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Knowledge Graphs in the Life Sciences - Registration closes soon - BioSB 13 - 17 March
by BeNeLux bioinformaticians forum 30 Jan '23

30 Jan '23

Dear colleagues, March 13 - 17 BioSB organizes (in Wageningen, NL) the course "*Knowledge Graphs in the Life Sciences*". Although many people indicated their interest in this course, not many people have signed up so far. Make sure to register *quickly* if you want to gain more experience and knowledge with/about Linked Data technologies. Experienced teachers (like Jasper Koehorst, Önder Babur and Anna Fensel) are ready to share their expertise with you! ***************************************************** More information about the course can be found **here <https://www.dtls.nl/courses/fair-linked-data-in-the-life-sciences/>**. **Registration (pref. before 3 Febr) can be done here <https://www.aanmelder.nl/139335/subscribe>. ********************************************************* You can expect the following learning outcomes: * Explain Linked Data technologies (Internet, Semantic Web, ontologies, graph databases), standards and recommendations (as URI, XML, RDF, OWL, SPARQL), and their use in forming a Web of Data; * Use Linked Data technologies for retrieving information in the Semantic Web (i.e. use of SPARQL); * Use of existing vocabularies for annotating data and endpoints for finding data for a particular domain; * Understand the FAIR principles and how to apply it to a research project; * Able to convert research metadata into FAIR Linked Datasets. The course is aimed at PhD students with a background in biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. Preparation material will be distributed dug the course. We wish you a warm welcome in Wageningen! Kind regards, Petra Aarnoutse community manager BioSB

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BioSB-NLSEB Symposium "Evolution in and of cell communities", 15 February 2023, Amsterdam
by BeNeLux bioinformaticians forum 30 Jan '23

30 Jan '23

Dear all, On Februari 15, BioSB HotTopics and NLSEB jointly organise a symposium on Evolution in and of cell communities. The symposium brings together speakers from backgrounds in microbial evolution and cancer research, including experimentalists and theorists. The symposium takes place at the VU Amsterdam from 9:30-18:00 and besides presentations also includes time for discussion and a poster session. More information and registration (free): https://forms.gle/5C6f2t9KDroXMu6s9<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforms.gle…> Thanks and hope to see you Feb 15! [BioSB_NLSEB_202302.png] ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org | e.bosdriesz(a)vu.nl

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PostDoc position in Bologna (IT)
by BeNeLux bioinformaticians forum 25 Jan '23

25 Jan '23

Dear all, Please find below a message on behalf of Emidio Capriotti on a postdoc position in Bologna, Italy. Best, Fabrizio ULB and IB2, Bruxelles *Computational infrastructure for the analysis of the rare disease genome* Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy The BioFolD unit (biofold.org) at the University of Bologna is seeking a post-doc with programming skills in the field of bioinformatics/computational biology. The ideal candidate should be able to analyze DNA and protein sequence as well as protein three-dimensional structure to develop new methods for predicting the impact of genetic variants. We offer a 24 months fellowship. Qualifications: PhD in Bioinformatics, Physics, Mathematics, Informatics, Start date : As soon as possible How to Apply : Information on the application are in Italian ( ricercatm.unibo.it/assegniricerca_segretari/_bandi/2008/Bando66137[194301]TutorColloquio.pdf ). In case it is needed please contact Emidio Capriotti to submit the official application through the website concorsi.unibo.it. The deadline for the application is February 28th. Contact Emidio Capriotti at gmail.com

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Opening for a Data Research Assistant position in the Bart de Strooper lab in UCL/London
by BeNeLux bioinformaticians forum 25 Jan '23

25 Jan '23

Dear all, We are looking for a Data Research Assistant for our UCL/Crick lab in London. Our lab focuses on research in to Alzheimer's Disease, the most prevalent form of dementia, using a number of different methods. We use the latest and greatest methods in spatial and single cell transcriptomics and proteomics. These methods generate a lot of data, and as such we are looking for somebody to play a central role in organizing data management, processing, analysis workflows and visiualization. As such you can provide a crucial role in our research, which will ultimately lead to novel drugs against Alzheimer's Disease. More details here: https://www.ucl.ac.uk/work-at-ucl/search-ucl-jobs/details?jobId=4533&jobTit… Best Mark

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Opening for an Assistant Professor Artificial Intelligence in Plant & Microbial Biology
by Abeln, S. (Sanne) 24 Jan '23

24 Jan '23

Dear colleagues, Utrecht University has an opening for an Assistant Professor position in Artificial Intelligence in Plant & Microbial Biology. We seek a new colleague who will perform research in machine learning and artificial intelligence to resolve big data-driven fundamental research questions in the green life sciences. The Assistant Professor will be part of the new interdepartmental AI Technology for Life group and the Plant-Microbe Interactions group. For more details, see: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/assist… Applications need to be received by 23 January 2023. It would be nice if you could share this position with potential candidates, Many thanks, Sanne --- Sanne Abeln Associate Professor in Bioinformatics Dep. of Computer Science - Vrije Universiteit +31 20 59 87816<tel:+31%2020%2059%2087816> https://www.few.vu.nl/~abeln/

