- BBClist - maillist.psb.ugent.be

(IB)2 Research Day, 16th November 2018
by Matthieu Defrance 18 Oct '18

18 Oct '18

(IB)2 Research Day 2018 16th November 2018, 9.30-5 pm U-Residence, Congrescentrum, green room, Campus VUB, Brussels Registration: https://goo.gl/forms/bDFUQyXp8R6baKIQ2 We are pleased to announce that the annual "(IB)2 Research Day 2018" will be held November 16th 2018 from 9.30am to 5.00pm at the VUB Congrescentrum U-Residence (VUB Campus Generaal Jacqueslaan 271, 1050 Brussels). This one-day meeting is organized by (IB)2 or Interuniversity Institute of Bioinformatics in Brussels is a interdisciplinary research institute and supported by ULB and VUB universities. 9.30 9.35 Welcome 9.35 10.35 Keynote 1 - Carl Herrmann, University of Heidelberg Multi-omics data integration for single-cell genomics 10.35 11.05 Charlotte Nachtegael, Unraveling the oligogenic potential of developmental disorders (IB)2, ULB 11.05 11.30 Coffee Break 11.30 12.00 Youssef Bouysran, Bioinformatic investigations of missense mutations in the FBN1 gene (IB)2, ULB 12.00 12.30 Nathaniel Mon Père, Quantitative Models for Cell Differentiation in Hematopoiesis (IB)2, ULB 12.30 12.45 Flash presentations 12.45 14.00 Lunch break and poster session 14.00 15.00 Keynote 2 - Hervé Isambert, Institut Curie Paris Learning causal and non-causal networks from large scale genomic and clinical data 15.00 15.30 Gipsi Lima Mendez, Ocean Eco-system biology through integration of heterogeneous data (IB)2, ULB 15.30 16.00 Closing remarks / Future of the (IB)2 16.00 17.00 Musical Coffee Up to date version of the program: https://ibsquare.be/research-day This meeting is free and open to every researcher or student but a quick online registration is required: https://goo.gl/forms/bDFUQyXp8R6baKIQ2 If you have any questions regarding this meeting please feel free to contact: Sophie de Buylsophie.de.Buyl(a)vub.be or Matthieu Defrance matthieu.dc.defrance(a)ulb.ac.be On behalf the (IB)2, Sophie de Buyl and Matthieu Defrance

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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
by Laurent Gatto 18 Oct '18

18 Oct '18

The Computational Biology (CBIO) unit at the de Duve Institute in Brussels, Belgium, seeks to appoint a full time research software engineer. The successful candidate will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of biomedically relevant topics in collaboration with researchers from the de Duve institute as well as other institutes on the biomedical campus of UCLouvain. The focus of the position is on rigorous research software engineering, analysis pipeline development and high-throughput biology data analysis, with the possibility of engaging in teaching activities. If you recognise yourself in any of the following profiles, please consider applying. - You have created/maintained/used software to address research problems in high throughput biology (such as, for example genomics, transcriptomics, epigenetics, proteomics and/or metabolomics). - You can rapidly assimilate understanding of new biomedical questions, and quickly connect research needs to software requirements. - You are committed to open source software development best practices and know how to adapt these to biomedical research contexts. Duties and activities The research software engineer will be expected to contribute to various activities, including : - Research projects: support and advise collaborators with their data analyses and contributed to scientific reports and publications. - Maintain and develop research software and repositories linked to the ongoing research in the group and collaborative projects. - Participate in the administration of the computing and data storage infrastructure. - Attend scientific conferences to present their research and development and workshops to improve and learn new sets of skills. - Contribute to bioinformatics teaching, both within the institute and the School of Biomedical Sciences. Required skills The ideal candidate would be either a researcher with a focus on research software and data analysis, or a software developer with an interest in research and biomedical sciences. We are looking for a motivated candidate with a PhD or a Master's degree in bioinformatics or equivalent, possessing computational and quantitative skills such as : - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience with the processing and analysis of omics data (important). - Experience in open and reproducible research, open source software and open data (important). - Experience in C/C++ (desirable). - Experience in JavaScript, specifically the development of online visualisation applications (desirable). - Experience in teaching, ideally the Data and Software Carpentry curricula or interest in training to become an instructor (desirable). - Experience in high performance computing (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. Contract on external resources, full time, with initial duration of 3 years (1 year renewable twice) - available immediately. We value equality, diversity and an open, collaborative and welcoming work environment. Please send your application by email to Laurent Gatto referencing this position, including a CV, 3 academic references, and a motivation letter. Don't hesitate to contact me for additional information. Original post advert: https://jobs.uclouvain.be/PersonnelAdministratif/job/Research-software-engi… Prof Laurent Gatto de Duve Institute - UCLouvain Avenue Hippocrate, 75 - bte B1.74.10 1200 Brussels, Belgium Tel: +32 (0)2 764 74 15

