- BBClist - maillist.psb.ugent.be

Systems Engineer position for ELIXIR-LU
by Christophe TREFOIS 04 Mar '21

04 Mar '21

Dear all, We are looking to extend our ELIXIR LU node by a great systems engineer to work on OpenStack, Kubernetes and other fun technologies. The link to apply: http://emea3.mrted.ly/2nexj Please see a description below. Thank you Your Role For our research activities and projects within LCSB and ELIXIR-LU, we are looking for a systems engineer to support our scientific IT infrastructures, including our virtual private clouds based on OpenStack and RHEV. In addition, the hired candidate will help with the development and setup of new state of the art solutions within our research activities. The candidate will need to research, design, and implement innovative IT solutions to enable our data integration and analytics platforms. - Research existing technologies and contribute to technology, benchmarks, selection and methodologies to apply to new and ongoing research projects. - Conceptually design innovative IT solutions within research projects. - Engage in research activities, new approaches and IT solutions in ELIXIR-LU. - Setup and provide support to ELIXIR-LU IT services. - Provisioning, installation/configuration, operation, upgrade and maintenance of systems hardware and software and related infrastructure in and for biomedical, translational, and clinical research. - Become a key actor of continuous improvement and innovation within the group. - Monitor performance, analyse and troubleshoot issues and outages/incidents. - Assist with system backup/recovery services, system administration processes, firewalls, networks, storage. - Maintain and monitor support information in ticketing systems and related tools. - Work closely with other team members aiming for a high level of quality and user satisfaction. - Write and maintain documentation for technical procedures. - Assist in the procurement of in-house services via external vendors, if/when so desired. Your Profile - Higher-educationn computer science, engineering or in another field but with equivalent proven experience as cloud engineer. - An interest in state-of-the-art technologies. - Autonomous, dynamic, and curious. - Proven experience with the following technologies: - Linux (RHEL/Ubuntu), Linux scripting (shell / bash) - OpenStack, Ceph, Keystone, ... - Docker, Kubernetes - RedHat Enterprise Virtualization / oVirt - NFS / Samba administration. - Good programming experience (Python, Perl). - Experience with Puppet, Ansible, git, Icinga / Nagios, RedHat IdM, LDAP / AD, AWS, Azure or GCP will be considered an asset. - Knowledge of modern web development technologies will be considered an asset. Excellent communication skills and the ability to articulate clearly the scientific and technical needs and to work within an interdisciplinary setting, communicating with other internal/external partners. *We offer* - A fully funded Cloud Engineer (Research & Development specialist) position with a competitive salary - Participate in the building of state-of-the-art IT infrastructure to enable precision medicine. - An opportunity to join the fast-growing Bioinformatics Core Facility group headed by Prof. Dr. Reinhard Schneider at LCSB. - An exciting international environment. In Short - Contract Type: Fixed Term Contract 36 Month - Work Hours: Full Time 40.0 Hours per Week - Location: Belval - Starting date: asap - Job Reference: UOL03671 Further Information Online applications should be addressed to: Prof. Dr. Reinhard Schneider Head of the Bioinformatics core facility and head of the ELIXIR Luxembourg node Applications (in English) should contain the following documents: - A detailed curriculum vitae - Cover letter mentioning the reference number - List of infrastructure/software projects and/or publications - Description of past experience and future interests - Name and addresses of three referees Early application is highly encouraged, as the applications will be processed upon reception. Please apply ONLINE formally through the HR system. Applications by email will not be considered. The University of Luxembourg embraces inclusion and diversity as key values. We are fully committed to removing any discriminatory barrier related to gender, and not only, in recruitment and career progression of our staff. -- Christophe Trefois, PhD

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Permanent position, NBIS Uppsala Sweden
by Lieven Sterck 04 Mar '21

