March 2021 - BBClist - maillist.psb.ugent.be

Online tutorials: modeling microbial ecology at multiple scales
by Daniel Garza 15 Mar '21

15 Mar '21

Dear all, we are organizing online tutorials to learn more and exchange information about modeling microbial ecology at multiple scales. If you are interested in microbiomes and would like to know more about how they can be modeled, then please join these tutorials. The first tutorial will be given by Veronika Dubinkina <https://scholar.google.com/citations?user=Td1pQmIAAAAJ&hl=ja>. She will discuss consumer-resource models. Including the classical examples of MacArthur and Tilman and recent explorations in modeling microbiome ecology ( e.g., https://go.nature.com/38ei5UT <https://www.google.com/url?q=https://go.nature.com/38ei5UT&sa=D&source=edit…> and https://bit.ly/3t5bdBx <https://www.google.com/url?q=https://bit.ly/3t5bdBx&sa=D&source=editors&ust…> ) The next tutorial will be announced in mid-April. The tutorials are free, but to receive the zoom link and the installation instructions for the practical session, please register <https://docs.google.com/forms/d/e/1FAIpQLSfSPDm8-eLfHrk1q9IRzucjp0JafZb083y…> . Tutorial I: <https://modelmems.github.io/#tutorials> Date: 06-Apr-2021 Time: 15-18:00h (CET) Schedule: 15:00 - 16:20 - Seminar by Veronika Dubinkina 16:20 - 16:30 - Coffee break 16:30-17:45 - Guided hands-on tutorial 17:45 - 18:00 - Wrap-up session more information at https://modelmems.github.io/# Organizing team, Akshit Goyal (MIT) Bram Van Dijk (MPI for Evolutionary Biology) Daniel Garza (KU Leuven) Veronika Dubinkina (University of Illinois at Urbana-Champaign)

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Senior Bioinformatician - AstraZeneca (Cambridge, UK)
by Sergio Martinez Cuesta 13 Mar '21

13 Mar '21

*Are you a quantitatively-minded scientist looking to apply bioinformatics and machine learning to design the next generation of therapeutics? 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 Cambridge!* We are currently looking for a Senior Bioinformatician to join us at AstraZeneca in Cambridge, UK as part of the Data Sciences and Quantitative Biology team in biopharma R&D: https://careers.astrazeneca.com/job/cambridge/senior-bioinformatician-data-… Deadline for applications *23rd March*! Please distribute with bioinformatics colleagues reaching their ends of contracts. Best wishes, Sergio

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Help EMBL-EBI maintain its services: articulating the value of open data
by Kim DE RUYCK 11 Mar '21

11 Mar '21

Dear , I would like to encourage you to participate in a survey that aims to assess the worldwide value of the bioinformatics resources available through [ https://www.ebi.ac.uk/ | EMBL’s European Bioinformatics Institute (EMBL-EBI) ] . The institute hosts some of the world’s most important collections of biological data including UniProt, Ensembl, ChEMBL, ENA and Europe PubMed Central. Your input is extremely important and will help EMBL-EBI maintain and develop its resources for the global scientific community. EMBL-EBI would be very grateful if you and other users in your organisation could contribute to this study by completing the following survey: [ https://www.surveymonkey.co.uk/r/EMBL-EBI_Impact_PE | https://www.surveymonkey.co.uk/r/EMBL-EBI_Impact_PE ] . The survey takes around 15 minutes and closes on 31 March 2021. T he results of the survey will be anonymized and all personal data treated as confidential. Please share this survey with colleagues and collaborators who use public data resources. If you have any questions or comments about the survey please contact impactsurvey(a)ebi.ac.uk. Kind regards, Kim De Ruyck -- Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB-UGent Center for Plant Systems Biology Technologiepark 71, 9052 Ghent, Belgium [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ]

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Registration open for ELIXIR-NL CWL Lesson Hackathon, March 22 and 23, 2021 , 13-17 CET
by Celia van Gelder 11 Mar '21