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Fwd: Junior Lecturer VU/UvA master’s programme Bioinformatics and Systems Biology JD
by BeNeLux bioinformaticians forum 24 Jan '23

24 Jan '23

Please see below announcement and link to online description. Please note, deadline next week: Wed Feb 1st. -------- Forwarded Message -------- Subject: JUNIOR LECTURER VU/UvA MASTER’S PROGRAMME BIOINFORMATICS AND SYSTEMS BIOLOGY JD Date: Fri, 23 Dec 2022 17:46:48 +0000 From: Marten Postma <M.Postma(a)uva.nl> To: bio-jobs.few(a)listserver.vu.nl <bio-jobs.few(a)listserver.vu.nl>, bbclist(a)psb.vib-ugent.be <bbclist(a)psb.vib-ugent.be> Dear Reader, There is a Junior Lecturer position available at the VU/UvA for teaching in Bioinformatics & Systems Biology Check out the VU website : https://workingat.vu.nl/ad/junior-lecturer-juniordocent-masters-programme-b… <https://workingat.vu.nl/ad/junior-lecturer-juniordocent-masters-programme-b…> Junior lecturer (juniordocent) Master’s Programme Bioinformatics and Systems Biology JD - >Working at VU <https://workingat.vu.nl/ad/junior-lecturer-juniordocent-masters-programme-b…> We are looking for a colleague who is passionate about education and dedicated to support the VU/UvA joint degree Master’s programme for Bioinformatics and Systems Biology<https://vu.nl/en/education/master/bioinformatics-and-systems-biology> Please apply... workingat.vu.nl Kind Regards, Marten Dr. Marten Postma Assistant Professor Chair Examinations Board BSc BMW/MSc BMS Leerlijncoördinator Omics en Systeembiologie BSc BMW Track coordinator Systems Biology MSc BioSB JD Member Admission CommitteeMSc BioSB JD Vice-chair Curriculum Committee MSc BioSB JD Member SILS Educational Committee (SEC) zoom : https://uva-live.zoom.us/j/2612815610 Room C2.102 (SILS) Swammerdam Institute for Life Sciences (SILS) University of Amsterdam (uVA) Science Park 904 1098 XH Amsterdam The Netherlands tel : +31 20 525 6225 e-mail : M.Postma(a)uva.nl website : http://www.martenpostma.nl/science/ -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1111 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +312059 87783 - skype: kafeenstra - room NU 12A31| | |Feenstra(a)few.vu.nl -www.few.vu.nl/~feenstra/ | | | "If we knew what it was we were doing, it would not | | | be called research, would it?" (Albert Einstein) | |_____________|_______________________________________________________|

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Postdoctoral position in structural bioinformatics (joint VUB and Confo therapeutics)
by BeNeLux bioinformaticians forum 24 Jan '23

24 Jan '23

Dear all, We have an open postdoctoral position in structural bioinformatics, jointly with Confo Therapeutics, for the design of dynamic proteins. The final aim is to prosecute GPCR drug targets, a challenging topic, so we are looking for a motivated computational researcher who wants to engage with the real life application of their research - if you are interested, or know someone who might be, have a look here: https://bit.ly/dyndesign. Please do share in your network! Best, Wim --------------------------------------------------------------------------------------- Prof. Dr. Wim Vranken Tel: +32 (0)2 6291952<tel:+3226291952> (VUB) VUB - Building E, 5th Floor, E5.02, Pleinlaan 2 1050 Brussels, Belgium Structural Biology Brussels/Artificial Intelligence/General Chemistry/Biomedical sciences Associate professor - http://bio2byte.be/ ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Member and former director - http://ibsquare.be/ ELIXIR - Bringing together life science resources across Europe Co-lead of ELIXIR IDP community, member of ELIXIR-Belgium management board ---------------------------------------------------------------------------------------

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ATCR2023 meeting : 3-4 May
by BeNeLux bioinformaticians forum 24 Jan '23

24 Jan '23

Dear all, We will be organising the third ATCR meeting in Antwerp, Belgium on the 3rd-4th of May, 2023. The aim of this meeting is to gather experts from academia and industry discuss T-cells from a T-cell receptor (TCR) perspective. The invited speakers include: Paul G Thomas, Victor Greiff, Nicole La Gruta, Phil Bradley, Diether Lambrechts, Aleksandra Walczak, Femke van Wijk, Thierry Mora, Maria Rodriguez Martinez, Petra Bacher, Andreas Mayer, Morten Nielsen and Hedda Wardemann. Our sponsors include: 10xGenomics, BD sciences and ImmuneWatch. We have an open call for abstracts covering new computational/experimental methods or new findings in the TCR field for both talks and posters. The submission deadline is the 30th of March. More information can be found here: https://www.uantwerpen.be/atcr23 In addition, there will be a free workshop on TCR data analysis using tools such as TCRex, ClusTCR, and TCRexplore, the preceding day on the 2nd of May: https://www.uantwerpen.be/en/conferences/third-antwerp-tcr-meeting/workshop/ Hope to see you all there! On behalf of the ATCR scientific committee, Benson Ogunjimi Pieter Meysman Co-chairs ATCR2023

