January 2023 - BBClist - maillist.psb.ugent.be

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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Welcome to 2023 🍾 !!! Get ready with our training sessions!
by BeNeLux bioinformaticians forum 16 Jan '23

16 Jan '23

[cid:image001.png@01D92992.711F9700] [signature_2008044598] 2023 is here 🍾! And to make it an even better year, join us for some training sessions! Dear colleagues, Coming up in in the next few months: Get started with introduction to Git & GitHub, learn how to use it and how it helps tracking versions of your code and writing. Make life easier and increase the impact of your work using Docker (and Singularity) for reproducible and automated data analysis. And don’t forget you can have scalable and reproducible pipelines with Nextflow for reproducible and automated data analysis. Last, but not least, join us for the hybrid session of Gentle hands-on introduction to Python programming , and start making your own codes. Find bellow the details you need to join us in any of the coming up trainings. Don’t forget to subscribe! Introduction to Git & GitHub ____________________________________________________________________________________ 8th February 2023 – Brussels Face to Face training This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers Registration and info: Link for Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-5> Docker (and Singularity) for reproducible and automated data analysis ____________________________________________________________________________________ 13th and 14th March 2023 – Leuven Face to Face training The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be highlighted as well. Registration and info: Docker and reproducibility<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> Nextflow for reproducible and automated data analysis ____________________________________________________________________________________ 30th and 31st March 2023 – Leuven Face to Face training You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Registration and info: NextFlow automated pipeline<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> Gentle hands-on introduction to Python programming ____________________________________________________________________________________ 12th , 19th and 26st April 2023 – Ghent Hybrid session This course gently introduces programming to new programmers. There are plenty of opportunuties to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn. Registration and info: Gentle hands-on python<https://training.vib.be/all-trainings/gentle-hands-introduction-python-prog…> Kind regards, Bruna Piereck ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium tel +32 0497 2988 73 [cid:image001.png@01D92992.711F9700][signature_2008044598] Bruna Piereck VIB Bioinformatics Core ELIXIR Belgium Training Coordinator Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium tel +32 0497 2988 73 [signature_2008044598] [cid:image001.png@01D92992.711F9700]

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Bioinformatics Awards & Call for abstracts at the [BC]2 conference - please share with your community
by BeNeLux bioinformaticians forum 13 Jan '23

13 Jan '23

Dear colleagues, On behalf of our SIB colleagues we want to share the information that SIB has just opened the *call for abstracts for the [BC]2 Basel Computational Biology Conference 2023 <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbc2.ch%2F…>*. It will take place from 11-13 September in Basel, Switzerland under the theme “Big data in biology: promises and challenges”, featuring *Elisabeth Bik* and *Fabian Theis* as keynote speakers. In addition, the call for entries for the *International Bioinformatics Awards 2023* is still running and will end on *31 January 2023*. The SIB Awards is a biennial competition open to worldwide early career bioinformaticians and ground-breaking resources of national and international standing, in the following three categories: o PhD Paper Award <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sib.s…> o Early Career Award <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sib.s…> o Innovative Resource Award <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sib.s…> Best Celia -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI Network Manager TDCC-LSH tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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BioSB 2023 conference - Call for abstracts!
by BeNeLux bioinformaticians forum 13 Jan '23

