November 2022 - BBClist - maillist.psb.ugent.be

Two calls for Tutorials - ISMB/ECCB and [BC]2
by Celia van Gelder 18 Nov '22

18 Nov '22

*FYI* Dear colleagues, Please note that there are two open calls for tutorials: 1. Tutorials for ISMB/ECCB 2023 <https://www.iscb.org/ismbeccb2023-submissions/tutorials> – deadline for submissions *19 December 2022*. 1. Tutorials and Workshops for [BC]2 2023 <https://www.bc2.ch/tutorials-workshops-calls> – deadline for submissions *8 January 2023*. You are most welcome to submit your proposals and forward this message to anyone. Many thanks and all the best, Patricia -- *Patricia Palagi, PhD SIB Training SIB | Swiss Institute of Bioinformatics Quartier Sorge, Bâtiment Amphipôle - 1015 Lausanne - Switzerland patricia.palagi(a)sib.swiss <patricia.palagi(a)sib.swiss> - www.sib.swiss <http://www.sib.swiss> * -- 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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EPB-ULB : full-time academic position
by GILIS Dimitri 17 Nov '22

17 Nov '22

Dear all, The Brussels School of Engineering will open a full-time academic position in Computational Modeling of Biomolecular systems. The job description is summarised below, and the full vacancy will be published on the following site from 1/12/2022 : https://www.ulb.be/fr/vacances-d-emplois-academiques-et-scientifiques/liste… 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> ------------------------------- Job description A mechanistic understanding of complex biological systems requires the consideration of multiple spatial and temporal scales, and their integration into holistic models or networks. Fluctuations play a major role in the dynamics of many of these processes and have to be considered to obtain a realistic description of these systems and their evolution. The large amounts of high-throughput biological data that are currently being produced, from the molecule to the organism scales, are an unprecedented source of information and a stepping stone to advance these issues. To address the key challenges of biomolecular modeling, innovative mathematical, computational and modeling approaches need to be developed. In this context, the candidate should be an expert in the modeling of: * Biomolecular systems (proteins, DNA, RNA, …) * Biological networks (interactome, gene regulatory networks, disease networks, …) and this expertise should cover multiples molecular scales He/she should also have a solid expertise in several of the following techniques: * Physics-oriented multi-scale modeling * Structural bioinformatics and biomolecular design * Dynamical and stochastic modeling of complex systems * Data-driven modeling of biological networks * State-of-the-art machine learning techniques * Evolutionary and coevolutionary techniques Area of Research: Transdisciplinary – bioinformatics, computational molecular biophysics, computational biology Educational and scientific goals: The successful candidate is expected to integrate into the existing teaching activities of the Schools of Engineering and Bioengineering, and to develop new, top-level, scientific activities in collaboration with other groups of the Schools of Engineering and Bioengineering and the Faculty of Sciences, in particular with the ULB/VUB Interuniversity Institute of Bioinformatics in Brussels ((IB)²). Courses covered at the time of recruitment: The appointed academic will take the responsibility of parts of the following courses: * In the Master 1 in Bioengineering and in the Master 2 in Biomedical Engineering * Introduction à la bioinformatique et à ses applications (partim of 18h in a 5 ECTS course) * In the Master 1 in Bioinformatics and Modeling * Biophysics and structural bioinformatics I (partim of 18h in a 5 ECTS course) * Biophysics and structural bioinformatics II (partim of 12h in a 5 ECTS course) After one year, the appointed academic will also take responsibility of a part of the following course: * In the Bachelor 1 in Bioengineering * Connaissances fondamentales et éléments de physique (partim of about 48h in a 10 ECTS course She/he will also have the opportunity in the future to contribute to other existing courses in the chemistry, bioengineering, physics, biomedical or informatics departments of the School of Engineering. Qualifications required : PhD Degree (with doctoral thesis) in Engineering or in Sciences. Skills required * Applicants should have at least 4 years of research experience at the time of their recruitment. * Post-doctoral experience and an excellent scientific record are required. * Exchange periods outside of the applicants’ home institution (during or after their PhD) will be taken into consideration when evaluating applications. * Experience in master and PhD thesis supervision, and grant submission and management are a plus. * Applicants who do not speak French (level C1) may be granted a period of adaptation, but they must be able to teach in French at the end of the 3rd year following their appointment. * Level C1 in English is expected. Candidates must be capable of teaching in English at the time of their appointment.