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Help Shape the Future of Training at Edinburgh Genomics.
by TRAIN edgenomics-training 17 Oct '18

17 Oct '18

Dear all At Edinburgh Genomics, we are always looking at ways we can improve the services we offer to you, the scientific community. We currently provide training courses covering a range of different genomics topics using the latest bioinformatics techniques. We want to keep these courses as relevant and as useful to you as possible, tailoring our training to best meet your needs. But, to do this we need your help! We want you to have your say in shaping the future of training provision at Edinburgh Genomics. Do you need more training in a particular programming language? Are you moving to a new type of analysis that feels bewildering without some expert advice? Let us know by completing this quick survey (20 short questions) and help us to better understand your needs: https://www.surveymonkey.co.uk/r/7M6QB2D The survey is completely anonymous unless you chose to share your contact details, your responses are used for developing training courses only, and are never shared with a third party. Thank you in advance: we value your opinions and preferences very highly. Kind Regards Nathan Medd Training and Outreach Manager Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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FW: Professorship KU Leuven Applied Bioinformatics in Microbial Ecology and related fields
by Hans Rediers 16 Oct '18

16 Oct '18

Dear, At KU Leuven's Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), there is an open position for a professor (Junior/Senior) in the field of 'Applied Bioinformatics in Microbial Ecology and related fields'. I dare to bring this vacancy to your attention. More information on the PME&BIM lab can be found on: https://iiw.kuleuven.be/onderzoek/pme-bim For all information regarding the job profile, consult: https://www.kuleuven.be/personeel/jobsite/jobs/54649637?hl=en&lang=en We are offering full-time employment in an intellectually challenging environment. KU Leuven is a research-intensive, internationally oriented university that carries out both fundamental and applied scientific research. You will work at Campus Group T in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Feel free to pass on this announcement to all possibly interested researchers (including former PhD students, post-docs, colleagues etc). The deadline is February 1st, 2019. A concise research plan defining main lines of research is requested as an annex to the application tool. For all your questions, please feel free to contact me Yours sincerely, Hans Rediers ------------- Prof. dr. ir. Hans Rediers Programme coordinator Master IW: Biotechnology Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM) Cluster for Bioengineering Technology (CBeT) Department of Microbial and Molecular Systems (M2S) Faculty of Engineering Technology KU Leuven - Campus De Nayer Fortsesteenweg 30A | BE-2860 Sint-Katelijne-Waver | Belgium Tel. +32 (0)15 30 55 90 Fax. +32 (0)15 30 55 99 Website: www.kuleuven.be/pme-bim<http://www.kuleuven.be/pme-bim> E-mail: hans.rediers(a)kuleuven.be<mailto:hans.rediers@kuleuven.be>

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Second Announcement NSBM Fall Meeting
by Nicolaes, G (BIOCH) 15 Oct '18

