- BBClist - maillist.psb.ugent.be

Learn more about Version control and Reproducibility
by BeNeLux bioinformaticians forum 09 Jul '24

09 Jul '24

Dear colleague, I bet you can relate with this image! [Image preview]Improve your versioning and research reproducibility! You have two opportunities to join uss! Check what fits you best! Click here to register: 29/Feb and 01/March - registration to: Introduction to Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-10> 16/May and 17/May - registration to: Introduction to Git & GitHub <https://training.vib.be/all-trainings/introduction-git-github-9> Come learn with us, at VIB<https://www.linkedin.com/company/vib/>, how to use Git and GitHub to a better version-control, code maintenance and to collaborate with your colleagues all together! Bruna Piereck Bioinformatics Training Expert VIB Technology Training ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent - Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated] [cid:image005.png@01DA5823.9AD438B0]

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Open PhD position in omics data integration and visualisation
by BeNeLux bioinformaticians forum 04 Jul '24

04 Jul '24

Good afternoon, We have an open PhD position on omics data integration and visualisation at our Augmented Intelligence for Data Analytics Lab at KU Leuven, Belgium. In this research, we will use a visual analytics approach (combining interactive data visualisation with unsupervised machine learning methods such as topological data analysis) to look at patterns in gut microbiome, environmental microbiome and pollutants in the water flea. For more information and to apply, see the KU Leuven jobsite at https://www.kuleuven.be/personeel/jobsite/jobs/60355154 The deadline for application is 28 July 2024. Looking forward to your applications, Jan Aerts -- Prof Jan Aerts Augmented Intelligence for Data Analytics (AIDA) Lab Department of Biosystems, KU Leuven, Belgium +32 16 32 21 40 https://www.biw.kuleuven.be/biosyst ; https://vda-lab.github.io

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Call for Papers: BNAIC/BeNeLearn 2024 Conference
by BeNeLux bioinformaticians forum 04 Jul '24

04 Jul '24

Dear Colleagues, We are pleased to announce the call for papers for the upcoming BNAIC/BeNeLearn 2024 conference, the premier AI and ML event for Belgium, the Netherlands, and Luxembourg. This year's combined 36th BNAIC and 33rd BeNeLearn conference will be held from November 18-20, 2024, at Utrecht, the Netherlands. We invite researchers to submit their unpublished original research in all areas of Artificial Intelligence and Machine Learning. We especially encourage submissions on interdisciplinary topics. High-quality research already published in international AI-related conferences or journals is also welcome for presentation and will be published as extended abstracts. Submission Categories: 1. Type A: Regular Papers – Original research, position, and review papers (up to 14 pages). 2. Type B: Encore Abstracts – Abstracts of recently published work (up to 2 pages). 3. Type C: Demonstration Abstracts – Proposals for demos with a short video (up to 2 pages). 4. Type D: Student Oral and Poster Abstracts – Research by Bachelor and Master students (up to 2 pages). 5. Type E: Late Breaking Poster Abstracts – Ongoing research (up to 2 pages). Important Dates: * Abstract Submission (Type A): August 23, 2024 * Paper Submission (All Types except Type E): August 30, 2024 * Bachelor/Master Thesis Fellowship Application: August 30, 2024 * Late Breaking Poster Submission (Type E): October 8, 2024 * Author Notifications: October 4, 2024 * Camera Ready Submission: October 25, 2024 Accepted contributions will be included in the non-archival conference pre-proceedings. Selected Type A papers will be invited to submit to the post-proceedings in the Springer CCIS series. For more details on submission guidelines and topics of interest, please visit the conference website at BNAIC/BeNeLearn 2024.<https://bnaic2024.sites.uu.nl/call-for-papers-2/> We look forward to your contributions and to welcoming you to Utrecht for an inspiring conference. Best regards, BNAIC/BeNeLearn 2024 Organizing Committee

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Submission Deadline Extension - 36th IEEE International Conference on Tools with Artificial Intelligence
by BeNeLux bioinformaticians forum 01 Jul '24

