January 2024 - BBClist - maillist.psb.ugent.be

ESSAI 2024 CALL FOR COURSE PROPOSALS
by BeNeLux bioinformaticians forum 17 Jan '24

17 Jan '24

ESSAI 2024 CALL FOR COURSE PROPOSALS (Apologies for multiple postings) The 2nd European Summer School in Artificial Intelligence - ESSAI 2024 July 15-26, 2024 Athens, Greece https://essai2024.di.uoa.gr/ IMPORTANT DATES 07 Feb 2024: Course Title submission deadline (mandatory) 14 Feb 2024: Final submission 06 Mar 2024: Notification ABOUT ESSAI 2024 is the second edition of the annual summer school on AI held under the auspices of the European Association for Artificial Intelligence (EurAI). ESSAI 2024 will provide an interdisciplinary setting in which courses are offered in all areas of Artificial Intelligence and also from wider scientific, historical, and philosophical perspectives. ESSAI is a central meeting place for students and young researchers in Artificial Intelligence to discuss current research and share knowledge. Courses will consist of five 90-minute sessions, offered daily (Monday-Friday) in a single week, to allow students to develop in-depth knowledge of a topic. The first edition of ESSAI was held in Ljubljana, Slovenia (https://essai.si/ ) between the 24th and 28th of July 2023 and was extremely successful, attracting over 500 participants. We look forward to a second edition of ESSAI that is at least as successful. TOPICS AND FORMAT ESSAI aims to cover all subdisciplines of AI and the interactions between them. Proposals for courses at ESSAI 2024 are invited in all areas of Artificial Intelligence, including but not limited to the following: * Autonomous Agents and Multi-agent Systems (MAS) * Causality and Causal Learning (CL) * Ethical, Legal and Social Aspects of AI (ELS) * Foundation Models (FM) * Knowledge Representation and Reasoning (KR) * Learning Theory (LT) * Natural Language Processing (NLP) * Neuro-Symbolic Learning and Reasoning (NSLR) * Planning and Strategic Reasoning (PLAN) * Reinforcement Learning (RL) * Robotics (ROB) * Safe, Explainable and Trustworthy AI (SET) * Search and Optimization (SO) * Supervised and Unsupervised Learning (ML) * Vision (VIS) Each course will consist of five 90-minute lectures, offered daily (Monday-Friday) in a single week. While introductory courses will typically focus on one subarea of AI, advanced courses are encouraged to present a broader perspective on AI and should be of interest beyond one specific area. CATEGORIES Each proposal should fall under one of the following categories. INTRODUCTORY COURSES Introductory courses are intended to introduce a research field to students, young researchers, and other non-specialists, and to foster a sound understanding of its basic methods and techniques. Such courses should enable researchers from related disciplines to develop some comfort and competence in the topic considered. Introductory courses in a cross-disciplinary area may presuppose general knowledge of the related disciplines. ADVANCED COURSES Advanced courses are targeted primarily to graduate students who wish to acquire a level of comfort and understanding in the current research of a field. PROPOSAL GUIDELINES To be considered, course proposals should closely adhere to the following guidelines: * Courses must be presented by lecturers who submitted the proposal. For courses with more than two lecturers, the role of each lecturer should be clearly explained and justified in the proposal. * Course proposals should explicitly state the intended course category. Proposals for introductory courses should indicate the intended level, for example, as it relates to standard textbooks and monographs in the area. Proposals for advanced courses should specify the prerequisites in detail. Proposals must be submitted in PDF format via: https://easychair.org/conferences/?conf=essai2024 and include all the following: 1. Personal information for each proposer: Name, affiliation, contact address, email, homepage (optional) 2. General proposal information: Title, category 3. Information about the course content: a. Abstract of up to 150 words b. Motivation and description (up to two pages) c. Tentative outline d. Expected level and prerequisites e. Appropriate references (e.g., textbooks, monographs, proceedings, surveys) f. Whether the course will appeal to students outside of the main discipline of the course 4. Information about the proposer(s): a. Short CVs of the proposer(s) b. Evidence that the proposer(s) are excellent lecturers with relevant teaching experience, in particular in delivering intensive courses in an interdisciplinary setting. To keep participation fees to a minimum, all the instructional and organizational work of ESSAI is performed on a completely voluntary basis. However, the registration fees of organizers and instructors will be waived. In addition, and where appropriate, ESSAI will seek to partially reimburse travel and accommodation expenses associated with delivering a course. If lecturers can cover their travel and accommodation expenses from other sources, this is greatly appreciated. SUBMISSION INFORMATION By February 7, 2024: Proposers must submit on EasyChair at least the name(s) of the lecturers(s), the ESSAI area and course level and a short abstract. By February 14, 2024: Submission must be completed by uploading a PDF with the actual proposal as detailed above. SUBMISSION PORTAL Please submit your proposals to https://easychair.org/conferences/?conf=essai2024 ORGANIZING COMMITTEE Chair: Brian Logan, Utrecht University Co-chair: Magdalena Ortiz, TU Wien Local Chair: Manolis Koubarakis, National and Kapodistrian University of Athens ESSAI Steering Committee Chair (EurAI Board representative): Giuseppe De Giacomo, Oxford University

