- BBClist - maillist.psb.ugent.be

BioSB course Integrated Modeling and Optimization - 14-18 December 2020 - register now!
by Femke Francissen 24 Nov '20

24 Nov '20

Dear colleague, It is still possible to register for the BioSB research school course: *Integrated Modeling and Optimization* 14-18 December 2020, online course 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. Read more <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…> --------------------- *About BioSB* The Netherlands Bioinformatics and Systems Biology research school (BioSB) is the national platform in which the Dutch community of researchers in bioinformatics and systems biology is organized. BioSB also organizes: 1. fundamental and advanced post-graduate courses <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…> 2. the yearly BioSB conference <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…> 3. hot topics meetings <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…> The aim of the BioSB research school is to offer PhD students, postdocs and senior researchers a vibrant environment for their scientific development as well as education in bioinformatics and systems biology. In addition, BioSB acts as a parent organization for YoungCB <https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngc…>, the official Regional Student Group (RSG) of the International Society of Computational Biology (ISCB).

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two open positions at UMC Utrecht (NL): bioinformatician and data scientist
by Drylewicz, J. 20 Nov '20

20 Nov '20

Dear all, We have two open positions within the Computational Immunology Core of the Center for Translational Immunology at the UMC Utrecht (NL). We are looking for two motivated and talented bioinformaticians to join our current team working in close collaboration with experimentalists and clinicians. We offer a full-time position for the duration of one year, starting beginning of 2021 and are looking for a candidate with a bioinformatics/biostatistics degree (data scientist position) and masters in bioinformatics (for bioinformatician position). Interested candidates can apply before December 15. Please see the two advertisements for more details. Best regards, Julia Drylewicz, PhD [/var/folders/5c/hdgch2797tb1s7mg4cf9t7880000gn/T/com.microsoft.Outlook/WebArchiveCopyPasteTempFiles/cid8EB5A84A-AA23-4821-88D5-84EDB7287447] University Medical Center Utrecht | Center for Translational Immunology Computational Immunology Core | Utrecht Center for Quantitative Immunology Visiting address: KC 02.046.0 | Lundlaan 6 | UTRECHT, the Netherlands Postal address: KC 02.085.2 | P.O. Box 85090| 3508 AB UTRECHT, The Netherlands T +31 (0)88 75 535 69 | J.Drylewicz(a)umcutrecht.nl<mailto:J.Drylewicz@umcutrecht.nl> |[2ZNPswyyHiBaelp6FUOVDTs5Sbf+ZZ7e28ojK2Q4dxHc0ahUJ8yBj19WiIEy6X4g6eo6KQZcNzwwrx7VZuVeKz3zV8zdyuiufMsexi8dxGPVX57aA1YBpt+eWwKLX1WZIgSAIgiAIgiAIgiAIgiAIgiAIUlX+B3GEF3qR7jyTAAAAAElFTkSuQmCC] LinkedIn<https://www.linkedin.com/in/julia-drylewicz-9b054024/> | [szEZ22KbsKR7ao5kzzlL69n8tTJnZrmUOXAAAAABJRU5ErkJggg==] Twitter<https://twitter.com/JuliaDrylewicz> ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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[Newsletter] Research Software Developers Day 2020
by Belgium Research Software Engineers 20 Nov '20

20 Nov '20

Full program now available! No images? Click here https://email.vibconferences.be/t/r-e-juitkuhk-uhtudkhjjk-o/ Research Software Developers Day 3rd December 2020 | Online Dear all, The first conference of the Belgium Research Software Engineers community - the Research Software Developers Day [https://www.be-rse.org/rsdd2020] - takes place on 3 December 2020. The aim of this conference is to foster a community of research software developers and to collectively improve the standard of software used for scientific research. For this, our first edition, we focus on three main themes: reproducibility, software quality and infrastructure which we will address in two parallel sessions with presentations and workshops. Full program is now available on our website [https://www.be-rse.org/rsdd2020] and tickets are free of charge! Kind regards, The organizers Belgium Research Software Engineers Preferences https://bits.updatemyprofile.com/r-juitkuhk-DCA2A3C5-uhtudkhjjk-b | Unsubscribe https://email.vibconferences.be/t/r-u-juitkuhk-uhtudkhjjk-n/