01 Jul '24

Dear Colleagues, The 36th IEEE International Conference on Tools with Artificial Intelligence (ICTAI) organizing committee is inviting you to submit your research papers. The conference will be held in person, from October 28th till October 30th, 2024, in Herndon, Virginia, USA. Topics include (but not limited to): 1. AI Foundations 2. AI in Domain-specific Applications 3. AI in Computer Systems 4. AI in Data Analytics, Data Mining and Big Data 5. AI in Smart Cities 6. Machine Learning 7. Knowledge Representation, Reasoning, Cognition 8. AI and Decision Systems 9. Uncertainty in AI 10. Natural Language Processing 11. AI and Societal Impact Website: https://ictai.computer.org/2024/ Important Dates Paper submission: July 15, 2024 Acceptance notification: August 25, 2024 Camera-ready: September 23, 2024 Conference: October 28th - October 30th To submit your manuscript, please use the following link: https://easychair.org/conferences/?conf=ictai2024 For more information, please don't hesitate to contact the General Chair Dr. Manolis Koubarakis (National and Kapodistrian University of Athens) at koubarak(a)di.uoa.gr, Co-Program Chairs Dr. Nikolaos Bourbakis (BAIF) at drbourbakis(a)gmail.com and Dr. Jessica Lin (George Mason University) at jessica(a)gmu.edu<mailto:jessica@gmu.edu> and Financial & Registration Chair Dr. Alexiou (Kennesaw State University) at malexiou(a)kennesaw.edu. We look forward to your submissions. Sachin Sharma ICTAI 2024 Publicity Chair

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BioSB course program 2024: YOU DON'T WANT TO MISS THIS!
by BeNeLux bioinformaticians forum 30 Jun '24

30 Jun '24

Dear Colleagues, We are proud to present our new course schedule in the BioSB series, please see the attachment. Be welcome to join us! Click on the links in the form for more information and possible registration Don't want to open an attachment? You definitely don't want to miss these courses: Multi-omics and Data Sciences in Complex diseases<https://www.dtls.nl/courses/multi-omics-and-data-sciences-in-complex-diseas…> (23-27 Sept, Maastricht) Computational Metagenomics<https://www.dtls.nl/courses/computational-metagenomics-advanced/> (14 - 16 Oct, Wageningen) Single-Cell Analysis<https://www.dtls.nl/courses/single-cell-analysis-2024/> (29 Oct - 01 Nov, Rotterdam) Intergrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-2024-funda…> (9-13 Dec, Wageningen) Constraint-based Modeling<https://www.dtls.nl/courses/constraint-based-modeling-introduction-and-adva…> (10 - 14 Feb 2025, Wageningen) Advance Notice BioSB Hot Topics Symposium: On 22 October another Hot Topic Seminar will be organized in Amsterdam (13:00 - 17:00) Bioinformatics methods for pathogen surveillance More information will follow soon on our Hot Topics website<https://www.dtls.nl/biosb/hottopics/> Did you know that our participants are always very enthusiastic about these informal but highly educational events? And these meetings are even for FREE! Build on your early career network: mark your calendar and register in August! I look forward to welcoming you at one of our events! Kind regards, Petra Aarnoutse, BioSB community managers [cid:part1.50wucx7R.RfXVaLoj@health-RI.nl]

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PhD Position at TUDelft on biologically-inspired machine learning
by BeNeLux bioinformaticians forum 26 Jun '24