04 Mar '21

on behalf of Henrik Lantz (joint head of NBIS support team): If you know of someone who would be crazy enough to move to Sweden, or if you have any possibilities of spreading the link in your networks, that would be appreciated a lot. [ https://www.uu.se/en/about-uu/join-us/details/?positionId=381399 | https://www.uu.se/en/about-uu/join-us/details/?positionId=381399 ] We know that this person will get to work with genome annotation, but depending on the projects we get, there could definitely be other types of analysis too. We do not require previous experience with genome annotation as we have staff around who could teach the new person. Experience and talent in DNA/RNA-based bioinformatics is more important! The position does not include research, this is a staff-scientist position focused on support to Swedish researchers. It is a permanent position. All the best, Henrik Lieven Sterck - Senior Postdoctoral Scientist Bioinformatics VIB Department of Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 21 [ http://bioinformatics.psb.ugent.be/ | http://bioinformatics.psb.ugent.be ] "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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Postdoctoral position in bioinformatics at ULB Brussels
by Fabrizio Pucci 03 Mar '21

03 Mar '21

The Computational Biology and Bioinformatics group of the Brussels University (ULB) is seeking candidates for a postdoctoral position. *Research context*: The understanding of the biophysical mechanisms that drive single nucleobase substitutions in different regions of the human genome is one of the key questions of the post-genomic era. These mutations, whether inherited or somatic, are potentially responsible for a huge range of rare and complex diseases. The rationalization of these mechanisms is highly intricate, since base substitutions depend on the nucleotide sequence context and can be triggered by a wide range of physical, chemical or biological factors. *Objective*: In the AtOme project, we will bridge the gap between the atomic-level characterization of mutagenesis processes and the resulting phenotypic traits. More specifically, we will investigate the role of DNA charge transport in mutational and pathogenic processes using a multiscale computational approach combining quantum chemistry, machine learning and genomics. *Offer*: A full time postdoctoral position for 2 years. Flexible starting date, between now and October 2021. Possibility of extension through an FNRS postdoctoral research grant or a Marie Curie EC grant. *Required:* - PhD degree in Sciences (Bioinformatics, Bioengineer, Physics, Chemistry, Informatics). - Excellent programming skills. - Excellent publication record. - Maximum 6 years research experience after PhD. - International mobility (maximum 24 months of residence in Belgium in the last 3 years). *Desirable:* - Experience in the area of quantum chemistry, machine learning, and/or genome bioinformatics. *Contact*: Please submit: (1) a cover letter detailing your background and interest in the position, (2) a full CV and (3) two references (with name, email, address, phone number), to M. Rooman (mrooman(a)ulb.ac.be) *Application deadline: *June 1, 2021.

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Tenure Track Assistant/Associate Professor Modelling and AI for Systems Medicine
by Riel, Natal van 01 Mar '21

01 Mar '21

We have a vacancy: Tenure Track Assistant/Associate Professor Modelling and AI for Systems Medicine at Eindhoven University of Technology https://jobs.tue.nl/en/vacancy/tenure-track-assistant-associate-professor-m… . We are looking for a creative and pro-active team player to initiate a new research line in biomedical systems biology. We unite data-driven and model-based approaches for biomedical research, engineering and healthcare. We search for candidates with a PhD degree in computational biology, biomedical engineering or other relevant disciplines. New directions could be the development and application of AI technology for learning and adaptation of dynamic models. This may enable the creation of ‘digital twins’ and contribute to personalized health and precision medicine. We search for candidates that want to play a leading role in this rapidly developing field. The TU/e provides an exciting ecosystem for healthcare engineering research and innovation, which includes close collaboration with local hospitals, industry and the cross-departmental artificial intelligence institute EAISI (www.tue.nl/ai<http://www.tue.nl/ai>). We offer a substantial start-up package to kick-off your career. Deadline for applications: 30/04/2021. Kind regards, Natal van Riel Prof. dr. ir. Natal A.W. van Riel [cid:image005.png@01D70EEF.4DC1FB50] Professor of Biomedical Systems Biology Head of Systems Biology and Metabolic Disease (SBMD) Computational Biology group Department of Biomedical Engineering Eindhoven University of Technology P.O. Box 513, 5600 MB Eindhoven, The Netherlands Internal address: Building Gemini-Zuid 3.109 Groene Loper, 5612 AZ Eindhoven route and map<http://www.tue.nl/en/our-university/departments/biomedical-engineering/the-…> T +31 40 247 5506 (5537) n.a.w.v.riel(a)tue.nl<mailto:n.a.w.v.riel@tue.nl> www.tue.nl/en/research/researchers/natal-van-riel/<https://www.tue.nl/en/research/researchers/natal-van-riel/> | www.tue.nl/cbio [cid:image006.png@01D70EEF.4DC1FB50] Professor of Computational Modelling Amsterdam University Medical Centers University of Amsterdam n.a.vanriel(a)amsterdamumc.nl<mailto:n.a.vanriel@amsterdamumc.nl>