11 Mar '21

Dear colleagues, It is my pleasure to announce that the registration is now open for the CWL Lesson Hackathon that is organised by ELIXIR-NL. The hackathon will take place on March 22 and March 23, from 13-17 CET. More information can be found further in this mail and also here: https://github.com/common-workflow-lab/cwl-novice-tutorial/wiki/2021-Lesson… Registration form: https://docs.google.com/forms/d/e/1FAIpQLSeniSgVCCUIAzPVey-uWcEBV0XAJWkf3CS… Organizing Committee: Michael R. Crusoe, Fotis Psomopoulos, Renato Alves, Toby Hodges, Hervé Ménager, Peter van Heusden, Celia van Gelder Introduction In the CWL community a lot of efforts have been made to set up lesson materials. Previous work consists of establishing episodes <https://github.com/common-workflow-lab/cwl-novice-tutorial/tree/gh-pages/_e…>, learning objectives <https://github.com/common-workflow-lab/cwl-novice-tutorial/blob/gh-pages/pa…> and learner profiles <https://github.com/common-workflow-lab/cwl-novice-tutorial/blob/gh-pages/pa…)>. In this CWL lesson hackathon we intend to build on that work and make significant steps towards creating CWL lessons that can be (re-) used by the CWL community and others who need to train in CWL. The newly developed lessons will be first used in two upcoming CWL courses in 2021 (by ELIXIR-GR and ELIXIR-NL). Audience & prerequisite knowledge Participants in this lesson hackathon are expected to have some familiarity either with workflows (with CWL being the case in study), and/or training / lesson development / pedagogical aspects. The lesson hackathon itself will be structured into parallel development sessions, and therefore complementary experiences will be particularly useful to address the challenges and exercises of the lesson, and create balanced teams. Finally, it is important to note that the hackathon is open to any contributors, and not limited only to the ELIXIR network. Programme Day 1, March 22, 2021, 13-17 CET 13.00: Welcome and introduction (Michael Crusoe) - Starting point: what is in place: Episodes/lessons, Exercises, Learning outcomes (sketched), Learner profiles (complete) - Plan of approach for the hackathon - Not making new episodes/lessons; finishing the existing episodes/lessons; Making exercises - Expectations of organiser and expectations of participants - Divide in groups for the breakouts (per lesson) 13:30 Hacking in breakouts (3 hours) Facilitators will rotate as need be - Write exercises - Send Pull Requests - When exercises are finished, write teaching material - Review PRs from other groups - Summarize results for reporting in the Wrap-up session 16.30 Wrap up - Each group reports back about what has been done and plans for Day 2. 17.00 Closing Day 2, March 23, 2021, 10-13 CET (optional) & 13-17 CET 9.00 - 13.00 No formal sessions. Optional hours are up to each individual; Toby Hodges and Michael R. Crusoe will be available starting from 09:00 Central European Time <https://www.timeanddate.com/worldclock/meetingdetails.html?year=2021&month=…> 13.00: Quick recap of Day 1 plus reshuffling of groups if needed/wanted 13.15: Hacking in breakouts; Facilitators will rotate as need be - Write exercises - Send Pull Requests - When exercises are finished, write teaching material - Review PRs from other groups - Summarize results for reporting in the Wrap-up session 16.00 Wrap up - Each group reports back about what has been done and plans for Day 2. 16.30 Next steps after the lesson hackathon 17.00 Closing We hope to see many of you at the Lesson Hackathon! Best regards, Celia, on behalf of the Organizing Committee -- Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL / Node 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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School on the Analysis of Microbial Time Series Data, 2-4th November 2021
by Karoline Faust 10 Mar '21

10 Mar '21

Dear all, We are happy to announce our School on the Analysis of Microbial Time Series Data, which will take place in Leuven (or online if necessary) from the 2-4th of November 2021. The school will explore the insights gained from longitudinal microbiome data, study different techniques to quantify community stability and look at whether and how drivers of community dynamics can be identified from time series. The mornings will start with a general introduction followed by lectures on the latest developments in the field, while the afternoons will be dedicated to hands-on practical sessions. A number of internationally known speakers have confirmed their contribution, including Zishu Liu, Libusha Kelly, Malte Herold, Gail Rosen, Dana Ofiteru, Alex Washburne, Ursula Gaedke, Johannes Björk, Jacopo Grilli, Ashley Shade and Aura Raulo. For more information and registration, please visit: https://tinyurl.com/microbetime Kind regards, Karoline, on behalf of the organisers Karoline Faust --------------------------------------------------- Email: karoline.faust(a)kuleuven.be<mailto:karoline.faust@kuleuven.be> Web: http://tinyurl.com/MicrobialSysBio --------------------------------------------------- Room 7.A130, Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology, Immunology and Transplantation KU Leuven, Campus Gasthuisberg Herestraat 49, postbus 1028 3000 Leuven Belgium ---------------------------------------------------

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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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