, known as BEAGLE, being implemented in C/C++ with CUDA C and C++, the C/C++ interface to the CUDA parallel computing platform. The first part of the project involves the continued development of an online Bayesian phylodynamic inference approach that allows incorporating novel data into an ongoing analysis. As such, the current implementation of such an approach in BEAST (https://arxiv.org/abs/2002.00245) will need to be extended towards more complex models with varying dimensionality and evaluated in terms of its statistical and computational performance. Other approaches to increase the performance of Bayesian phylodynamic inference can also be investigated, such as through parallelization (and interfacing with the BEAGLE library) and the design of novel transition kernels (e.g. Hamiltonian Monte Carlo) aimed at exploring (posterior) distributions of interest in a more efficient manner. In a second part of the project, useful software applications that complement Bayesian phylogenetic and phylodynamic inference will need to be designed and implemented. The main goal is to focus on assessing and interpreting the exploration of tree space, and think of useful and easy-to-interpret visualizations to do so. Novel approaches to visualizing the results of phylodynamic analyses altogether, along with the associated uncertainty on all parameters of interest and accompanying metadata, are also an important aspect of the position, with our group having previous experience in this area (for example, in developing SPREAD and SpreaD3). To this end, web-based applications can also be developed, and knowledge of JavaScript and/or Python is also considered a plus. The topics proposed are not carved in stone however, and we are certainly open to exploring new ideas and concepts. The candidate will be able to perform research in a dynamic and multidisciplinary team (computer scientists, data analysts and evolutionary biologists), housed in the brand-new facilities of the Rega institute at the Gasthuisberg University hospital campus, and guided by prolific supervisors. The candidate will be able to contribute to the continued development of the BEAST software package - used by many researchers in the fields of phylogenetics, phylodynamics and molecular evolution - and collaborate with top researchers in the field. Additionally, at the Division of Clinical and Epidemiological Virology, the candidate will be able to interact with several top researchers in the field of epidemiology, virology and metagenomics, and work on important infectious disease problems from an evolutionary perspective. The targeted starting date will be June/July 1st 2020, although both earlier and later starting dates can be negotiated, and the candidates should obtain his/her master’s and/or PhD degree by that time. All applicants are expected to submit a motivation letter, overview of their study results and two references (with their contact details). Funding is available for 4 years to perform a PhD, and between 2-3 years in case a post-doctoral researcher is selected. The position will remain open until a suitable candidate has been selected. -- Guy Baele, Assistant Professor Department of Microbiology, Immunology and Transplantation Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

1 0

Open position at Janssen Belgium
by Joke Reumers 25 Feb '20

25 Feb '20

Dear all, Janssen Belgium has an open fixed position in R&D IT. The position would be very suited for a (junior) bioinformatics researcher with a strong interest in the technical aspects of the job (machine learning, cloud operations). The full job description can be found here<https://jobs.jnj.com/jobs/2005800870W?lang=en-us&previousLocale=en-US>. Prior industry experience is not required. Best regards, Joke Reumers Joke Reumers, PhD Team Lead Computational Biology @ Discovery Sciences Janssen Pharmaceutica, Beerse -- +32 14 60 33 24

1 0

Containers & Workflow pipelines course
by Tuur Muyldermans 25 Feb '20

25 Feb '20

Dear, On Monday 11 and Tuesday 12 May 2020 ELIXIR Belgium and VIB are organizing a 'Containers and Workflow Pipelines for reproducible and automated data analysis<https://training.vib.be/containers-and-workflow-pipelines-reproducible-and-…>' course in Ghent. For this two day course we invited the Bioinformatics core of the Centre for Genomic Regulation, Barcelona! The first day is dedicated to Containers (Docker & Singularity) which are great tools for code portability and analysis reproducibility. You will learn how to build a container from scratch, share it with others and how to re-use and modify existing containers. On the second day, you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. With the rising interest in these topics, we hope this might be of interest to you. We start from scratch, however will build up fast and expect prior bioinformatics & programming knowledge. The full program is online and registrations are open via this link<https://training.vib.be/containers-and-workflow-pipelines-reproducible-and-…>. Best, Tuur Muyldermans On behalf of the ELIXIR Belgium team Tuur Muyldermans - ELIXIR Bioinformatics Trainer ELIXIR Belgium | VIB Bioinformatics Core Rijvisschestraat 126, 9052 Ghent | +32 9 248 16 01 www.elixir-belgium.org<https://www.elixir-belgium.org/> | https://corefacilities.vib.be<https://corefacilities.vib.be/> Subscribe to our mailing list<http://eepurl.com/cl-xOX> [ELIXIR logo]

1 0

FW: Global BioImaging - Training Programme Manager
by Alexander Botzki 18 Feb '20

