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Special issue of TCS/C on Foundational Methods in Systems Biology: call for papers
by Ion Petre 04 Nov '22

04 Nov '22

** Please distribute this call for papers also in your own groups/networks ** Special issue of Theoretical Computer Science (track C) on Foundational Methods in Systems Biology Submission: continuous, cut-off date May 15, 2023 ================================================================= Dear Colleague, With this email we would like to invite you to submit a paper to the special issue of the Theoretical Computer Science journal (series C: Natural Computing) on “Foundations of Systems Biology”. This special issue is aligned with the conference series on “Computational Methods in Systems Biology (CMSB)” and shares its topics of interests. We look for original research articles on foundational aspects of systems biology and their applications. Topics of interest include, but are not limited to: • formalisms for modelling biological processes; • methods and tools for biological system analysis, modelling and simulation; • frameworks for model verification, validation, analysis, and simulation of biological systems; • high-performance methods for computational systems biology; • identification of biological systems; • network modelling, analysis, inference; • automated parameter and model synthesis; • multi-scale modelling and analysis methods; • design, analysis, and verification methods for synthetic biology; • methods for biomolecular computing and engineered molecular devices; • data-based approaches for systems and synthetic biology; • optimality and control of biological systems; • machine learning for systems biology. Submitted papers should not be under consideration for publication elsewhere. Extended versions of manuscripts that have been published in conference proceedings (CMSB or other conferences) can be submitted to this special issue if they have been extended by at least 30% and the differences between the two versions are explained in the introduction. The manuscripts should include all content in the article, rather than in appendices or in supplementary information. Please prepare your article in LaTeX in the Elsevier journal paper format (https://www.elsevier.com/authors/author-schemas/latex-instructions) and submit it using the editorial manager (https://www.editorialmanager.com/TCS/default.aspx) The tile of the special issue is “Foundations of Systems Biology” (short title VSI: FoundSysBio). In order to properly assign your submission to the special issue we are preparing, it is crucial to select VSI: FoundSysBio twice, as Article Type (starting the submission procedure) and Requested Editor (in Review Preferences). All papers for the special issue will be reviewed following the standard refereeing procedure for Theoretical Computer Science. Submissions will be reviewed on a continuous basis, with a cut-off date set for May 15, 2023. We suggest an upper limit of 40 pages on the length of the paper in the LaTeX style of the journal; please contact us if you need more pages for your manuscript. To keep track of the papers, please inform us of after the submission with an email to ion.petre(a)utu.fi and apaun(a)fmi.unibuc.ro. With best wishes, Ion Petre and Andrei Paun Guest editors of the special issue of TCS/C on Foundations of Systems Biology

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BioSB course Integrated Modeling and Optimization, 12-16 December 2022, Wageningen, the Netherlands
by Celia van Gelder 04 Nov '22

04 Nov '22

Dear colleagues, Also in this academic year the BioSB research school, Wageningen University & Reserach and Eindhoven University of Technology will organize the course: *Integrated Modeling and Optimization* 12-16 December 2022, Wageningen University Website: https://www.dtls.nl/courses/integrated-modeling-and-optimization-2022/ Computational modelling is an absolute requisite to gain understanding of the biological mechanisms underlying patterns observed in experimental data. However, one could say that modelling is a craftsmanship, that can only be learned via intense exercising and ‘learning by doing’. In this course we offer the participants the possibility to learn and exercise the modeling process and the optimization techniques needed to fit models to data. In the course the students will learn: - to understand the common ground and the differences for applications of dynamic modeling in metabolic, regulatory, signaling, and multi-scale biological processes - how to set-up a dynamic model to represent biological networks using different interaction mechanisms - to implement, simulate and analyze dynamic network models - to understand the wide variety of problems in modelling that can be solved with optimization · - to apply different types of numerical optimization methods: global and local search methods: steepest descent, Levenberg-Marquardt, genetic algorithms, linear programming. - the combination of dynamic modeling and optimization to integrate experimental data in modelling, estimate model parameters and design experiments. - to understand how numerical optimization (linear programming) works in flux balance analysis to simulate metabolic network models. Lecturers: · Prof. Natal van Riel, Eindhoven University of Technology (course coordinator) · Dr. Aalt-Jan van Dijk, Wageningen University & Research · Prof. Jaap Molenaar, Wageningen University & Research · Dr. Hans Stigter, Wageningen University & Research · Dr. Robert Smith, Wageningen University & Research · Dr. Dragan Bosnacki, Eindhoven University of Technology Target audience: The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis.  -- 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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Virtual course: Systematising complex and combined metabolic analyses with COBREXA.jl
by Venkata Pardhasaradhi SATAGOPAM 28 Oct '22

