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DTSTART;TZID=Europe/Stockholm:20261027T110000
DTEND;TZID=Europe/Stockholm:20261027T120000
DTSTAMP:20260916T093614Z
CREATED:20260916T093613Z
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SUMMARY:When every hypothesis is published: AI and the exploitation of Open Science Assets
DESCRIPTION: Open science has given us a shared public good\, in the form of publications and public datasets\, free to access and reuse by anyone. But AI can now generate\, test and write up hypotheses against those assets faster than our community can evaluate them. This seminar looks at what happens to open repositories when they become inputs to industrial-scale hypothesis generation. We will also provide case studies of outputs that can be generated in under an hour\, and examples of the impact on the literature (including the de facto banning of some open science resources altogether). It also asks what data stewards\, funders and publishers can realistically do about it. \n\n\n\nPresenters:  \n\n\n\nMatt Spick Institute for People-Centred AI\, University of Surrey\, UK \n\n\n\nMatt Spick is a Lecturer in Health and Biomedical Data Analytics at the University of Surrey and a member of the Institute for People-Centred AI. His research focuses on AI\, research integrity\, Open Science and the detection of problematic scientific publishing. \n\n\n\n Danny Maupin School of Health Sciences\, University of Surrey\, UK \n\n\n\nDanny Maupin is a Research Fellow in Health Data Sciences at the University of Surrey. His research spans digital health\, AI and research integrity\, including how generative AI is changing research practices and the use of Open Science resources. \n\n\n\nThe session will conclude with an open Q&A\, providing an opportunity to ask questions and interact with presenters. \n\n\n\nMore Information\n\n\n\nThis event is part of the SciLifeLab Open Science seminar series\, an event series by the SciLifeLab Data Centre and NBIS joint Data Management team.The goal of the events in this seminar series is to provide interesting interactive seminars around topics related to Research Data Management and Open Science in general\, and to foster discussions around best practices. \n\n\n\nResearch Data Management (RDM) concerns the organization\, storage\, preservation\, and sharing of data that is collected and analyzed during a research project. Proper planning and management of research data will make project management easier and more efficient while projects are being performed. It also facilitates sharing and allows others to validate as well as reuse the data.Open Science is a set of principles and practices that aim to make scientific research from all fields accessible to everyone for the benefits of scientists and society as a whole. Open science is about making sure not only that scientific knowledge is accessible but also that the production of that knowledge itself is inclusive\, equitable and sustainable. \n\n\n\nThe events are open to everyone working at or affiliated with a Swedish research institute or university. We welcome all researchers\, educational professionals\, staff\, RDM professionals\, and others with an interest in life sciences\, from all university levels. The events are informal and inclusive\, so feel welcome to join and participate in our interesting discussions! \n\n\n\nThe events will be recorded and published openly after the seminars on the SciLifeLab YouTube channel. The slides will be made available at our SciLifeLab Data Repository.More information about SciLifeLab Data Centre and NBIS joint Open Science seminar series: https://www.scilifelab.se/data/scilifelab-data-management-seminar-series/ \n\n\n\nIf you have suggestions for topics or presentations\, please contact us at data-management@scilifelab.seFor more information or inquiries\, please contact us at  data-management@scilifelab.se
URL:https://www.scilifelab.se/event/when-every-hypothesis-is-published-ai-and-the-exploitation-of-open-science-assets/
LOCATION:Online event via Zoom
ORGANIZER;CN="Open Science Seminar Series":MAILTO:data-management@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261102T100000
DTEND;TZID=Europe/Stockholm:20261102T153000
DTSTAMP:20261006T200937Z
CREATED:20260916T073033Z
LAST-MODIFIED:20261006T200937Z
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SUMMARY:Hands-on Workshop: Developing AI Agents in Life Sciences (Lund)