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Postdoctoral position in bioinformatics of the human gut microbiome - VIB
by BeNeLux bioinformaticians forum 12 Jan '24

12 Jan '24

> Begin forwarded message: > > From: Jeroen Raes <jeroen.raes(a)kuleuven.be> > Subject: Postdoctoral position in bioinformatics of the human gut microbiome - VIB > Date: 11 January 2024 at 15:52:08 CET > > > Postdoctoral position in bioinformatics of the human gut microbiome > Leuven VIB-KU Leuven Center for Microbiology > > https://jobs.vib.be/j/69697/postdoctoral-position-in-bioinformatics-of-the-… > > > > — > Prof. Jeroen Raes, PhD > > Group leader, Bioinformatics and (eco-)systems biology lab > Department of Microbiology and Immunology, Rega institute, KU Leuven > > Vice-director, VIB Center for Microbiology > > KU Leuven - Campus Gasthuisberg > Herestraat 49 - box 1028 > 3000 Leuven > Belgium > > jeroen.raes(a)kuleuven.be <mailto:jeroen.raes@med.kuleuven.be> > Phone: +32 (0)16 330678 <tel:%2B32%20%280%2916%20330678> > http://www.raeslab.org <http://www.raeslab.org/> > > NOTE: All mail on my KU Leuven address is monitored by my PA, Elisa van der Zande (elisa.vanderzande(a)kuleuven.be <mailto:elisa.vanderzande@kuleuven.be>) - for personal matters, please contact me in person >

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Job Offer - Bioinformatics Scientist at BASF Nunhems Vegetable Seeds
by BeNeLux bioinformaticians forum 12 Jan '24