28 Oct '22

Dear all, You may be interested in the virtual course “Systematising complex and combined metabolic analyses with COBREXA.jl” on constraint-based reconstruction and analysis (COBRA) of large metabolic networks using COBREXA.jl High-Performance Computing framework on November 15th. Feel free to contact Wei or Miroslav (in CC) for any questions. To learn more about the course and register please go here: https://permedcoe.eu/training/virtual-course-systematising-complex-and-comb… Best, Venkata — Dr. Venkata Satagopam 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)uni.lu<mailto:venkata.satagopam@uni.lu> http://lcsb.uni.lu ----- 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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IRIBHM - ULB is hiring three postdocs
by DETOURS Vincent 28 Oct '22

28 Oct '22

Dear all, The IRIBHM, an institute from the Universite Libre de Bruxelles, is hiring three postdocs, including a computational biologist. See the announcements here: https://owncloud.ulb.ac.be/index.php/s/i94aCWkUVP2NuPH Feel free to forward this mail. All the best, Prof. Vincent Detours, Ph. D. 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 E-mail: vincent.detours at ulb.be

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BSC: New vacancies - November 2022
by Laura Delshams Munoz 25 Oct '22

25 Oct '22

Hello, My name is Laura Delshams, I am part of the HR team at the Barcelona Supercomputing Center - Centro Nacional de Supercomputación. I am contacting you because we have opened several vacancies in the Life Sciences and CASE departments, and we would be grateful if you could share them with your contacts: * Junior Research Engineer for Social Link Analytics (RE1) <https://www.bsc.es/join-us/job-opportunities/35122lsslare1> - Life Sciences: Deadline 16th of November * Web Front-end Developer (RE2) <https://www.bsc.es/join-us/job-opportunities/38122lsinbre2> - Life Sciences: Deadline 16th of November * Post-doctoral Researcher in Computer and Biomedical Data Science (R2-R3) <https://www.bsc.es/join-us/job-opportunities/40322lsiconbir2-3>- Life Sciences: Deadline 16th of November * CI/CD Research Engineer (RE2) <https://www.bsc.es/join-us/job-opportunities/27622casepnmre2> - CASE Department: Deadline 16th of November If you need further information regarding any of our vacancies, or you need any additional steps from my side in order to disseminate it, please let me know. Thank you! Best regards, -- Laura Delshams /Human Resources - Talent & Development Officer/ *Barcelona Supercomputing Center – Centro Nacional de Supercomputación* <mailto:anais.delastre@bsc.es>Tel. +34- 93 413 40 72<mailto:anais.delastre@bsc.es> <mailto:anais.delastre@bsc.es>laura.delshams(a)bsc.es <mailto:laura.delshams@bsc.es><http://www.bsc.es/> <http://www.bsc.es/>www.bsc.es <http://www.bsc.es/>

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Fellowship in Bologna
by Fabrizio Pucci 25 Oct '22

25 Oct '22

Dear all, Please find below a message on behalf of Emiodio Capriotti on a fellowship in Bologna. Best, Fabrizio Pucci, 3BIO, École polytechnique de Bruxelles, ULB Interuniversity Institute of Bioinformatics in Brussels (IB)2 >>> Research Associate - Department of Pharmacy and Biotechnology, University of Bologna <<< The BioFolD unit (https://biofold.org) at the University of Bologna is seeking a Research Associate with programming skills in the field of bioinformatics. 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 12 moths fellowship starting on November 2022 Qualifications Master in Bioinformatics, Physics, Mathematics, Computer Science and related degrees. How to apply: If you are interested please contact Emidio Capriotti ( emidio.capriotti(a)unibo.it) The deadline for the submission of the application is November the 6th. Online announcement in Italian is available at https://bandi.unibo.it/ricerca/assegni-ricerca?id_bando=65676