DESCRIPTION:We are delighted to invite you to join our upcoming workshop on “Developing AI Agents in Life Sciences”\, organized by SciLifeLab Data Centre and SciLifeLab Lund site in collaboration with the eScience Hub at Lund University. AI agents are emerging as autonomous systems that orchestrate scientific workflows by interacting with digital tools and data sources. These have various implications for life science research. They can\, for example\, simplify complex analyses by automating data integration\, run computational models\, and coordinate experimental steps\, making research pipelines more efficient and reproducible. In this on-site hands-on workshop held at Belfragesalen\, BMC D15 (Klinikgatan 32) in Lund\, we will introduce and discuss AI Agents in life science\, and engage in collaborative practical sessions. Welcome! \n\n\n\nDate: 2026-11-02Time: 10.00-15.30 (coffee will be served from 9.30). Fika and lunch provided free of charge. Location: room Belfragesalen\, BMC D15\, Klinikgatan 32\, Lund. No remote participation. \n\n\n\nTarget audience: Researchers\, PhD students\, research infrastructure interested in learning more about and trying hands-on exercises with AI Agents. Participants with any university affiliation and industry researchers are welcome. Basic Python programming skills are required; previous experience working with Jupyter notebooks would be helpful. Participants must bring their own laptop. \n\n\n\nRegistration: We expect many to be interested in attending this event. After we reach max capacity\, we will open a waitlist. If you cannot join\, please cancel your registration as soon as possible to make your spot available for someone else. Please add dietary restrictions to your registration. \n\n\n\n\nRegister for the workshop\n\n\n\n\nSpeakers and Facilitators:  Chris Long Huynh (PhD candidate\, Uppsala University)\, and Mahbub Ul Alam and Johan Alfredéen (Data Engineers (AI) at SciLifeLab Data Centre). \n\n\n\nThe workshop will feature a series of engaging presentations\, interactive discussions\, and collaborative sessions focusing on: \n\n\n\n\nIntroduction to AI agent technologies\n\n\n\nApplications\, opportunities and challenges of AI Agents in life science\n\n\n\nHands-on tutorials with reasoning models\, LangChain and MCP servers\n\n\n\nDiscussions on the role of AI agents in shaping the future of life science\n\n\n\n\nAgenda \n\n\n\n09:30-10:00 Light breakfast and networking \n\n\n\n10.00-10.15 Presentation session 1: Introduction: Exploring how AI agents can transform life sciences. Speaker: Johan Alfredéen. \n\n\n\n10.15-10.30 Demonstration Session: AI agents in action. Facilitators: Mahbub Ul Alam. \n\n\n\n10:30-12:00 Hands-on Session 1: Developing AI agents with LangChain & ReAct. Session Facilitators: Dinh Long Huynh\, Mahbub Ul Alam.  \n\n\n\n12:00-13:00 Lunch and networking \n\n\n\n13:00-13:30 Continuation of Hands-on Session 1: Developing AI agents with LangChain & ReAct. \n\n\n\n13:30-15:00 Hands-on Session 2: AI agent collaboration with the Model Context Protocol (MCP). Session Facilitators: Mahbub Ul Alam\, Johan Alfredéen\, Dinh Long Huynh. \n\n\n\n15:00-15:15 Presentation Session 2: Deploying AI Agents: Legal\, Technical\, and Practical Considerations. Speaker: Johan Alfredéen. \n\n\n\n15:15-15:30 Concluding Session: Open Q&A  \n\n\n\n15:30 Fika and networking \n\n\n\nRegistration: Please add dietary restrictions to your registration. If you cannot join\, please cancel your registration. \n\n\n\nThis event is a organised by SciLifeLab Data Centre and SciLifeLab Lund in collaboration with the eScience Hub at Lund University. For questions please contact  open-llm@scilifelab.se .
URL:https://www.scilifelab.se/event/ai-agents-in-life-science-lund/
LOCATION:Belfragesalen\, BMC D15\, Klinikgatan 32\, Lund\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261103T100000
DTEND;TZID=Europe/Stockholm:20261103T170000
DTSTAMP:20261006T100551Z
CREATED:20260618T112246Z
LAST-MODIFIED:20261006T100551Z
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SUMMARY:Research Data Management in Life Science - Gothenburg
DESCRIPTION:Make the most of your research data\n\n\n\nHow can you effectively manage\, share and safeguard your research data while following current requirements and best practices? \n\n\n\nJoin SciLifeLab Data Centre\, National Bioinformatics Infrastructure Sweden (NBIS) and SciLifeLab Gothenburg for an interactive event on research data management in the life sciences. Local and national experts will provide practical guidance and discuss available support for research data handling\, GDPR\, FAIR principles and Open Science. \n\n\n\nThe event is aimed at life-science researchers and research infrastructure staff in the Gothenburg area who want to strengthen their data management practices and learn more about available support. \n\n\n\nThe format will be informal and interactive\, with plenty of opportunities to ask questions\, share experiences and join the discussion. \n\n\n\nWelcome to join us! \n\n\n\nRegister here\n\n\n\nRegistration deadline: Tuesday\, October 27\, 2026 \n\n\n\nPROGRAM\n\n\n\n10.00-10.15: Welcome coffee/tea \n\n\n\n10.15-10.30: Introduction \n\n\n\n10:30-12:00: Writing a strong Data Management Plan (DMP) – Improving the lifecycle of your research data in an AI-aware research