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WABI 2021 -- Call for Papers
by El-Kebir, Mohammed 25 Feb '21

25 Feb '21

WABI 2021 Call for Papers 21th Workshop on Algorithms in Bioinformatics Chicago, USA (virtual), August 2-4 2021 https://acm-bcb.org/WABI/2021/ SCOPE WABI is an international Conference covering research in algorithmic work in bioinformatics, computational biology and systems biology. The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that provide evidence of their potential usefulness in practice, preferably by testing on appropriately chosen simulated or real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. PAPER SUBMISSION Submissions must be formatted in LaTeX using the LIPIcs style <https://submission.dagstuhl.de/styles/download-tag/lipics/v2021.1/authors/z…> and must not exceed 15 pages excluding references. For details please see the information for authors <https://submission.dagstuhl.de/documentation/authors>. Each paper must contain a succinct statement of the issues and of their motivation, a summary of the main results, and a brief explanation of their significance, all accessible to non-specialist readers. All submissions must be made online, through the EasyChair submission system, at: https://easychair.org/conferences/?conf=wabi2021 For scientific information, please contact one of the WABI program committee co-chairs, Alessandra Carbone (Alessandra.Carbone(a)lip6.fr) or Mohammed El-Kebir (melkebir(a)illinois.edu) For organizational information, please refer to the ACM-BCB 2021 <https://acm-bcb.org/> website. You will need to register on the EasyChair web site before submitting. A standard .pdf file must be received by April 16, 2021 (time zone of your choice) in order for your submission to be considered. Re-submission of already submitted papers will be possible until April 18, 2021 (time zone of your choice). Simultaneous submission to another conference with published proceedings is not permitted, but simultaneous submission to a journal is allowed, provided that the authors notify the program chairs; if published in a journal, such a contribution will be published as a short abstract in the WABI proceedings. Depositing in arxiv.org <http://arxiv.org/> or biorxiv.org <http://biorxiv.org/> is allowed. By submitting a paper the authors acknowledge that in case of acceptance at least one of the authors must register at ACM-BCB 2021 or WABI 2021, attend the conference, and present the paper. PROCEEDINGS Accepted papers will be published in WABI proceedings in the LIPIcs Leibniz International Proceedings in Informatics <https://www.dagstuhl.de/publikationen/lipics/>. Selected papers will be invited for an extended publication in a thematic series in Algorithms for Molecular Biology (AMB) <http://almob.biomedcentral.com/>. Previous proceedings of WABI appeared in LNCS/LNBI volumes until 2015. As of 2016, they appeared in LIPICS volumes. IMPORTANT DATES Paper submission deadline: April 16, 2021 Submitted papers can be updated or withdrawn until April 18, 2021 Notification of paper acceptance: May 21, 2021 Final version of accepted paper due: May 31, 2021 Conference: August 2 - 4, 2021, virtual PROGRAM COMMITTEE Tatsuya Akutsu, Kyoto University, Japan Marco Antoniotti, Universita di Milano-Bicocca, Italy Anne Bergeron, Universite du Quebec a Montreal, Canada Paola Bonizzoni, Universita di Milano-Bicocca, Italy Christina Boucher, University of Florida, USA Alessandra Carbone, Sorbonne Universite, France (co-chair) Leonid Chindelevitch, Imperial College London, UK Lenore Cowen, Tufts University, USA Daniel Doerr, University of Duesseldorf, Germany Mohammed El-Kebir, University of Illinois at Urbana-Champaign, USA (co-chair) Nadia El-Mabrouk, University of Montreal, Canada Anna Gambin, Warsaw University, Poland Bjarni Halldorsson, deCODE genetics and Reykjavik University, Iceland Katharina Huber, University of East Anglia, UK Carl Kingsford, Carnegie Mellon University, USA Gunnar Klau, Heinrich Heine University Dusseldorf, Germany Gregory Kucherov, University of Paris Est, France Manuel Lafond, Universite de Sherbrooke, Canada Elodie Laine, Sorbonne Universite, France Yu Lin, Austrialia National University, Australia Stefano Lonardi, University of California Riverside, USA Veli Makinen, University of Helsinki, Finland Tobias Marschall, Heinrich Heine University, Germany Erin Molloy, University of Maryland College Park / UCLA, US Bernard Moret, Ecole Polytechnique Federale de Lausanne, Switzerland Vincent Moulton, University of East Anglia, UK Francesca Nadalin, EMBL-EBI / ITT, Italy, England Mihai Pop, University of Maryland College Park, USA Teresa Przytycka, NCBI, NIH, USA William Stafford Noble, University of Washington, USA Aida Ouangraoua, Universite de Sherbrooke, Canada Ion Petre, Turku University, Finland Nadia Pisanti, University of Pisa, Italy Solon Pissis, CWI Amsterdam, the Netherlands Alberto Policriti, University of Udine, Italy Sven Rahmann, University of Duisburg-Essen, Germany Knut Reinert, FU Berlin, Germany Sebastien Roch, University of Wisconsin Madison, US Giovanna Rosone, University of Pisa, Italy Marie-France Sagot, INRIA Rhone-Alpes, France Alexander Schoenhuth, Bielefeld University, Germany Mingfu Shao, Penn State, US Jens Stoye, Bielefeld University, Germany Krister Swenson, CNRS & Universite de Montpellier, France Ewa Szczurek, Warsaw University, Poland Sharma Thankachan, University of Central Florida, USA Alexandru Tomescu, University of Helsinki, Finland Helene Touzet, CNRS, France Esko Ukkonen, University of Helsinki, Finland Gianluca Della Vedova, University of Milano-Bicocca, Italy Tomas Vinar, Comenius University, Slovakia Prudence W.H.Wong, University of Liverpool, UK Tandy Warnow, University of Illinois at Urbana-Champaign, USA Simone Zaccaria, UCL Cancer Institute, UK Louxin Zhang, National University of Singapore, Singapore Xiuwei Zhang, Georgia Tech, US -- Mohammed El-Kebir<http://www.el-kebir.net> Assistant Professor 3216 Siebel Center Computer Science Department University of Illinois Urbana-Champaign 217-300-7369