18 Feb '20

From: Training-coordinators <training-coordinators-bounces(a)elixir-europe.org> On Behalf Of Gabriella Rustici Sent: Tuesday, 18 February 2020 12:24 To: training-coordinators(a)elixir-europe.org Subject: [Training-coordinators] Global BioImaging - Training Programme Manager Dear All, Global BioImaging is looking for a Training Programme Manager. This is a great community to work with so please disseminate this opportunity within your networks!!!!!! See attached document for more details Regards Gabry -- Gabriella Rustici, PhD Associate Director of Training, HDR UK Head of Bioinformatics Training, University of Cambridge Department of Genetics Downing Street Cambridge CB2 3EH United Kingdom Email: gr231(a)cam.ac.uk<mailto:gr231@cam.ac.uk> Tel: +44 (0)1223 333614 URL: http://bioinfotraining.bio.cam.ac.uk

1 0

advanced bachelor programme bioinformatics in Bruges (Belgium) (60 ECTS)
by Demeyere Mieke 18 Feb '20

18 Feb '20

Dear Madam/Sir HOWEST University of Applied Sciences starts in September 2020 with a remote bioinformatics study programme! Advanced bachelor of Bioinformatics ... a small summary. Why? Bioinformatics is an emerging field, adding this extra degree to your curriculum, will have an added value to your resume. Aim? Teaching dry-lab skills to people with a molecular biological background in order to function as a fully trained bioinformatician. Content? · Working with databases (build them, retrieve, access and store data in it) · High throughput analysis (working on pipeline, data analysis in R) · Construction of a bioinformatics tool (using php for web application, writing python scripts) · Other: comparative genomics analysis, data mining, structural analysis in pymol, ... For more detailed information please access: http://bioinformatictools.howest.be/programme.pdf For Who? We recruit everyone who holds a diploma of higher education stating sufficient knowledge of molecular biology on (minimal) bachelor level (e.g. Bachelor biomedical Laboratory Technology, bachelor biochemistry, bachelor biotechnology, ...) also relevant Master and PhD degrees are eligible. Duration? One year in daytime education Two year in remote education (starts in September 2020) Want more information? Contact us: Bit(a)howest.be<mailto:Bit@howest.be>, visit our website<https://www.howest.be/en/programmes/advanced-bachelor/bioinformatics> or watch our video<https://www.youtube.com/watch?v=THTK1S-LH34> or presentation in attachment. With kind regards Mieke Demeyere Opleidingscoördinator Biomedische Laboratoriumtechnologie/Programme coordinator Advanced Bachelor of Bioinformatics [cid:image001.png@01D5E67B.A4D954D0] Howest University of Applied Sciences Campus Brugge Station Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 Fax: +32 50 38 11 71 www.howest.be/blt<http://www.howest.be/blt> en https://www.howest.be/nl/opleidingen/banaba/bio-informatica Bekijk onze navormingen en opleidingen via deze link<https://www.howest.be/nl/opleidingen/navormingen/biomedische-laboratoriumte…>. Denk aan het milieu vooraleer je dit bericht of de bijlagen uitprint!

1 0

IRIBHM/ULB PhD program
by Vincent Detours 18 Feb '20

18 Feb '20

Dear all, IRIBHM, a major molecular biology lab in Belgium, launches an international graduate programme. Topics include computational Biology. More here: http://iribhmphd.ulb.be All the best, Vincent Detours, Ph. D. https://iribhm.org/v-detours/ IRIBHM - Université Libre de Bruxelles Bldg C, room C.4.116 ULB, Campus Erasme, CP602 808 route de Lennik B-1070 Brussels Belgium Phone: +32-2-555 4220 Fax: +32-2-555 4655 Skype: vdetours E-mail: vdetours at ulb.ac.be

1 0

Job vacancy applied bioinformatics
by Warris, Sven 17 Feb '20

17 Feb '20

Dear reader, We are looking for a Bioinformatics Assistant to join our research team in Applied Bioinformatics. The group combines wet-lab and bioinformatics expertise. We focus on innovative approaches to genomics analyses, with projects on genome reconstruction, gene annotation, comparative genomics and tool development. Applied Bioinformatics is part of Bioscience, one of the business units of the Wageningen Research foundation of the Plant Sciences Group. Wageningen Research, together with Wageningen University forms Wageningen University & Research. At Bioscience, we study at the molecular level the regulation of metabolic and developmental processes of plants and plant genomics to meet the needs of our growing society. We are developing tools that allow to efficiently use plant genetic resources. Wageningen UR is an internationally renowned research institute in the fields of life sciences and sustainable production. More information: https://www.wur.nl/en/vacancy/Bioinformatics-Research-Assistant.htm Best, Sven Warris Wageningen University & Research

1 0