landscape\nManaging research data involves a complex web of decisions. How do you ensure that nothing falls through the cracks\, that your data remains secure and organised\, and that your project supports FAIR data principles from start to finish? A strong Data Management Plan (DMP) helps researchers think through these questions before problems arise. \n\n\n\nThis hands-on workshop emphasises data management planning across all phases of a research project\, from data collection and documentation to storage\, sharing\, preservation\, and reuse. Participants will gain direct access to the Data Stewardship Wizard (DSW) tool and begin drafting a customised DMP tailored to life science research projects. \n\n\n\nNew for this year\, the workshop will also briefly address the growing role of AI tools in DMP writing. Many researchers can now ask an AI system to generate a DMP in seconds\, but a well-written text is not the same as a well-considered plan. We will discuss how AI can support drafting\, reflection\, and quality control\, while also highlighting the risks of generic\, incomplete\, or misleading answers. The focus will remain on helping researchers understand the decisions behind their DMPs and use available tools responsibly. \n\n\n\n \n\n\n\n \n\n\n\n\n12.00-13.00: Lunch \n\n\n\n13.00-14.30: Handling personal data in Life Science – Navigating GDPR\, Swedish legislation\, and responsible AI use in research\nAre you confident in how your research project documents\, processes\, and protects personal data? Life science research often involves complex data flows\, multiple actors\, and sensitive information\, making it essential to understand both the legal requirements and the practical responsibilities involved. \n\n\n\nThis seminar guides participants through the legal landscape\, from the GDPR to relevant Swedish national legislation. Using a practical research scenario\, we will clarify essential roles and concepts\, including: \n\n\n\n\nResearch principal (forskningshuvudman): Understanding the role and responsibilities of the organisation hosting the research.\n\n\n\nData controllers vs. processors: Identifying who is responsible for each stage of data processing\, including storage\, analysis\, sharing\, and long-term management.\n\n\n\nSensitive data: Understanding how biomedical research data should be handled\, protected\, and shared securely\, including practical considerations for services such as FEGA Sweden.\n\n\n\n\nNew for this year\, the seminar will also briefly address how GDPR affects the use of AI tools such as ChatGPT in research. Generative AI can support tasks such as drafting\, summarising\, coding\, documentation\, and project planning\, but it can also introduce risks when personal data\, sensitive data\, unpublished research material\, or confidential project information are entered into external tools. \n\n\n\nWe will discuss why AI use is not only a technical question\, but also a legal and organisational one: Who is responsible for the processing? What data can be shared with an AI tool? What should never be entered? How do researchers balance the benefits of AI with confidentiality\, accountability\, and compliance? \n\n\n\nThe aim is to help researchers make informed decisions when handling personal data in life science research\, including in an increasingly AI-supported research environment. \n\n\n\n\n14.30-15.30: Marketplace: an interactive exhibition – including fika\nVisit the Interactive Marketplace to explore local and national research data management services in an engaging and informal setting. Meet experts\, discover practical support and tools\, join interactive discussions\, and learn how different services can support your research — all through inspiring stands\, conversation-focused posters\, and hands-on activities like the Data Management Ferris Wheel.Interested in contributing to the Marketplace and showcasing your data management support services? Please contact gothenburg@scilifelab.se. \n\n\n\n\n15.30-17.00: Open source for research – Sharing code the right way\nResearch depends on code\, but without open and FAIR practices\, code can be difficult to understand\, reproduce\, and reuse. Open-source refers to code that is not only available\, but also licensed for free use\, modification\, and sharing. This workshop provides an overview of open and FAIR practices for research code\, and provides practical resources at three different levels; beginner\, intermediate and advanced. Participants will apply these principles in a hands-on tutorial to improve the openness\, transparency\, and reusability of their research code. \n\n\n\n\n \n\n\n\nMore information on Research Data Management and Open Science\n\n\n\nResearch Data Management (RDM) concerns the organization\, storage\, preservation\, and sharing of data that is collected and analyzed during a research project. Proper planning