12 Jan '24

Dear all, We have a new vacancy for a bioinformatics scientist at BASF (Nunhems) Vegetable Seeds. At BASF | Nunhems it is our ambition to make healthy eating enjoyable and sustainable. Together and in collaboration with partners we are eager to improve our vegetable varieties and solutions for our customers, the vegetable value chain and consumers worldwide. To further develop and grow this ambition we are looking for a Scientist Bioinformatics. Your Job As Bioinformatics Scientist you build knowledge and insights from digital data. Together with bioinformatics colleagues at BASF Nunhems Vegetable Seeds, you are responsible for managing our genome-wide digital genetic resources, such as gold standard reference genomes, high quality gene annotation and population-wide re-sequencing. Together with our genomics and molecular biology colleagues, you create pipelines and tools for data acquisition and processing. You provide elegant and intuitive methods to create, explore and analyze large genetic resources, geared towards next-generation and long-read sequencing. Major Accountabilities • Create and maintain unsupervised data-analysis pipelines • Develop user-facing data applications • Data processing, ensure quality and delivery of routine analysis experiments • Design and execute bespoke analyses on multi-omics datasets • Provide specialized technical expertise and technical advice in relation to data management, workflow development and data analysis methods • Innovation; propose out-of-the-box solutions for the utilization, storage and management of data Key activities: Tool and Pipeline development • Use industry-standard methods to create and maintain data-analysis applications (e.g. git, test-driven, agile/scrum) • Develop client-server applications for data delivery and exploration using various interfaces (scripting clients, Web, API, etc) Routine and bespoke data processing • Align with molecular scientists on experimental design, project goals and applications. • Ensure analysis activities are focused and delivered on time Technology scouting and innovation • Identify computational methods and other opportunities to improve speed, quality and extract more value from our datasets. • Evaluate new technologies and create business cases for implementation. Together with Genomics and Molecular Genetic teams collaborate in developing databases, gold standard reference genomes, high quality gene annotation and functional genomics integrative tools that facilitate gene discovery. Your profile • Ph.D. in Bioinformatics, Systems Biology, Genomics, Molecular Biology, Plant Sciences, with a clear computational component, or computer sciences with a clear interest in plant biology • Proven expertise in creating and support digital solutions for biological challenges • Strong ability to create scalable and maintainable software in python • Above-average knowledge of at least one other programming language (R, SQL, Rust, C) • Proven competence in usage of software-development best practices (version control, TDD etc) • Knowledge of Linux HPC environments • Proficiency in data analysis and interpretation using relevant software and tools Do you recognize yourself in the following competencies and skills? • Strong communication and presentation skills to effectively collaborate with internal and external stakeholders • Self-motivated, innovative, and able to work both independently and collaboratively fast-paced research environment • Solution-driven, with attention to detail and quality • Curiosity and drive to understand the new genomic technologies • Strong entrepreneurial and innovative spirit are crucial Interested in this job? You will be successful in this position when you are able to create efficient applications for data processing and access, playing a crucial role in implementing the ‘big-data genomics’ side of the digitalization strategy. This position contributes to speed and novelty in variety development and trait and gene discovery by enabling genetic and genomic data to integrated breeding teams, also ensuring gene discovery securing IP for BASF. Ready to join this team and contribute to our ambition to make healthy eating enjoyable and sustainable for everyone worldwide? Send us your resume (CV) and motivation letter to contact Michiel Weijters, Senior Global Talent Acquisition Specialist via michiel.weijters(a)vegetableseeds.basf.com<mailto:michiel.weijters@vegetableseeds.basf.com> What’s in it for you? Adding value to our customers begins with adding value to you. At BASF we believe that people are the key to our long-term success and that talent is in everyone. That’s why we empower you with the tools, guidance and opportunities you need to advance and succeed in work and life. Giving you the support that you need to be your best and fulfill your personal ambitions is what helps us achieve our ambitions. After all, our success is linked to yours. Whatever path you envision, BASF is a great place to build a rewarding, successful career. For BASF, diversity is one of the essential keys to business success and the well-being of our employees. We promote an inclusive culture that accepts the diversity of people, experiences and capabilities. By embracing talents and abilities of all kinds, we aim to boost creativity and motivation, and enhance our teams’ performance. Personal Data When processing your personal data during the applicant’s procedure, Nunhems Netherlands BV adheres to the applicable law and regulations, amongst others the General Data Protection Regulation (“GDPR”). For more information about the processing of your data and your rights, we would like to refer you to our privacy notice for applicants on our website www.nunhems.com.

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Selected VIB Training Activities in February and March: register now
by BeNeLux bioinformaticians forum 10 Jan '24

10 Jan '24

Dear colleague, Happy New Year! As we step into 2024, we're excited about the opportunities that lie ahead. May this year bring you success, growth, and new horizons. Explore a selection of our upcoming courses and embark on a journey of learning and development. Introduction to Git & GitHub 5 & 6 February, Brussels<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Research Data Management: Your Ally on the Way to Your Publication 12 & 13 February, Ghent<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Apply Scop3PTM Web-interface to Understand PTMs of Proteins 6 March, Leuven<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Apply MutationExplorer to Study Mutation of Proteins and Visualize their Energetic Impact 6 March, Leuven<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Enjoy your training! Best regards, Alex

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Call for submissions: Disease Maps Community Meeting, 25th-27th of March 2024, Luxembourg
by BeNeLux bioinformaticians forum 09 Jan '24

