November 2020 - BBClist - maillist.psb.ugent.be

PhD position in Integrating of multiple -omics datasets
by Claesen Jürgen 04 Jun '24

04 Jun '24

Dear all, SCK CEN and UHasselt are looking for candidates for a PhD project with the title: "Integromics - Towards integration of big biomolecular data to enable systems biology" Description The last decades, development of high-throughput technologies such as next-generation sequencing, microarrays and mass spectrometry has led to a paradigm shift in biology and life sciences. Where previously one biomolecule (for example, a gene, or a protein) was studied as a single entity, these experimental techniques allow to study a set of biomolecules (for example, the genome or the proteome) in one go and in a limited amount of time. While, at first, experiments were analyzed independently from each other, combining information of several experimental techniques, and correlating them with environmental and/or clinical parameters, is, nowadays, of great interest. As a consequence, novel statistical and computational methodologies for the analysis of multi-omics datasets have to be developed, allowing a multi-dimensional view on complex biological processes. In this PhD project, we aim at the development of computational methods for the analysis of multi-omics datasets, that are commonly generated by the three biology units of SCK*CEN, which will improve the understanding and valorization of the data, and which will keep the biology units up to date with current developments in biology and bioinformatics. Profile and diploma As a doctorate researcher you will join the dynamic bioinformatics team at SCK CEN and CenStat (UHasselt). A successful candidate should have : * A master degree in biostatistics/applied statistics/bioinformatics/statistical bioinformatics. * You are acquainted with statistical methodologies and had exposure to computer programming in SAS/R/Winbugs/Python. * You can work independently and within a team. * You have excellent communication skills. * You are interested to develop new methodology from both theoretical and applied aspects. * You enjoy working in a multidisciplinary and multicultural environment. * You are willing to closely collaborate with biologists/biostatisticians. * You speak and write English fluently. * You have work experience with at least two different "omics" platforms. For more information contact: Dr. Claesen Jürgen (SCK-CEN), jclaesen(a)sckcen.be<https://academy.sckcen.be/en/Mailform?contactid=b22040b5-cf18-496f-a82a-3bc…> Prof. Shkedy Ziv (Hasselt University), ziv.shkedy(a)uhasselt.be<https://academy.sckcen.be/en/Mailform?contactid=51ae7733-8006-4347-b211-9a4…> Link to the project in SCK-CEN: https://academy.sckcen.be/en/Your_thesis_internship/AllTopics/Integromics--… Kind Regards, Jürgen

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NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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BSC: Life Sciences vacancy
by BSC Human Resources 27 Nov '20

27 Nov '20

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - Frontend Developer - Spanish National Bioinformatics Institute (RE1). Deadline: 31 December, 2020 Link here <https://www.bsc.es/join-us/job-opportunities/38620lsinbre1> We would appreciate that you share the information with your contacts. Sincerely, /Human Resources/* Barcelona Supercomputing Center – Centro Nacional de Supercomputación* Tel. +34- 934137745 <mailto:anais.delastre@bsc.es>www.bsc.es <http://www.bsc.es/> http://bsc.es/disclaimer

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last CFP OLA'2021 @Sicilia Italy
by El-ghazali Talbi 26 Nov '20

26 Nov '20

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2021 International Conference on Optimization and Learning 21-23 June 2021 Catania (Sicilia), Italy http://ola2021.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2021 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2021 welcomes presentations that cover any aspects of optimization and learning research such as big optimization and learning, optimization for learning, learning for optimization, optimization and learning under uncertainty, deep learning, new high-impact applications, parameter tuning, 4th industrial revolution, computer vision, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Invited session organization Dec 18, 2020 Paper submission deadline Dec 18, 2020 Notification of acceptance March 24, 2021 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings. A SCOPUS and DBLP indexed Springer book will be published for best accepted long papers. All proceedings will be available at the conference. -- *********************************************************************** OLA'2021 International Conference on Optimization and Learning 23-25 June 2021, Catania, Italy http://ola2021.sciencesconf.org *********************************************************************** ********************************************************************** META'2021 International Conference on Metaheuristics and Nature Inspired Computing 27-30 Oct 2021, Marrakech, Morocco http://meta2021.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS guide2research.com

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CMSB 2021 - first call for papers
by Karoline Faust 25 Nov '20

25 Nov '20

CMSB 2021 ========= First Call for Papers The 19th conference on Computational Methods in Systems Biology (CMSB 2021, https://cmsb2021.labri.fr) will take place on September 22-24, either in person in Bordeaux (France), or online, depending on the evolution of the Covid-19 pandemic. CMSB is a well established conference series. It brings together researchers from across biological, mathematical, computational, and physical sciences who are interested in the modelling, simulation, analysis, inference, design, and control of biological systems. Invited speakers: - Diego di Bernardo (TIGEM, Italy) - Laurence Calzone (Institut Curie, France) - Giulia Giordano (University of Trento, Italy) - Yang-Yu Liu (Harvard Medical School, US) - Ion Petre (University of Turku, Finland) CMSB 2021 solicits contributions on the following or related topics: - 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 - applications of machine learning - network modelling, analysis, inference - automated parameter and model synthesis - model integration and biological databases - 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 - modelling, analysis and control of microbial communities More information on the program is available at https://cmsb2021.labri.fr. The CMSB 2021 proceedings will be published in the Springer LNCS/LNBI series and indexed by ISI Web of Science, Scopus, ACM Digital Library, DBLP, and Google Scholar. A selection of best papers will be invited to be extended and submitted to a special issue of BMC Bioinformatics at a discounted Author Processing Charge. IMPORTANT DATES * April 12, 2021: regular and tool paper submission * May 31, 2021: highlight talks proposals * June 7, 2021: acceptance notifications * June 14, 2021: poster abstract submission * September 22-24, 2021: conference Each contribution will be reviewed by at least three members of the program committee, soon available at https://cmsb2021.labri.fr/organization/. Please refer to the conference website for details on the different types of contributions at https://cmsb2021.labri.fr/call-for-contributions/. Looking forward to receiving your contributions, The chairs of CMSB 2021, Loïc Paulevé <https://loicpauleve.name> and Eugenio Cinquemani <https://team.inria.fr/ibis/eugenio-cinquemani>

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Position as bioinformatics academic research assistant
by Tobias Fehlmann 24 Nov '20

24 Nov '20

Dear all, We have an opened position for a bioinformatician at the chair for clinical bioinformatics of Saarland University in Germany. We offer exciting topics in the fields of single cell genomics and biomedical machine learning. All details can be found at: https://www.uni-saarland.de/fileadmin/user_upload/verwaltung/stellen/wissen… With kind regards, Tobias Fehlmann -- M.Sc. Tobias Fehlmann Chair for Clinical Bioinformatics Saarland University Building E2 1 R214 66123 Saarbrücken, Germany +49 681 302 68603

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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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