and management of research data will make project management easier and more efficient while projects are being performed. It also facilitates sharing and allows others to validate as well as reuse the data. \n\n\n\nOpen Science is a set of principles and practices that aim to make scientific research from all fields accessible to everyone for the benefits of scientists and society as a whole. Open science is about making sure not only that scientific knowledge is accessible but also that the production of that knowledge itself is inclusive\, equitable and sustainable. \n\n\n\nContact information: NBIS\, SciLifeLab Data Centre – Data Management\, and SciLifeLab Gothenburg. For questions\, please contact gothenburg@scilifelab.se
URL:https://www.scilifelab.se/event/research-data-management-in-life-science-gothenburg/
LOCATION:Birgit Thilander Lecture Hall\, Academicum\, Medicinaregatan 3\, Gothenburg
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2025/05/OpenScience-scaled.jpeg
ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261109T113000
DTEND;TZID=Europe/Stockholm:20261110T123000
DTSTAMP:20261016T081140Z
CREATED:20260413T092109Z
LAST-MODIFIED:20261016T081140Z
UID:10001800-1794223800-1794313800@www.scilifelab.se
SUMMARY:DDLS Annual Conference 2026
DESCRIPTION:The Data-Driven Life Science (DDLS) program\, funded by the Knut and Alice Wallenberg Foundation (KAW)\, warmly welcomes you to the 5th DDLS Annual Conference\, taking place November 9-10\, 2026\, at Aula Magna\, Frescati Campus\, Stockholm. \n\n\n\nTarget Group: Anyone interested in data-driven life science is welcome to attend the Conference. You don´t need to be part of the SciLifeLab & Wallenberg National Program for Data-Driven Life Science\, even though the conference focuses on achievements and highlights program activities. \n\n\n\nThis two-day\, in-person event will highlight DDLS research and activities\, showcase new technologies and services available to researchers across Sweden\, and provide a forum for knowledge exchange and collaboration. Participants will have the opportunity to: \n\n\n\n\nShare and discuss research findings\n\n\n\nExplore ideas and insights across disciplines\n\n\n\nBuild networks for collaboration and career development\n\n\n\nGain perspectives beyond their own fields of expertise\n\n\n\n\nThe conference begins with a light network lunch and registration on November 9 (11:30–12:30) and concludes with a networking lunch on November 10 (12:30–13:30). \n\n\n\nKeynotes\n\n\n\n\n\nLindsay EdwardsDr Lindsay Edwards\, Chief Technology Officer and President of PlatformsRelation Therapeutics\n\n\n\n\n\nKaroline FaustAssociate Professor and head of the Lab of Microbial Systems BiologyKU Leuven\n\n\n\n\n\nPreliminary program\n\n\n\nNovember 9\n\n\n\n11:00Registration opens11:30Light lunch12:30Introduction and WelcomeThree Impactful Problems in Drug Discovery That Might Be Solvable with Machine Learning (and What We Are Doing About Them at Relation Therapeutics)Lindsey Edwards\, CTO & President of Platforms\, Relation Therapeutics\, London\, UKPanel DiscussionModerators: Ola Engkvist\, Executive Director AstraZeneca & Adjunct Professor Chalmers University of Technology; Tuuli Lappalainen\, Professor\, KTH/SciLifeLab1. Gianfranco Grompone\, PhD\, CSO\, BioGaia AB & Affiliated Scientist\, Univ. of Gothenburg2. Lina Hultin Rosenberg\, Director Data & Analytics\, R&D\, Olink / Thermo Fisher3. Peetra Magnusson\, PhD\, Assoc. Prof.\, Dept. of IGP & DDLS Director\, Uppsala Univ.4. Patrik Rydén\, PhD\, Prof. of Math Statistics & IDS Director\, Umeå University5. Lindsey Edwards\, CTO & President of Platforms\, Relation Therapeutics\, London\, UK14:00Poster session I (odd numbers) with Coffee15:00DDLS Fellows talksSteering AlphaFold through the distogramNicholas Pearce\, UUPredictors of genome-wide variation in the effects of new mutationsJennifer James\, UUTowards autoregularization of reconstruction and datamining in cryo-EMBjörn Forsberg\, LiU16:00Meet the new DDLS Fellows16:15Presentation of NAISSErik Lindahl\, LiU\, director of NAISS16:30Poster session II (even numbers) with Mingle17:30End of day 1\n\n\n\nNovember 10\n\n\n\n09:00DDLS Fellows talksJosé Cerca\, NRMLeveraging population genomic data to understand clonal hematopoiesis and blood cancer riskAbhishek Niroula\, GU10:00Coffee break10:45Top-Down and Bottom-Up Exploration of Alternative Community Types in the Human Gut MicrobiomeKaroline Faust\, Associate Professor\, KU Leuven\, Belgium12:40Presentations of DDLS funded projectsLearning 3D genome dynamics from heterogeneous dataJohan Elf\, UUMultimodal AI-based Precision Diagnostics and Decision Support for Breast Cancer (AID4BC)Mattias Rantalainen\, KITIMED: Time-Resolved Imaging and Multi-Channel Evaluation of Cellular DynamicsRocio Mercado\, ChalmersOla Spjuth\, UUMicroscopy Foundation Model & AI-Ready Data Hub for Smart MicroscopyHanzhao