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Vacancy BaseClear
by Mark Bessem 17 Nov '22

17 Nov '22

BaseClear is expanding! If you're interested in working as a bioinformatician in the microbiome field, apply now. https://www.baseclear.com/career-jobs/12385/ [https://www.baseclear.com/wp-content/uploads/shutterstock_25532056.jpg]<https://www.baseclear.com/career-jobs/12385/> Junior Bioinformatician - BaseClear B.V.<https://www.baseclear.com/career-jobs/12385/> Senior/Key Account Manager. JOIN US AS SENIOR/KEY ACCOUNT MANAGER BaseClear was founded in 1993, and ever since has been a pioneer in genomic analysis. www.baseclear.com Met vriendelijke groet, Kind regards, Mark Bessem Manager Bioinformatics [cid:d866a073-e347-4696-8457-90896207d829] <https://www.baseclear.com/> General: +31(0) 715 23 39 17 www.baseclear.com<https://www.baseclear.com> [cid:79b34ba4-3d15-4eb0-a9a5-d578c6fac3d8] Please consider the environment before printing this email. Disclaimer<https://www.baseclear.com/disclaimer>

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VIB is looking for a Head of BioImaging Core
by Alexander Botzki 12 Nov '22

12 Nov '22

Dear colleagues on the BBC list, VIB is looking for someone to lead the Bioimaging Core. Yesterday, the vacancy for this position was published. You can find it here: https://jobs.vib.be/j/52537/head-vib-bioimaging-core?social=1668152433 If you think about someone who could be interested in such a position, please feel free to forward it in your network. Thank you very much. Best regards, Alex Alexander Botzki – Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [signature_2070832211]

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FW: Postdoctoral position at Luis Graca Lab, Lisbon
by Dileep Kumar, Saumya 08 Nov '22

08 Nov '22

Hello, Please can you help advertising this postdoc position? If any more information required, I can help. Best Regards, Saumya From: Luis Graca <lgraca(a)medicina.ulisboa.pt> Date: Saturday, 5. November 2022 at 13:52 To: Saumya Dileep Kumar <saumya.dileepkumar(a)helmholtz-hzi.de> Subject: Postdoctoral position at Luis Graca Lab, Lisbon Dear Saumya, I would appreciate your help in advertising a post-doctoral position at my lab in Lisbon, open until November 30. The attached PDF has detailed information. In brief, we are seeking highly motivated postdocs with a background in computational biology. The research will use single-cell and spatial transcriptomics technologies to investigate the regulation of antibody production following vaccination. In parallel, equivalent datasets from biopsies of autoimmune patients will provide an opportunity to explore the immune dysregulation leading to autoimmunity. The host laboratory, led by Luis Graca, has recognized expertise in studying immune regulation and the role of specialized populations of regulatory T cells (Nature Comms 2017, Science Immunol 2017). The lab focuses on investigating various regulatory mechanisms in immune biology, with particular interest in the regulation of the germinal centre (GC) responses, key for antibody production following infection, vaccination, and autoimmunity (Nature Rev Rheumat 2019; Immunol Rev 2019). The group has developed sophisticated methods and protocols that allow detailed investigation of GCs in mice and humans, while making use of single-cell -omics technologies and various statistical, machine learning, and computational methods to examine the detailed profile of GC cells and propose new models of regulation (Science Immunol 2021). Our expertise in computational and mathematical approaches has been used to address problems ranging from cell biology (bioRxiv 2022) to human populations (N Engl J Med 2022). More information about the host laboratory (with link to job application form): https://imm.medicina.ulisboa.pt/investigation/laboratories/luis-graca-lab/#… Thanks for your help, Luis Prof. Luis Graca, MD PhD Full Professor | Professor Catedrático Vice-Dean | Subdiretor, FMUL Group Leader, iMM Head of Lymphocyte Regulation Laboratory [Image removed by sender.] Faculdade de Medicina da Universidade de Lisboa Avenida Professor Egas Moniz . 1649-028 Lisboa . Portugal iMM Lisboa general contact (+351) 217 999 411<tel:%28%2B351%29%E2%80%8B%20217%E2%80%8B%20999%E2%80%8B%20411> - ext: 47241 Direct contact: (+351) 217 999 467 imm.medicina.ulisboa.pt Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Dirk Heinz - komm. Administrative Geschäftsführerin: Elisabeth Gerndt Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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PhD position in Wageningen: Computational Mass Spectrometry for Food Safety
by Hooft, Justin vander 08 Nov '22