15 Oct '18

Second Announcement [ogo.png] NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Fall meeting 3D Protein Structures: what sequences cannot tell you November 16th 2018 Venue: Boothzaal, University Library De Uithof, Utrecht The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands and beyond, that work on three dimensional structures of biomolecules and biomolecular simulations. This is a first announcement of our Fall meeting to which you are cordially invited. During the meeting, the floor will be given to students, PhD students, post-docs and a number of invited guest speakers who study protein structure and/or structural bioinformatics or related topics. Location and dates * Date: November 16th, 2018, 10:00-17:00 * Venue: Boothzaal, University Library De Uithof, Heidelberglaan 3, 3584 CS Utrecht * http://www.uu.nl/universiteitsbibliotheek/locaties<http://www.uu.nl/universiteitsbibliotheek/locaties%20> Deadlines * Registration deadline for posters or to be considered for a short talk: November 5th * Registration deadline (including lunch): November 9th Application procedure * Participants should send an email to register (required but free registration) to: g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> * Submission of an abstract is required if you want to present a poster. * Indicate in your email if you want to be selected for a short oral presentation. Note: The maximum number of participants is limited to 75! So please register on time. Lead contact * Dr. Gerry Nicolaes - g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> http://www.3dstructure-function.nl/nsbm-fall-meeting/<http://www.3dstructure-function.nl/?page_id=912&preview=true> Confirmed speakers are: o Dr. Vlad Cojocaru (Hubrecht Institute) - "Molecular simulations of DNA recognition by transcription factors" o Dr. Marc Baaden (Institut de Biologie Physico-Chimique) - " 3D protein structures in virtual molecular reality" o Dr. Chris Oostenbrink (Institute of Molecular Modeling and Simulation, BOKU Vienna) - "Binding molecules in free-energy calculations" o Prof. Peter Peters (Maastricht University) - "Beauty and Benefits of cryo-EM; our new endeavors in vitrification of proteins and cells" Abstract submission is still open and we have several free slots in the sessions for students, PhD students and post-docs Costs Attendance is free of charge but registration is required. Lunch and coffee will be provided thanks to the financial support of the Nijmegen Centre for Molecular and Biomolecular Informatics. A flyer is enclosed. With kind regards, Gerry Nicolaes [cid:image001.jpg@01CC2F5C.EA047880] Gerry Nicolaes, PhD Associate Professor Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.3dstructure-function.nl<http://www.3dstructure-function.nl/> [cid:image002.jpg@01CC2F5C.EA047880]Please consider your environmental responsibility before printing this e-mail.

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professor position applied bioinformatics Leuven
by Vera van Noort 15 Oct '18

15 Oct '18

At KU Leuven¹s Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), there is an open position for a professor (Junior/Senior) in the field of Applied Bioinformatics in Microbial Ecology and related fields¹. More information on the PME&BIM lab can be found on: https://iiw.kuleuven.be/onderzoek/pme-bim <https://iiw.kuleuven.be/onderzoek/pme-bim> For all information regarding the job profile, consult: https://www.kuleuven.be/personeel/jobsite/jobs/54649637?hl=en&lang=en <https://www.kuleuven.be/personeel/jobsite/jobs/54649637?hl=en&lang=en> We offer full-time employment in an intellectually challenging environment. KU Leuven is a research-intensive, internationally oriented university that carries out both fundamental and applied scientific research. You will work at Campus Group T in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam. Feel free to pass on this announcement to all possibly interested researchers (including former PhD students, post-docs, colleagues etc). The deadline is February 1st, 2019. A concise research plan defining main lines of research is requested as an annex to the application tool. For more information contact Hans Rediers <hans.rediers(a)kuleuven.be>. Best wishes, Vera van Noort

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PhD position Bioinformatics - KU Leuven
by Vera van Noort 12 Oct '18

12 Oct '18

The Computational Systems Biology group at KU Leuven is looking for a PhD student in the DART pathways project supported by the NC3Rs. The student will work on phylogenetic reconstructions for genes in pathways relevant to Developmental And Reproductive Toxicity, to improve the orthology assignments between human, animal test species and alternative test models. These will be used in a tool that aids in the selection of alternative models for toxicity testing and the reduction of animal tests. If you have a background in Bioinformatics and want to apply your knowledge to a societally relevant problem, contact prof. dr. Vera van Noort vera.vannoort(a)kuleuven.be https://www.kuleuven.be/personeel/jobsite/jobs/54891123 Bw, Vera van Noort

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Edinburgh Genomics - R for Genomics Workshop
by TRAIN edgenomics-training 11 Oct '18