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CFP META'2021 @Marrakech
by El-ghazali Talbi 25 Feb '21

25 Feb '21

Dear colleagues, please distribute the CFP of META Conf. in your networks. Thanks for your collaboration. Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. ********************************************************************** META'2021 International Conference on Metaheuristics and Nature Inspired Computing 27-30 Oct 2021 Marrakech, Morocco http://meta2021.sciencesconf.org/ ********************************************************************** META is one of the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, META’2021 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. All selected long papers will be published in the Springer (SCOPUS, ISI, DBLP) conference proceedings. At least, 2 special special issues in ISI and SCOPUS journals are also confirmed. META'2021 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. META'2021 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. The scope of the META conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm intelligence, bio-inspired algorithms, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Quantum computing * Parallel and distributed algorithms * Decomposition methods * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, cloud, bio-medical, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, stochastic optimization, … * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Hyper-heuristics, cross-domain metaheuristics * Software frameworks for metaheuristics and nature inspired computing Submission of papers: ____________________ - Submission of papers via the website S1) Short papers: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages. S2) Long papers: Original research contributions of a maximum of 10 pages. S3) Journal papers: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication. For this special case, the submission should have the same title that the accepted work, the abstract AND the complete reference of the work. - Proceedings of the conference will be provided. Selected papers of type S2 will be published in a Springer book (SCOPUS, ISI, DBLP). - Predefined styles are available on the website http://meta2021.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline April 9, 2021, contact meta2021(a)sciencesconf.org Important dates: _______________ - Submission deadline: April 30, 2021 - Notification of acceptance: June 11, 2021 -- ********************************************************************** 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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Senior Bioinformatician for Oligonucleotide Therapeutics in AstraZeneca - Gothenburg (Sweden)
by Sergio Martinez Cuesta 24 Feb '21