08 Nov '22

Dear fellow colleagues, Could I raise your attention for an exciting opportunity: between Wageningen Food Safety Research and the Bioinformatics Group at Wageningen University, there is a funded PhD position available. Do you know a suitable and motivated candidate that has (some) experience with setting up computational mass spectrometry / metabolomics workflows? Or would you be interested yourself? Please have a look at the details below, and follow the link to apply. Kind regards from Wageningen, Justin —— Integration of computational mass spectrometry and risk-based datamining in food safety analysis Wageningen University Bioinformatics Group & Wageningen Food Safety Research, Wageningen, NL General info: www.wur.nl/nl/vacature/phd-candidate-in-computational-mass-spectrometry-for…<http://www.wur.nl/nl/vacature/phd-candidate-in-computational-mass-spectrome…> Brief Description: High-resolution mass spectrometry generates extensive data sets contain much more information than we can currently extract from them. Complementary to looking for single chemical compounds, identifying patterns in mass spectra that can be associated with chemical risks might give additional insights about potential hazards in our food and feed. To do so, the candidate will set up a computational mass spectrometry workflow to find yet unknown food safety hazards in high-resolution mass spectrometry data. In addition, using toxicity prediction tools and sample meta-data, the most relevant food toxicants will be filtered from 1000s of annotated compounds. Various new, exciting high end mass spectrometers are available to obtain part of the input data. Tasks include: - setting up a pipeline to structurally annotate high-resolution mass spectrometry data - designing a toxicity prediction tool based on chemical structure databases - developing a toxicity-based data mining workflow based on both spectral and structure input - applying the entire workflow to a real-life analytical data set for food safety Qualifications: Candidates should hold a successfully completed MSc in (bio)informatics, metabolomics, (bio)analytical chemistry or related area, with a strong interest and demonstrable skills in programming (in Python), (computational) metabolomics, and/or analytical chemistry, preferably high-resolution mass spectrometry. We are specifically seeking candidate with excellent communication skills, both oral and written, who like to work in a multidisciplinary setting, and are critical, accurate and efficient way. Start date: As soon as possible How to Apply Please fill out the application form on our website, www.wur.nl/nl/vacature/phd-candidate-in-computational-mass-spectrometry-for…<http://www.wur.nl/nl/vacature/phd-candidate-in-computational-mass-spectrome…>. Applications are dealt with in order, so please do not defer submission. —— Dr Justin J.J. van der Hooft Assistant Professor in Computational Metabolomics Visiting Professor at the Biochemistry Group, University of Johannesburg, South Africa Member of Wageningen Young Academy | Member of Young NMC & Netherlands Metabolomics Center | Member of Metabolomics Society Follow me on Twitter for the latest science updates: @jjjvanderhooft Our most recent group effort is a preprint on Good Practices and Recommendations for Using and Benchmarking Computational Metabolomics Metabolite Annotation Tools: https://www.researchsquare.com/article/rs-1662223/v1 - let us know what you think! :-) Group Website: https://vdhooftcompmet.github.io Follow us on Twitter! —> @vdHooft_CompMet Bioinformatics Group, Department of Plant Sciences, Wageningen University justin.vanderhooft(a)wur.nl<mailto:justin.vanderhooft@wur.nl> Tel: +31317483061 Building.room 107/W2.Aa.083, Droevendaalsesteeg 1, 6708PB Wageningen - NL Post: PO Box 633, 6700AP Wageningen, NL http://www.wur.nl/en/Expertise-Services/Chair-groups/Plant-Sciences/Bioinfo… [cid:A2E4220B-C100-4E32-8374-5C81294AE480@home] Working with genomics and/or metabolomics data and wondering how to turn it into structure and function?! Consider joining the NPLinker eScience Genome & Metabolome Mining workshop organised in March 2023 in Wageningen, NL. Find more information here: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinfor… Working with mass spectrometry and/or NMR data to discover novel and known chemistry in complex natural mixtures? Have a look at our most recent review on how computational metabolomics approaches support the mapping of chemical space based on networking and substructure-based analyses: https://pubs.rsc.org/en/content/articlehtml/2021/np/d1np00023c Working with metabolomics data? Without realizing, you are using spectral similarity scoring all the time. For example, during library matching to annotate structures in your profile. Spec2Vec similarity scoring is the first machine learning based spectral similarity score outperforming classical scores! Find our paper in Plos Computational Biology here: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008… Spec2Vec’s supervised cousin MS2DeepScore was published in 2021 in Journal of ChemInformatics: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00558-4 Do you have metabolomics data of sequenced organisms or of communities or complex samples uploaded in open databases? Please consider to record their links in our just in Nature Chemical Biology published platform: https://www.nature.com/articles/s41589-020-00724-z And thinking of linking genome mining to metabolome mining analysis? Please find our tutorial review here highlighting opportunities and pitfalls: https://pubs.rsc.org/en/content/articlelanding/2020/CS/D0CS00162G#!divAbstr… Do you want to streamline your metabolomics analyses even more? Use ReDU and FBMN! ReDU offers consistent metadata across many public mass spectrometry fragmentation data files. FBMN brings together qualitative and quantitative analyses! ReDU: https://www.nature.com/articles/s41592-020-0916-7 FBMN: https://www.nature.com/articles/s41592-020-0933-6 Did you hear about molecular networking? But you don’t know how to create them? Look no further and start with our protocol that is describing how to for various instruments and platforms: https://rdcu.be/b4Qo6 —— [cid:image001.gif@01D340E8.1630BEC0]