26 Jun '24

Enhancing plant resilience through biologically-inspired machine learning Delft University of Technology Delft Bioinformatics Lab Netherlands ZH Delft www.tudelft.nl/over-tu-delft/werken-bij-tu-delft/vacatures/details?jobId=17…<https://www.tudelft.nl/over-tu-delft/werken-bij-tu-delft/vacatures/details?…> Description We are seeking a highly motivated PhD candidate to join our research team focused on enhancing plant resilience using cutting-edge data analysis and machine learning techniques. This exciting opportunity will involve designing and integrating biological knowledge into machine learning models to uncover mechanisms controlling plant resilience. The ultimate goal is to connect these findings with simulation models to predict how plants respond to environmental stresses such as drought and extreme temperatures, supporting plant breeding industry to develop crops that can withstand combinations of stresses brought by a changing climate. The project is part of the Crop-XR program, a highly collaborative 10-year national initiative of universities and industry, with a mission to grow resilient crops developed by a data-driven design. Key Challenges: - Develop and implement biologically-inspired machine learning algorithms aimed at identifying gene regulatory networks that influence plant resilience. - Integrate spatial and temporal data to establish connections between gene modules and specific plant organs and developmental stages. - Utilize predictive modeling to identify key genes with significant impacts on stress resilience, thereby pinpointing potential targets for the breeding of more resilient plant varieties. - Collaborate closely with modelers and plant biology experimenters to validate and enhance computational models, ensuring their accuracy and applicability. - Contribute to the integration of mechanistic and machine learning models to simulate how plants respond to environmental changes and leverage these simulations to propose new experiments that generate "smart data" for ongoing model refinement and improvement. Benefits: - Opportunity to work on cutting-edge research with significant real-world impact. - Collaborative and dynamic research environment. - Access to state-of-the-art facilities and resources. - Support for professional development and attendance at international conferences. This PhD position is positioned within the Delft Bioinformatics Lab, part of the Computer Science department of the Delft University of Technology under supervision of Prof. Marcel Reinders. The PhD will be done in close collaboration with the Bioinformatics Group at Wageningen University, and co-supervised by Prof. Dick de Ridder. ________________________________ Qualifications - A Master's degree in Computer science, Artificial Intelligence (AI), Computational Biology, Bioinformatics, or a related field with an affinity to plant sciences. - Strong background in machine learning and data analysis. - Experience with biological data integration and simulation modeling. - Excellent programming skills (e.g., Python, R) and familiarity with machine learning libraries. - Strong analytical and problem-solving skills. - Ability to work independently and as part of a multidisciplinary team. - Strong interpersonal communication and collaboration abilities - Good communication skills and proficiency in English. Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis. For more details please check the Graduate Schools Admission Requirements. ________________________________ Start date As soon as possible ________________________________ How to Apply Please use the online application form on the vacancy website: www.tudelft.nl/over-tu-delft/werken-bij-tu-delft/vacatures/details?jobId=17…<https://www.tudelft.nl/over-tu-delft/werken-bij-tu-delft/vacatures/details?…> ________________________________ Contact Marcel Reinders m.j.t.reinders(a)tudelft.nl<https://careers.iscb.org/jobs/view/%3ca%20%20href=%22mailto:m.j.t.reinders@…>

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youngNMC Symposium 2024 in Ghent!
by BeNeLux bioinformaticians forum 26 Jun '24

26 Jun '24

📣 Exciting Opportunity for Early Career Scientists! Are you passionate about metabolomics and eager to enhance your skills? Join us at the YoungNMC Symposium 2024 in Ghent, Belgium! 📅 Event Date: September 4th, as a pre-meeting of the Benelux Metabolomics Days 2024 📍 Location: Ghent, Belgium 🗣️ Keynote Speakers: Prof. Kris Laukens (University of Antwerp) and Dr. Marco Giampà (VIB Metabolomics Core Leuven) Don't miss out on this chance to learn from leading experts and connect with peers. Register here by July 31st! With kind regards, On behalf of the YoungNMC committee, Sandrien Desmet Sandrien Desmet, PhD - Metabolomics expert VIB Metabolomics Core Ghent VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 61<callto:+32(0)9%20331%2038%2061> https://metabolomicscore-gent.sites.vib.be/en [240516 youngnmc_banner]

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Course: Multi-omics and data sciences in complex diseases - registration open!
by BeNeLux bioinformaticians forum 24 Jun '24

24 Jun '24

We are happy to inform you that registration is open for our exciting new five-day course: Multi-omics and data sciences in complex diseases Date: September 23-27, 2024. Venue: Randwijck campus, Maastricht University, The Netherlands. Target audience: PhD candidates, postdocs, and senior researchers from academia as well as industry. Organisers: Collaboration between Maastricht University and BioSB, the Netherlands Bioinformatics and Systems Biology research school. Course contents: The course will cover experimental technologies and integrative data analysis approaches for the study of complex phenotypes. We will address approaches to study genetic and environmental interactions; new developments in NGS and epigenomics applications and workflows; integrative multi-omics data analysis using multivariate and machine learning approaches; as well as knowledge integration tools and methods to extract biologically meaningful information. Registration and more information: BioSB: https://www.dtls.nl/courses/multi-omics-and-data-sciences-in-complex-diseas… Further questions: Course organisers Dr. Lars Eijssen (l.eijssen(a)maastrichtuniversity.nl<mailto:l.eijssen@maastrichtuniversity.nl>) or Dr. Rachel Cavill (rachel.cavill(a)maastrichtuniversity.nl<mailto:rachel.cavill@maastrichtuniversity.nl>) _________________________ Lars M.T. Eijssen Assistant professor Dept. of Bioinformatics-BiGCaT Dept. of Psychiatry and Neuropsychology Maastricht University