24 Feb '21

*Are you a quantitatively-minded scientist looking to apply bioinformatics and machine learning to design oligonucleotides for therapeutic use? Do you wish to join a growing team where you will have the possibility to further exploit our drug discovery platforms? If yes, we have the position for you at AstraZeneca in Gothenburg!* We are currently looking for a Senior Bioinformatician for Oligonucleotide Therapeutics to join us at AstraZeneca in Gothenburg, Sweden. In this position you’ll be a part of the Data Sciences and Quantitative Biology team that works as part of the Discovery Sciences organisation, within BioPharma R&D. https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-… *Application deadline February 28th!* Thanks, Sergio

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Register now for 2 Helis Academy FAIR data stewardship events
by Celia van Gelder 24 Feb '21

24 Feb '21

DTL Newsletter - View this email in your browser <https://mailchi.mp/dtls/register-now-for-2-helis-academy?e=f6e850c160> *for data-driven life sciences* Register now for 2 Helis Academy FAIR data stewardship events *Are you interested in capacity building in data stewardship in the life sciences? We would like to bring your attention to two events of the Helis Academy.* *Are you a professional advancing digital skills in the life sciences? * Then join the Helis Academy event March 15th. You will learn about the portfolio of courses in Data Analysis & Data Stewardship and the possible next steps to close the gap for digital skills in life sciences and health. For more information and registration please click here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> . *Are you a researcher, (starting) data steward or generally interested in the topic of FAIR Data Stewardship?* Then make sure to join this 6 half day introductory course organised by the Helis Academy which runs in the period March 17-31. Make sure to register soon, as only 30 participants can join. Find more information here. <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 © *2021 Dutch Techcentre for Life Sciences content is open. Please reuse under CC0, 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 Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM 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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Five (5) AI4B.io PhD positions TU Delft
by Thomas Abeel 22 Feb '21

22 Feb '21

Dear all, In the context of AI4B.io, we have 5 PhD positions available at Delft University of Technology in collaboration with DSM. https://www.academictransfer.com/en/298076/phd-position-machine-learning-fo… https://www.academictransfer.com/en/298075/phd-position-machine-learning-fo… https://www.academictransfer.com/en/298080/phd-position-reinforcement-learn… https://www.academictransfer.com/en/298080/phd-position-reinforcement-learn… https://www.academictransfer.com/en/298077/phd-position-digital-twin-and-sm… kind regards, Thomas

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HIDSS4Health PhD program Heidelberg/Karlsruhe
by Marc Jan Bonder 19 Feb '21

19 Feb '21

Dear all, I hope this email finds you well. The HIDSS4Health research school performs an annual candidate selection process. We are looking for excellent graduates holding master degrees, received by July 2021 at the latest, in computer science, mathematics, engineering, physics or related quantitative sciences (e.g., bioinformatics or medical informatics). Suitable candidates are selected in a three-step process: (1) the written application, (2) a virtual one-day selection event for short-listed applicants, and (3) matching projects and candidates. Please find a description of the 2021 project proposals here ( https://www.hidss4health.de/documents/Proposals_2021.pdf) Evaluation criteria for the candidates are an excellent academic record and a strong motivation for the interdisciplinary nature of the projects. The institutions are committed to increasing the percentage of female scientists and encouraging female applicants to apply. If you are interested please apply by the 1st of march: https://www.hidss4health.de/#apply More information can be found here: https://www.hidss4health.de/ Best regards, Marc Jan Bonder

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