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Stay tuned! Upcoming trainings
by Bruna Piereck Moura 07 Nov '22

07 Nov '22

[cid:image001.png@01D8F2BE.411D7FF0] [signature_2008044598] Stay tuned! Amazing opportunities to improve yourself! Dear colleague, Coming up in the following months (November-January) , come check the trainings open for registration. In November you have your last opportunity to make A tour of machine learning: classification<https://training.vib.be/all-trainings/tour-machine-learning-classification-1>. And what could be better than getting some help with managing your data in December with Research Data Management: your ally on the way to your publication<https://training.vib.be/all-trainings/research-data-management-your-ally-wa…>. And, last but not least, you can start January 2023 with our Gentle hands-on introduction to Python programming<https://training.vib.be/all-trainings/gentle-hands-introduction-python-prog…>. Find bellow the details you need to join us in any of the coming up trainings. Don't forget to subscribe! A tour of machine learning: classification. ____________________________________________________________________________________ 14th to 15th November 2022 - Ghent Face to Face training In the current age of data, advanced analysis offered by Machine Learning research is essential for transforming this data into new knowledge and useful tools. In this two-day workshop I explain the principles underlying Machine Learning and teach you how to build accurate prediction models from data through hands on exercises, with a focus on building classification models. Subscription and info: https://training.vib.be/all-trainings/tour-machine-learning-classification-1 Research Data Management: your ally on the way to your publication __________________________________________________________________________________ 12th to 13th December 2022 - Ghent Face to Face training It is better to start with the publication in mind! In this course you will learn how to use Research Data Management (RDM) in order to improve the writing of your publications and potentially increase its impact. Starting from basic concepts together with hands-on activities and discussions, during two days you will learn how to standardize, document and submit your data in a repository and how all of this will help you to underpin your publication! Subscription and info: https://training.vib.be/all-trainings/research-data-management-your-ally-wa… Gentle hands-on introduction to Python programming ____________________________________________________________________________________ 04th, 11th and 18th of January 2023 Online This course gently introduces programming to new programmers. There are plenty of opportunities 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. Subscription and info: https://training.vib.be/all-trainings/gentle-hands-introduction-python-prog… Kind regards VIB and ELIXIR Belgium Training Coordinator Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium [signature_2008044598] [cid:image001.png@01D8F2BE.411D7FF0]

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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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