09 Jan '24

Call for submissions for the 8th Disease Maps Community Meeting 2024 on 25th-27th of March 2024 in Luxembourg. https://disease-maps.org/DMCM2024 Submit your abstracts via the EasyChair link<https://easychair.org/cfp/dmcm2024> by 24 January 2024. Register via this registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…> by 24 February 2024. DMCM’24 a joint event of the Disease Maps Community (https://disease-maps.org<https://disease-maps.org/>) and the ELIXIR Systems Biology Community (https://elixir-europe.org/communities/systems-biology) We plan intensive exchanges during panel discussions, poster sessions and focus group workshops. See the agenda<https://disease-maps.org/DMCM2024/programme/> for more details. Keynote speakers * James Glazier, Professor of Intelligent Systems Engineering, Professor & Director of Biocomplexity Institute Biophysics, Indiana University, Bloomington, USA * Liesbet Geris, Collen-Francqui Research Professor in Biomechanics and Computational Tissue Engineering, University of Liège and KU Leuven, Belgium * Henning Hermjakob, Head of Molecular Systems Services, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK * Reinhard Schneider, Head of Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg Featured workshop imSAVAR Symposium: Disease maps and irAOPs in the immune system effects of immunomodulatory therapies. Scope We will focus on systems medicine topics, including tools, standards, and applications of bioinformatics, computational and systems biology to research on human diseases. Join us to discuss challenges of building reliable models of disease mechanisms from prior knowledge and data, and applying their predictions. The topics include, but are not limited to: * Curation of diagrammatic models of diseases using systems biology standards * Visual analytics of systems biology diagrams * Modelling of disease mechanisms: network-based, Boolean or continuous * Interpreting multi-omics data using systems biology diagrams * Using omics data for model building and parameterisation Abstract Submission Deadline: 24 January 2024 (the EasyChair link<https://easychair.org/cfp/dmcm2024>) Registration Deadline: 24 February 2024 (registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…>) When: 25th-27th of March 2024 Where: University of Luxembourg, Campus Belval, Maison du Savoir 2, avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg https://www.uni.lu/en/about/campuses/belval-campus For all details see https://disease-maps.org/DMCM2024<https://disease-maps.org/DMCM2024> With warm regards, on behalf of the organisers --- Marek Ostaszewski University of Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval | House of Biomedicine 6, avenue du Swing, L-4367 Belvaux, Luxembourg Tel: +352 46 66 44 5604 http://lcsb.uni.lu<http://lcsb.uni.lu/>

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Bioinformatics Jobs at Berlin Institute of Health
by BeNeLux bioinformaticians forum 06 Jan '24

06 Jan '24

Hi everybody, the Robinson lab has just relocated to Berlin Institute of Health at the Charité University Hospital. We are recruiting several positions that will be funded by an Alexander von Humboldt Professorship in Artificial Intelligence. The Robinson lab create created the Human Phenotype Ontology<http:///www.human-phenotype-ontology.org> and the Medical Action Ontology<https://pubmed.ncbi.nlm.nih.gov/37503136/> and has led the development of the Phenopacket Schema<https://pubmed.ncbi.nlm.nih.gov/35705716/> for the Global Alliance for Genomics and Health<https://www.ga4gh.org/>. We have developed software for genomic diagnostics, genomic applications such as ChIP-seq and RNA-seq, machine-learning algorithms for various applications. Please see the links on this page for the first two job descriptions (our lab is described on the rest of the page): https://robinsongroup.github.io/careers/ Thanks & groetjes, Peter ___________________________ Peter Robinson Professor for Medical Computer Science A.v.Humboldt professorship Berlin Institute of Health at Charité (BIH) Rahel Hirsch Center for Translational Medicine Luisenstraße 65 10117 Berlin peter.robinson(a)bih-charite.de https://robinsongroup.github.io/

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Job Offer - Junior Research Engineer for Computational Biology (RE1)
by BeNeLux bioinformaticians forum 05 Jan '24

05 Jan '24

Hello, I hope this email finds you well. I am contacting you because we have opened a new PhD Student vacancy in the Life Sciences department, and we would be grateful if you could share them it with your contacts and post them in your website: * *Junior Research Engineer computational Biology (RE1): *https://www.bsc.es/join-us/job-opportunities/58923lscbre1 o Deadline 31th of January 2024 If you need further information regarding any of our vacancies, or you need any additional steps from my side in order to disseminate it, please let me know. Thank you! Best regards, -- Aldara Cárdenas Pereira /HR UNDERGRADUATE STUDENT /*Barcelona Supercomputing Center - Centro Nacional de Supercomputación* aldara.cardenas(a)bsc.es www.bsc.es <http://www.bsc.es/>