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Hartwig is hiring!
by Daphne van Beek 21 Oct '22

21 Oct '22

Hi all, Hartwig is hiring! We're looking for a Senior Software Engineer and a Software Developer to help us advance our work to get the right patient the right treatment at the right time. We've been working for the past couple of years on building an extensive database and a cutting-edge toolset that is quick, cheap and the best for our data. We're a very ambitious group of people, so we're looking to expand to make our dreams come true. Are you motivated to help us realise our mission? Apply using the below links! Senior Software Engineer: https://lnkd.in/e4eiaNUi Software developer: https://lnkd.in/euht2bCe With kind regards, Daphne van Beek IT Manager Absent on Monday [Hartwig Medical Foundation]<https://www.hartwigmedicalfoundation.nl/en/> A Science Park 408, 1098 XH Amsterdam T +31 (0)20 226 9712 W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl/en/> | oncoact.nl<https://oncoact.nl/?lang=en> N Subscribe to our newsletter<https://mailchi.mp/475bfde5c6f3/nieuwsbrieven-hartwig-medical-foundation> [Facebook]<https://www.facebook.com/HartwigMedicalFoundation> [LinkedIn] <https://www.linkedin.com/company/hartwig-medical-foundation> [Twitter] <https://twitter.com/hartwigmedical> [Instagram] <https://www.instagram.com/hartwigmedicalfoundation/?hl=en> [YouTube] <https://www.youtube.com/channel/UCK8juCiUGC1OsEXPtdEEwPA> It is our mission to realize that every cancer patient receives a personalized treatment using a complete DNA test<https://oncoact.nl/?lang=en>.

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Vacancy bioinformatician / computer scientist - genomics data infrastructure
by Kevin Vanneste 18 Oct '22

18 Oct '22

Dear all, The Bioinformatics Platform at the Belgian Institute of Health (www.sciensano.be<http://www.sciensano.be>) currently has a vacancy for a bioinformatician or a computer scientist to work on setting up services and infrastructure within the context of the Genomics Data Infrastructure project. More info and applications are available on our job site: https://jobs.sciensano.be/content/jobpage.asp?a=DETAIL&jdkid=1029&l=DUTCH Sincerely, K Kevin Vanneste, PhD Senior scientist - Responsible Bioinformatics Platform Transversal activities in Applied Genomics (TAG) T + 32 2 642 50 65 [cid:image001.jpg@01D4595B.6D6E05D0] Rue Juliette Wytsmanstraat 14 * 1050 Brussels www.sciensano.be<http://www.sciensano.be/> P Please consider the environment before printing this e-mail

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EMBL-EBI Postdoctoral Fellowship - Protein Science Machine Learning with AstraZeneca
by Sergio Martinez Cuesta 18 Oct '22

18 Oct '22

Postdoc for a recently graduated PhD in computational biology / structural bioinformatics. https://www.embl.org/jobs/position/EBI02081 The aim of the project, which is a collaboration between EMBL-EBI and AstraZeneca, will be to investigate the applications of machine learning and AI in predicting the results of recombinant protein expression experiments and develop computational tools thereof. Thanks, Sergio

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bioinformatician vacancy post
by Miao Chien 11 Oct '22

11 Oct '22

Hi, I am currently looking for bioinformaticians (PhD or postdoc). Can you help me post the following vacancy link? Thank you! https://www.academictransfer.com/nl/318345/phd-postdoc-in-bioinformatics-on… Best, Miao Miao-Ping Chien Principal Investigator, Oncode Institute Assistant professor, Department of Molecular Genetics Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands Room 834a; Tel: +31 10 704 3073 m.p.chien(a)erasmusmc.nl<mailto:m.p.chien@erasmusmc.nl> www.mpchienlab.org

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