11 Oct '18

Starting out analysing genomic data in the R environment? There are still some spaces available for 'R for Genomics' at Edinburgh Genomics, Monday 26th and Tuesday 27th November 2018. This is a two-day workshop on the use of the statistical programming language ‘R’ in genomics, taught by experienced Edinburgh Genomics’ Bioinformaticians. By the end of the workshop, you will be comfortable with the basics of R; know how to use it as smartly as possible, avoiding common mistakes; apply it to manipulate various genomic data structures; add and extract annotation; and visualize your data to generate publication-ready plots. Instructors: Dr Katie Emelianova (Bioinformatician) Nathan Medd (Training and Outreach Manager) To register or for more information on this, and other courses available at Edinburgh Genomics, please visit our training page at https://genomics.ed.ac.uk/services/training Kind Regards Nathan Medd Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Open position in Research Data Management and Science Reproducibility at VIB
by Alexander Botzki 09 Oct '18

09 Oct '18

Dear all, We are welcoming a new colleague helping us in the area of Research Data Management and Science Reproducibility - check out our job offering at https://jobso.id/bis4 Best regards, Alexander 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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FW: 4-year PhD Theoretical Systems Biology & Bioinformatics @ Imperial College London Oct 2018
by Alexander Botzki 09 Oct '18

09 Oct '18

From: Sternberg, Michael J E <m.sternberg(a)imperial.ac.uk<mailto:m.sternberg@imperial.ac.uk>> Date: Mon, Oct 8, 2018 at 2:38 PM Subject: FW: 4-year PhD Theoretical Systems Biology & Bioinformatics @ Imperial College London Oct 2018 To: Dear colleague I would be grateful if you could forward this exciting opportunity to your undergraduates If possible, please could put the poster - that would be great. Thanks Mike Sternberg Imperial College London A 4-year PhD in Theoretical Systems Biology and Bioinformatics at Imperial College London The opportunity This 4-year PhD programme<https://www.findaphd.com/common/clickCount.aspx?theid=1005&type=185&url=htt…>, supported by The Wellcome Trust, will provide an exciting training opportunity to acquire multidisciplinary skills to develop and then apply modelling to biological and clinical problems at the molecular and cellular levels. The programme aims to facilitate discipline hopping into this area and we welcome undergraduates from biological and medical sciences, physical sciences, mathematics, statistics, engineering and computing. The course will enable you, whatever your first degree, to acquire the breadth of skills to undertake stimulating research using theoretical systems biology and bioinformatics to advance biological and clinical research. As a member of the programme you will join a large community at Imperial applying modelling to study biological and biomedical problems. [cid:1665856e0806917eb1] The training programme You will begin your studies by being registered on our highly-successful, year-long MSc in Bioinformatics and Theoretical Systems Biology. This course starts with training and you will acquire core biological, computational and mathematics skills and have lectures in bioinformatics and theoretical systems biology. This is followed by three different rotation projects which enable you to discover and experience different modelling methodologies and experimental laboratory environments. During the first year you will benefit from working with many other students studying for this MSc. The subsequent three PhD years will involve research developing novel theoretical methodologies and applying them to solve biological and biomedical problems. You will have two supervisors throughout your PhD – one theoretical and one experimental – to provide multidisciplinary training. You will have an opportunity to spend time with the experimental group so you understand the data-generating protocols and you can undertake laboratory work to test hypotheses generated from your modelling. We will offer you a wide range of research topics for your PhD as Imperial College has many vibrant research groups working in theoretical systems biology and bioinformatics and their application to bioscience and biomedical problems. Application Procedure The next 4-year programme starts in October 2018. There are 5 fully funded places (stipend, fees and generous research support including travel) for home/EU students and there is one scholarship to provide the additional fees required for an exceptional overseas student. The stipend for 2017 will start at no less than £22,278 in year one, rising to at least £26,839 in year four. Deadline for receipt of applications is 23:00 GMT on Monday 4 December 2017. For further details and application procedure: Google “Wellcome Bioinformatics Imperial” or go to http://www.imperial.ac.uk/wellcome-bioinformatics-phd/

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