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Vacancy PhD position visual analytics in multilayer networks LAST WEEK TO APPLY
by BeNeLux bioinformaticians forum 03 Jan '24

03 Jan '24

Dear all, == LAST WEEK BEFORE SUBMISSION DEADLINE == We have an exciting new PhD position in visual analytics of multi-layer networks The Visual Data Analysis research group at KU Leuven (University of Leuven) is part of the department of Biosystems at the Faculty of Bioscience Engineering. The group focusses on complex data exploration in the domain of biological and agricultural sciences, through the use of visual analytics and topological data analysis. The group is currently looking for a dynamic and highly motivated PhD student. Project Networks and graphs - both static and dynamic - play an important role in data science. Not only can they represent primary relational data (e.g. gene interactions) but many algorithms generate networks either as intermediate or final output (e.g. DBSCAN clustering and topological data analysis). In particular, these data structures are critical when investigating (biological and other) systems as a whole. We can quantitatively compare networks at different resolutions, and distinguish between changes in topology and changes in characteristics of the nodes and links themselves. Although many measures exist to do so (including degree, closeness, betweenness, etc), they mainly focus on the amount of difference but fall short in giving real insight in the quality of that difference. We want to focus on this qualitative understanding of networks rather than only a quantitative one. We want to develop a human-in-the-loop visual analytics toolkit to support the user in exploring differences between two or more networks in depth. Visual Analytics (VA) is often described as the science of analytical reasoning facilitated by the visual interface and combines interactive data visualisation and novel visual design on one hand with machine learning on the other. The methodology will involve - among other things - custom visual design, definition and implementation of interestingness features, as well as definition of novel distance metrics for topological data analysis. This will be applied to different types of multi-layer networks (e.g. with/without ordering in 2 or more dimensions). Keywords: graph, network, topological data analysis, visual analytics, data visualisation, multilayer networks Example papers on the topic of multi-layer networks and topological data analysis: * McGee et al. The State of the Art in Multilayer Network Visualization. Computer Graphics Forum 38, no. 6 (2019): 125–49. https://doi.org/10.1111/cgf.13610 * Lum et al. Extracting Insights from the Shape of Complex Data Using Topology. Scientific Reports 3 (2013): 1236. https://doi.org/10.1038/srep01236 Profile The Ideal Candidate * has a Master's degree in Computer Science, Bioscience Engineering or similar, with distinction (required) * has a solid understanding of network analysis / graph theory and a strong foundation in general data visualisation principles and techniques * has experience in topological data analysis (TDA) * has good programming and data analysis skills (incl using Python and if possible Javascript) * can work independently as well as part of a collaborative cross-domain research team * is proficient in oral and written English, possess excellent communication and multi-tasking skills, is team-oriented, proactive and result-driven. Interested Candidates Should Submit The Following * curriculum vitae * digital copy of the diplomas, including a list of courses followed and grades * contact information of 2 or 3 referees * motivation letter, which specifies why they apply to this position, and clearly illustrate possible past experience in the area. Offer * A fully funded, full-time PhD position for one year; after a positive evaluation, the contract can be extended to three additional years (four years in total) * A working climate where trust, (international) collaboration, and commitment are essential * An excellent young, stimulating and supportive international research environment * High level scientific training at a top-ranked university; training in academic, thematic and soft skills. How to apply For more information on this opportunity, please contact Prof Jan Aerts, tel.: +32 16 32 21 40, mail: jan.aerts(a)kuleuven.be<mailto:jan.aerts@kuleuven.be> You can apply via the KU Leuven jobsite at https://www.kuleuven.be/personeel/jobsite/jobs/60288125 Deadline for submitting: 11/1/2024 --- Prof Jan Aerts Visual Data Analysis Lab Department of Biosystems KU Leuven, Belgium jan.aerts(a)kuleuven.be https://www.biw.kuleuven.be/biosyst ; http://vda-lab.io

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