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Position bioinformatician - single cell analysis and data processing
by M.A. Sanders 15 Nov '20

15 Nov '20

Dear all, We would like to draw your attention to our recently opened position for bioinformatician at the department of Hematology, Erasmus MC. Full details and option to apply at: https://www.werkenbijerasmusmc.nl/en/vacancy/43521/bioinformatician-44.14.2… With kind regards, Mathijs Sanders We offer: We offer a 36 hour/week position as bioinformatician at the department of Hematology, Erasmus MC, with a primary focus on single cell data analyses and the implementation of cutting edge technology. We ask: You are an enthusiastic and skilled bioinformatician (BSc/MSc), motivated to work in a collaborative academic environment and willing to learn new skills to make a lasting impact on our research with the goal improve patient care. Department: The advent of new high-throughput technologies and the increased pace of sequencing has expanded the volumes of data that require bioinformatical analyses. We now seek to expand our computational biology team with a bioinformatician who will assist in processing sequencing data, participate in a number of research programs as bioinformatics support and contribute to the development of software and pipelines. Our primary focus is on processing data derived from single-cell technologies including spatial transcriptomics, genetics, epigenetics and other high-throughput applications. You will be tasked with improving the utility of these technologies to further our research.

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New plugin available for ImageJ / FIJI (microscopy / histology)
by Yves Sucaet 13 Nov '20

13 Nov '20

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job opening for a BSc/MSc_Bioinformatics
by Vos-3, H.R. 12 Nov '20

12 Nov '20

Dear All, We have a job opening for a BSc/MSc_Bioinformatics We offer: We are offering a position in bioinformatics (BSc/MSc) in proteomics, in an excellent research environment at the Center for Molecular Medicine, with innovative technology, and high-quality research and support. We ask: You are a recently graduated Bachelor/Master in Bioinformatics, motivated to work in a collaborative academic environment in fundamental biomedical research. Department The Center for Molecular Medicine is a research center that focuses on understanding the molecular and cellular basis of disease. More than 160 researchers perform multidisciplinary fundamental and translational research in relation to various diseases, including cancer and genetic disorders. The aim of the CMM is to train the next generation of biomedical scientists by performing internationally leading, fundamental biomedical research and by offering stimulating and excellent education. Within the CMM there are several core facilities, providing scientists access to high end technologies, among which is the facility for (single cell) proteomics. Job description You will work in an interdisciplinary team, with experts in nano-LC, mass spectrometry, flow cytometry, tissue culture and signaling in cancer. You will work together with wet-lab team members to design proteomics experiments for clients, processes mass spectrometry based data and help the client to interpret those data using bioinformatic analysis methods that are in-house but also which you have developed. Requirements You are motivated to work in a collaborative academic research environment in a facilitatory role in the field of proteomics. You are a creative, outgoing person, and enjoy working in a team. You have recently obtained your Bachelor/Master degree in bioinformatics, and would like to develop and implement innovative analysis methods for (single cell) proteomics in a multi-disciplinary team. You have experience in collaborating with wet-lab researchers, from whom you are eager to learn some wet-lab skills. This job is based on a temporary position, starting for 2.5 years, and option for extension upon positive evaluation. Starting date is January 1st, 2021. Contact: Harmjan Vos, H.R.Vos-3 at umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Vacancy for a structural bioinformatician at Radboudumc Nijmegen
by Hanka.Venselaar＠radboudumc.nl 11 Nov '20