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AIHA 2024 - 3rd International Workshop on Artificial Intelligence for Healthcare Applications (AIHA 2024)
by BeNeLux bioinformaticians forum 21 Jun '24

21 Jun '24

*Call for papers: **International Workshop on Artificial Intelligence for Healthcare Applications <https://aida.unicas.it/AIHA2024/index.html#motivation-section>**(AIHA 2024) <http://lia.unicas.it/patrech2019/> - December 1, 2024"* (PDF <https://aida.unicas.it/AIHA2024/download/CFP-AIHA2024.pdf>) The workshop will be held in conjunction with ICPR 2024 <https://icpr2024.org/> (27th International Conference on Pattern Recognition, Kolkata, India, December 1-5, 2024) AIHA 2024 will be held in* hybrid mode*, but the organizers encourage the participants to attend the workshop physically. The workshop aims to present recent advances in AI techniques for healthcare applications. The workshop aims to bridge artificial intelligence and machine learning researchers and practitioners with clinicians interested in exploiting AI potentialities in their clinical practice. *TOPICS* Topics include, but are not limited to, the following: - Biomedical image analysis - Data analytics for healthcare - Automatic disease prediction - Automatic diagnosis support systems - Genomic and proteomic data analysis - Artificial Intelligence for personalized medicine - Machine Learning as a tool to support medical diagnoses and decisions - Machine learning for diagnosis and rehabilitation - Neural signal analysis for diagnosis assistance - Physiological signals processing - Gait analysis - Therapy selection - Brain-computer interface for healthcare - Biomechatronics for medicine - Neuromotor rehabilitation - Machine learning approaches in rehabilitation - Motion analysis for healthcare *DATES* Paper Submission: July 12, 2024 Notification of Acceptance: September 6, 2024 Full Paper Submission: September 27, 2024 *SUBMISSION DETAILS* Contributions may be submitted in one of the following forms: - Full research papers (12-15 pages) - Short research papers (6-11) - Simple Abstracts (1-4 pages) Full research papers should present original unpublished work. Simple abstracts should describe original work in progress or a summary of a full paper. At least one author of each accepted work has to register for the conference, attend the conference, and present his work. *Accepted papers will be included in the ICPR 2024 Conference Proceedings*, which will be published by Springer in the Lecture Notes in Computer Science series (LNCS). Accepted abstracts describing unpublished work will be considered for publication of extended versions (at least 6 pages) in the same volume. Submission instructions are available at this link <https://aida.unicas.it/AIHA2024/submission.html#sub-id> *CHAIRS * Nicole Dalia Cilia <https://www.researchgate.net/profile/Nicole-Cilia>, Kore University of Enna, Italy Francesco Fontanella <https://sites.google.com/unicas.it/fontanella/>, University of Cassino and Southern Lazio, Italy Claudio Marrocco <https://unicas-public.gomp.it/PublicData?mode=professor&name=Claudio&lastNa…>, University of Cassino and Southern Lazio, Italy *CONTACT* Prof. Francesco Fontanella, fontanella(a)unicas.it -- Francesco Fontanella, PhD Associate Professor The University of Cassino and Southern Lazio, Italy https://sites.google.com/unicas.it/fontanella/

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Secure your seat at the Computational protein design course in Brussels 11-12 September
by BeNeLux bioinformaticians forum 20 Jun '24

20 Jun '24

Hi all, Take your chance to immerse yourself in computational protein design: predicting the effect of point mutations on protein stability using Rosetta, creating protein fusions and chimeras as well as protein design with RFDiffusion and ProteinMPNN. Secure your seat via https://training.vib.be/all-trainings/introduction-computational-protein-de… Looking forward to welcoming you in Brussels on September 11th and 12th. Cheers, Alex

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