June 2024 - 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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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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ESSAI 2024 Early Registration deadline extended
by BeNeLux bioinformaticians forum 17 Jun '24

17 Jun '24

ESSAI 2024 EARLY REGISTRATION DEADLINE EXTENDED TO JUNE 30TH European Summer School on Artificial Intelligence (ESSAI&ACAI 2024) - Call for participation https://essai2024.di.uoa.gr/ -------------------------------------------------------------------------------------------- (Apologies for multiple postings) The European Summer School on Artificial Intelligence and the Advanced Course on Artificial Intelligence invite participants from all over the world to attend its courses and advanced tutorials from July 15 to July 26, 2024 (two weeks). The school offers 30 week long courses and 11 two hour long advanced tutorials. Registration is now open at https://essai2024.di.uoa.gr/registration.html Participants can register for one week only or for the whole school. There is also the option of attending the schools remotely. The provisional schedule of the school is available at https://essai2024.di.uoa.gr/schedule.html Fellowships funded by EurAI covering registration will be offered to 30 selected students. Details are available at https://essai2024.di.uoa.gr/EurAI-travel-grants.html If you are affiliated with an organization which is a member of the Network of Excellence TAILOR (https://tailor-network.eu/) you will be able to attend with a free registration (details appear on the registration page and have been sent to TAILOR members). If you have any questions, please reach out to the Local Chair Manolis Koubarakis at koubarak(a)di.uoa.gr

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Call For Papers - 36th IEEE International Conference on Tools with Artificial Intelligence - Oct. 28 - Oct. 30 2024 - Herndon, VA, USA
by BeNeLux bioinformaticians forum 14 Jun '24

14 Jun '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 1, 2024 Acceptance notification: August 18, 2024 Camera-ready: September 16, 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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CFP: MCMI 2024 - Workshop on Multi- and Cross-Modal Information for Enhanced Pattern Recognition
by BeNeLux bioinformaticians forum 06 Jun '24

06 Jun '24

[image: logo-icpr-2024.png] CALL FOR PAPERS *MCMI Workshop 2024* - Multi- and Cross-Modal Information for Enhanced Pattern Recognition Co-located with the 26th International Conference on Pattern Recognition (ICPR 2024). MCMI 2024 @ ICPR 2024 Website: mcmi2024.unikore.it December 1, 2024, Kolkata, India *Important Dates* Full papers submission: July 1, 2024 Notification of paper acceptance: September 1, 2024 Camera-ready of accepted papers: September 27, 2024 Workshop: December 1, 2024 *Goal of the Workshop* The MCMI workshop aims to explore the convergence and fusion of information from multiple modalities, forming the backbone of modern AI systems for robust pattern recognition and understanding. This interdisciplinary workshop encourages collaboration across fields such as audio processing, computer vision, and natural language processing. It serves as a venue to discuss recent findings, share innovative methodologies, and address future directions in multimodal pattern analysis. *Topics of interest*We invite submissions of high-quality papers reporting original research and significant new work not under review or published elsewhere in the following areas: Technological Advancements in Multimodal Systems Multimodal Fusion Strategies Deep Learning Architectures for Multimodal Fusion Cross-Modal Feature Extraction and Learning Audio-Visual Speech Recognition Scene and Object Recognition from Audio-Visual Cues Temporal Dynamics in Multimodal Data Processing Robustness and Generalization across Diverse Modalities Applications and Interaction in Multimodal Systems Emotion Recognition in Multimodal Data Natural Language Processing for Multimedia Content Multimodal Datasets and Benchmarks Novel Interaction Paradigms for Multimodal Data Acquisition Security, Ethics, and Transparency in Multimodal Systems Ethical Considerations in Multimodal Data Processing Privacy-Preserving Multimodal Learning Explainable AI (XAI) in Multimodal Systems Security and Robustness in Multimodal Systems Adversarial Attacks and Defense in Multimodal Systems *Submission Guidelines* Papers must be formatted according to Springer's LNCS template and submitted via the workshop's submission system. Submissions should present substantial new work and should not be under review elsewhere: *Paper length*: up to 10 pages in Springer LNCS format, including figures, tables, and references. *Submission link*: https://cmt3.research.microsoft.com/MCMI2024/ *Peer review*: Single-blind Accepted papers will be published in the Lecture Notes in Computer Science series by Springer, and at least one author of each accepted paper must register for the workshop by the camera-ready deadline. *Workshop Organizers* Moreno La Quatra, Kore University of Enna, Italy Nicole Dalia Cilia, Kore University of Enna, Italy Vincenzo Conti, Kore University of Enna, Italy Salvatore Sorce, Kore University of Enna, Italy Giovanni Garraffa, Kore University of Enna, Italy Valerio Mario Salerno, Kore University of Enna, Italy For questions regarding the submission process, please contact the organizers at mcmi(a)unikore.it. *Diversity and Inclusion Statement* MCMI 2024 is committed to fostering an inclusive environment that values diversity. We thank our participants for their cooperation in helping us create a safe and positive workshop experience for everyone.

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