13 Jan '23

Submit your abstract and join us for the 9th edition of the BioSB conference, Hotel Zuiderduin, Egmond aan Zee. View this email in your browser <https://mailchi.mp/dtls/save-the-date-biosb-5382372?e=6c7bbf5973> <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Call for abstracts BioSB 2023 conference, 9-10 May 2023 The 9th edition of the Dutch Bioinformatics & Systems Biology conference <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> (BioSB 2023) will be organized *9-10 May 2023* at *Hotel Zuiderduin, *Egmond aan Zee, the Netherlands. The conference will have a highly diverse programme featuring: - Keynote lectures - Parallel thematic sessions (featuring selected and invited talks) - Workshops - Poster & demo sessions - Network breaks a conference dinner & evening programme On *8 May 2023* the YoungCB will organize the yearly *PhD retreat*. Information will follow in January 2023. Registration opens soon! Call for abstracts You can now submit an abstract for a presentation at the BioSB 2023 conference <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> . You can submit for an oral presentation, a poster presentation or a demo (tools/software) presentation. The main programme of the conference will feature several parallel sessions that will be set up via abstract selection. Submission topics You can submit an abstract for one of the following topics. Find a more detailed description of the topics on the submission topics webpage: <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> - Cancer research - Other health research - Plant and animal research - Microbes and microbial communities - Viruses and phages - Synthetic biology - Multi-scale modeling of patterning - Mechanistic modeling - Big data and omics - Structural biology/bioinformatics - Artificial intelligence - Phenotyping - Single-cell techniques - Evolutionary Systems Biology and Bioinformatics - ELIXIR - Education - Miscellaneous Submission deadlines - Oral presentations & flash talks: *3 March 2023* - Notification oral presentations: 24 March 2023 - Demo presentations: 14 April 2023 - Poster presentations: 14 April 2023 Submit your abstract <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Sponsor opportunities Would you like to be visible at our conference? We invite you to present your company to our diverse scientific public. We offer a number of attractive sponsorship packages, as well as exhibit space, but also custom made packages can be discussed. Find our sponsor & exhibitor packages here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> About The 9th edition of the Dutch Bioinformatics & Systems Biology conference <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> (BioSB 2023) will be organised on May 9-10 2023 at *Hotel Zuiderduin*, Egmond aan Zee, the Netherlands. The Dutch Bioinformatics & Systems Biology conference 2023 (BioSB 2023) discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition. Subscribe to the Digital Life Sciences newsletter <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> to stay up to date about the conference. You can also follow us on Twitter: #BioSB2023 and LinkedIn <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Visit the conference website <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Organized by The conference will be organized by the BioSB research school <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> together with Wageningen University & Research <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> , DTL <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> and ELIXIR-NL <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…>. <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Twitter] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Website] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> *Copyright © 2023 Citing us where appropriate.* update your preferences <https://dtls.us3.list-manage.com/profile?u=3cef2d6f6da8f8059e2288298&id=d62…> - unsubscribe from this list <https://dtls.us3.list-manage.com/unsubscribe?u=3cef2d6f6da8f8059e2288298&id…> - DTL privacy statement <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI Network Manager TDCC-LSH tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Job Vacancy for (bio)informaticians at the Microverse Cluster
by BeNeLux bioinformaticians forum 09 Jan '23

09 Jan '23

Dear sir or madam, The Cluster of Excellence Balance of the Microverse invites applications for two postdoctoral researcher position (in Correlative Image Data Analysis and in Integrative Research Data Management). The Microverse Cluster combines expertise in life, material, optical and computational sciences to elevate microbiome studies from descriptive to hypothesis-driven and functional analyses. Were looking for candidates with a PhD (or equivalent) in computer science, software engineering, (bio-)informatics, or other programming-affine fields. Both two-year full-time positions will be funded through the Excellence Strategy of the German federal and state governments. Application deadline is 7 February 2023. Further information can be found in the attachements or on our website: https://www.microverse-cluster.de/en/jobs.html We would appreciate it if you could forward our offer to your members and/or interested (bio)informaticians. Thanks a lot. Kind regards, Katja Präfcke *********************************************** Friedrich Schiller University Jena Jena School for Microbial Communication Neugasse 23 07743 Jena, Germany Phone: +49 (0) 3641 - 949 541 E-Mail: <mailto:apply@jsmc.info> apply(a)jsmc.info Website: <http://www.jsmc.uni-jena.de/> www.jsmc.uni-jena.de Follow us on Twitter: twitter.com/JSMC_Info

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Postdoc and PhD position in epigenomics available within Epi-Guide-Edit NWO Key Technology consortium
by BeNeLux bioinformaticians forum 09 Jan '23