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Upcoming BioSB courses and events!
by BeNeLux bioinformaticians forum 19 Jan '23

19 Jan '23

Dear Colleagues, Check this out! BioSB still has a few places available in some very interesting courses/events. Be fast if you want to join! * BioSB course: Constraint-based modeling This course will introduce computational modeling of large (genome-scale) metabolic reaction networks through a scalable framework known as constraint-based modeling. Emphasis will be on the usage in both biotechnology and systems biomedicine. Main topics will be fundamental constraint-based modeling methods, omics data integration, multi-scale modeling and microbial community modeling. The course will combine theoretical lectures with tutorial exercises and computational exercises in Python. Where: Wageningen Campus, the Netherlands When: 13 - 17 February 2023 More information and registration>><https://www.dtls.nl/courses/constraint-based-modeling-introduction-and-adva…> * BioSB course: Knowledge graphs in the life sciences This course aims to teach how to: * Explain Linked Data technologies (Internet, Semantic Web, ontologies, graph databases), standards and recommendations (as URI, XML, RDF, OWL, SPARQL), and their use in forming a Web of Data; * Use Linked Data technologies for retrieving information in the Semantic Web (i.e. use of SPARQL); * Use of existing vocabularies for annotating data and endpoints for finding data for a particular domain; * Understand the FAIR principles and how to apply it to a research project; * Able to convert research metadata into FAIR Linked Datasets. Where: Wageningen Campus, the Netherlands When: 13 - 17 March 2023 More information and registration>><https://www.dtls.nl/courses/fair-linked-data-in-the-life-sciences/> * BioSB Hot Topics Symposium: Evolution in and of Cell Communities Where: O2 building, Vrije Universiteit Amsterdam When: Wednesday 15/02/2022 from 9:30 - 18:00 Registration deadline: 1 February 2023! More information and registration>><https://www.dtls.nl/events/hottopics-symposium-evolution-in-and-of-cell-com…> [https://lh5.googleusercontent.com/nqFEz-_iODu6tP17diW6X46KTIS9bIPMaA_BeHl8n…] Kind regards, Petra Aarnoutse BioSB community manager

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Upcoming BioSB courses and events!
by BeNeLux bioinformaticians forum 19 Jan '23

19 Jan '23

Dear Colleagues, Check this out! BioSB still has a few places available in some very interesting courses/events. Be fast if you want to join! * BioSB course: Constraint-based modeling This course will introduce computational modeling of large (genome-scale) metabolic reaction networks through a scalable framework known as constraint-based modeling. Emphasis will be on the usage in both biotechnology and systems biomedicine. Main topics will be fundamental constraint-based modeling methods, omics data integration, multi-scale modeling and microbial community modeling. The course will combine theoretical lectures with tutorial exercises and computational exercises in Python. Where: Wageningen Campus, the Netherlands When: 13 - 17 February 2023 More information and registration>><https://www.dtls.nl/courses/constraint-based-modeling-introduction-and-adva…> * BioSB course: Knowledge graphs in the life sciences This course aims to teach how to: * Explain Linked Data technologies (Internet, Semantic Web, ontologies, graph databases), standards and recommendations (as URI, XML, RDF, OWL, SPARQL), and their use in forming a Web of Data; * Use Linked Data technologies for retrieving information in the Semantic Web (i.e. use of SPARQL); * Use of existing vocabularies for annotating data and endpoints for finding data for a particular domain; * Understand the FAIR principles and how to apply it to a research project; * Able to convert research metadata into FAIR Linked Datasets. Where: Wageningen Campus, the Netherlands When: 13 - 17 March 2023 More information and registration>><https://www.dtls.nl/courses/fair-linked-data-in-the-life-sciences/> * BioSB Hot Topics Symposium: Evolution in and of Cell Communities Where: O2 building, Vrije Universiteit Amsterdam When: Wednesday 15/02/2022 from 9:30 - 18:00 Registration deadline: 1 February 2023! More information and registration>><https://www.dtls.nl/events/hottopics-symposium-evolution-in-and-of-cell-com…> [https://lh5.googleusercontent.com/nqFEz-_iODu6tP17diW6X46KTIS9bIPMaA_BeHl8n…] Kind regards, Petra Aarnoutse BioSB community manager

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