11 Nov '20

Dear all, we would like to draw your attention to this vacancin our structural bioinformatics group at Radboudumc Nijmegen. Full tekst and details can be foud here: https://www.radboudumc.nl/en/vacancies/89341-postdoc-diagnostics-in-3d GRTZ from Nijmegen, Hanka "Job description The increasing pace at which genomes are being sequenced and at which protein 3D structures are being solved opens the possibilities to predict the effect of mutations on the functioning of a protein at an unprecedented scale. Furthermore, advances in Artificial Intelligence (AI) allow us to efficiently exploit that information to make reliable predictions about disease causing mutations. Such predictions can be applied in diagnostics, solving the many variants in patients' genomes for which we do not know whether they are responsible for disease. The project, named Diagnostics-in-3D, will therewith have a significant impact on diagnosis of (rare disease) patients. Your role in this project is to investigate how to optimally exploit protein 3D structure information in an AI framework that discriminates between benign and damaging mutations in human genomes. For that you will use our protein 3D modeling project HOPE, our deep learning platform for 3D protein structures DeepRank and our expertise in deep learning approaches to protein structures, comparative genomics and diagnostic classifiers. You will be working with a scientific programmer to turn your solutions into professional software. You will furthermore be collaborating with two companies, one from which you will to obtain relevant 3D data and sequence alignments and one with which we will implement parallel/distributed CPU/GPU computing solutions for this data and computation intensive project. Your job thus entices both scientific research into the effect of protein 3D structures and regular communication with the scientific and industrial partners. Tasks and responsibilities Obtain relevant data and find the best representation of 3D structure data for deep learning. Modeling effects of mutations on protein 3D structure. Extend DeepRank to work with single protein structures. Developing and training classifiers using DeepRank to predict the effect of mutations on protein function. Communicate with a scientific programmer about implementation of software. Reporting your results in the form of publications and presentation. Profile You either have a PhD in computational structural biology, with a strong computational background in modeling and interpreting 3D structures, or you have a PhD in machine learning and AI with a proven interest in protein 3D structures and biochemistry. Furthermore, you are enthusiastic about genetics and biomedical research. Lastly, you have strong communication skills and you have a collaborative mindset. " De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 41055629.

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a postdoc vacancy for computational structural biology and genetics
by Li Xue 10 Nov '20

10 Nov '20

Dear all, We have a postdoc vacancy for computational structural biology ad genetics: https://www.radboudumc.nl/en/vacancies/89341-postdoc-diagnostics-in-3d Could you help us to distribute the vacancy to anyone interested in or via your preferred communication channels? Thanks. Best, Li Assistant Professor Center for Molecular and Biomolecular Informatics Radboud University Medical Center Nijmegen the Netherlands

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Opening for a data scientist/bioinformatician at Princess Maxima Center for Pediatric Oncology
by Kemmeren-2, P.P.C. 05 Nov '20

05 Nov '20

Dear all, We have an opening for a data scientist/bioinformatician within the Princess Maxima Center for Pediatric Oncology! Interested in contributing to our efforts in providing state-of-the-art precision oncology for pediatric cancer patients as well as contribute to our whole-genome driven biobanking efforts, please apply using the link below. https://werkenbijprinsesmaximacentrum.nl/vacature/data-scientist-bioinforma… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_902055192] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Training on Visual Analytics for Life Sciences & Health
by Marques Neves, A.R. 05 Nov '20

05 Nov '20

Helis Academy: Training on Visual Analytics for Life Sciences & Health On the 1st of December 2020, Helis Academy and TU/e will organize an online course on Visual Analytics for Life Sciences & Health. This online program provides the opportunity to get insights on theory, current practice in industry and expected possible future Practice in industry within just one day, right from behind your own PC. More information and registration is available here: https://helisacademy-trainingonvisualanalytics.eventbrite.nl [A picture containing text Description automatically generated] Kind regards, [Eindhoven University of Technology] Rita Neves, M.Sc. Researcher | Eindhoven University of Technology | Department of Mathematics and Computer Science M: +351 914 878 562 | +31 (0)6 838 33 047<tel:+351%20914%20878%20562%20|%20+31%20(0)6%20838%2033%20047> E: a.r.m.marques.neves(a)tue.nl<mailto:a.r.m.marques.neves@tue.nl> A: Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven [https://img.mysignature.io/s/v3/0/d/a/0da47aae-d980-5ecc-919d-f6cbbc5bd6e2.…]<https://www.linkedin.com/in/rita-neves/>

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