09 Jan '23

Dear all, Within the NWO Key Technology funded Epi-Guide-Edit consortium dedicated to developing tools for durable epigenetic editing across different applications including health and agriculture, we have a postdoc and a PhD position (both 4 years) available focused on using single-cell resolution pooled epigenetic CRISPR/dCas screens to study epigenetic reprogramming in (breast cancer) cell lines. Both positions offer ample possibilities for the development and application of state-of-the art bioinformatics methods. For the details on the two positions, please see (application deadline: January 15): - Postdoc: https://vacatures.uva.nl/UvA/job/Postdoctoral-Researcher-in-Epigenomics/760… - PhD candidate: https://vacatures.uva.nl/UvA/job/PhD-Candidate-in-Epigenetic-Editing/760962… The positions are embedded in the group of the program coordinator, Prof. dr. Pernette Verschure, Swammerdam Institute for Life Sciences and the Dept. of Medical Biochemistry, Amsterdam University Medical Centers (AUMC), University of Amsterdam (UvA), NL. For computational analyses you will work closely together with Dr. Perry Moerland, Bioinformatics Lab, Dept. of Epidemiology and Data Science, AUMC, UvA, NL and Dr. Remco Loos, Informatics & Predictive Sciences, Bristol Myers Squibb, Spain. Best wishes, Perry --- Dr. ir. P.D. Moerland Bioinformatics Laboratory | Epidemiology and Data Science (EDS) Amsterdam UMC | Location AMC | J1B-225 | Meibergdreef 9 | 1105 AZ AMSTERDAM E: p.d.moerland(a)amsterdamumc.nl<mailto:p.d.moerland@amsterdamumc.nl> W: https://bioinformaticslaboratory.eu/ ______________________________________________________ AmsterdamUMC disclaimer : www.amsterdamumc.org/disclaimers

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2023 🍾 Check what is coming up.
by BeNeLux bioinformaticians forum 05 Jan '23

05 Jan '23

[cid:image001.png@01D91546.6FFD3720] [signature_2008044598] 2023 is in around the corner! 🍾 Check what is coming up. Dear colleagues, Coming up in 2023 we are offering trainings that can help you with different stages of the Research Data Management (RDM) of your project, you can start keeping track of versions of your code and writing by following introduction to Git & GitHub. And you can make your analysis reproducible using Docker (and Singularity) for reproducible and automated data analysis. Without forgetting that you can have scalable and reproducible pipelines built with Nextflow for reproducible and automated data analysis. Find bellow the details you need to join us in any of the coming up trainings. Don’t forget to subscribe! Introduction to Git & GitHub ____________________________________________________________________________________ 8th February 2023 – Brussels Face to Face training This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers Registration and info: Link for Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-5> Docker (and Singularity) for reproducible and automated data analysis ____________________________________________________________________________________ 13th and 14th March 2023 – Leuven Face to Face training The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be highlighted as well. Registration and info: Docker and reproducibility<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> Nextflow for reproducible and automated data analysis ____________________________________________________________________________________ 30th and 31st March 2023 – Leuven Face to Face training You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Registration and info: NextFlow automated pipeline<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> Kind regards, Bruna Piereck ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium tel +32 0497 2988 73 [cid:image001.png@01D91546.6FFD3720][signature_2008044598]

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1 year Post-doctoral position in Computational biology
by BeNeLux bioinformaticians forum 05 Jan '23

05 Jan '23

Dear colleagues, We are looking for a highly motivated post-doctoral researcher to develop artificial intelligence (AI) methods (1) to design de novo ligands that target a given olfactory receptor and (2) to predict the olfactory receptors targeted by a given molecule. You will find the complete job description in the PDF file attached to this email. Best regards ---------------------------------------------------------- Dimitri Gilis Professeur 3BIO-Bioinfo École polytechnique de Bruxelles Phone: +32 2 650 36 15 E-mail: dimitri.gilis(a)ulb.be<mailto:dimitri.gilis@ulb.be>

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