Zhang\, LiUSwedish Metabarcoding Network (SMN)Tobias Andermann\, UUTissUUmaps RDCPCarolina Wählby\, UUCRITICAL MICROBES – Comprehensive Research on InfecTIons Complications Across the Lifespan – MICROBiology Epidemiology in SwedenAnne-Marie Connolly\, UmUConclusion12:40Lunch and networking13:30Optional workshops organised by SciLifeLab Data Centre:– Workshop 1: How to use LLMs to present results from your research project as a web application (register here)– Workshop 2: Public hosting of Shiny apps: hands-on workshop (register here)\n\n\n\nSee separate registration page to sign up for workshops on November 10. \n\n\n\nKeynotes\n\n\n\nLindsey Edwards\nTitle: Three impactful problems in drug discovery that might be solvable with machine learning (and what we are doing about them at Relation Therapeutics).Bio: Lindsay is an internationally recognised leader at the interface of AI\, machine learning\, computational biology\, and drug discovery. Across both academia and industry\, he has consistently advanced the translation of science into medicine using computational sciences. In his academic career in Australia and at King’s College London\, he developed innovative computational approaches to human metabolism\, hypoxia\, and respiratory physiology. His teams pioneered methods for modelling metabolic and transcriptomic data\, applying these to diverse clinical contexts including respiratory disease\, diabetes\, hypertension\, Parkinson’s disease\, and critical illness. In industry\, Lindsay founded one of the first pharmaceutical data science divisions at GSK\, embedding machine learning and data science into every stage of the discovery pipeline. As CTO of Relation Therapeutics\, he has raised over $200M\, creating one of the most significant TechBio companies rooted in scientific translation (including forging a landmark platform multi billion dollar collaboration with GSK). His role on the Scientific Advisory Board of the Schmidt Centre at the Broad Institute of Harvard and MIT further reflects his international collaborative reach\, engaging with leading global scientists at the intersection of AI and life sciences. His publication record—over 40 papers in top biomedical journals (NEJM\, JAMA\, PNAS) and premier AI/ML venues (NeurIPS\, ICML\, ICLR)—is exceptionally rare\, demonstrating dual impact across medicine and computational science. He was recently elected a Fellow of the Academy of Medical Sciences. \n\n\n\n\nKaroline Faust\nTitle: Top-down and bottom-up exploration of alternative community types in the human gut microbiome.Bio: Karoline Faust is an Associate Professor at KU Leuven who heads the Lab of Microbial Systems Biology\, which focuses on investigating microbial community dynamics in silico and in vitro. In particular\, her team is studying interactions between human gut bacteria and the resulting dynamics with synthetic communities in controlled conditions. In addition\, the team develops new tools for the analysis of microbiome data\, specifically the analysis of microbial networks. The group’s work is thus situated at the intersection of bioinformatics\, systems biology\, and microbial ecology.Abstract: The human colon is home to a diverse microbial community\, the gut microbiome\, which impacts the host’s health and well-being. The composition of the gut microbiome varies across persons\, forming distinct groups known as enterotypes\, which have been linked to differences in host characteristics and behavior such as diet. However\, these environmental factors do not explain observations of transient perturbations leading to community shifts\, which persist even after the perturbation ceased. In my talk\, I will discuss multi-stability as an alternative hypothesis to explain enterotypes. I will present simulations and in vitro experiments that support the idea that alternative community types observed in the gut can be interpreted as different states of a multi-stable community. Investigating the causes behind alternative community types is relevant\, since they affect the interpretation of microbiome data. In particular\, multi-stability implies that different gut microbial community compositions can be due to past perturbations rather than current differences between hosts.Affiliation: Molecular Bacteriology Unit (Rega Institute)\, Department of Microbiology\, Immunology and Transplantation\, KU Leuven \n\n\n\n\nErik Lindahl\nTitle: Presentation of NAISS \n\n\n\nBio:  \n\n\n\nAbstract: \n\n\n\nAffiliation: LiU\, director of NAISS \n\n\n\n\nDDLS Fellows Talks\n\n\n\nBjörn Forsberg\nTitle: Towards autoregularization of reconstruction and datamining in cryo-EM \n\n\n\nBio: Researcher in structural biology and method development in cryo-EM \n\n\n\nAbstract: Cryo-EM is the method of choice for visualization of proteins and biomolecules with molecular detail\, permitting multiple states\, binding partners and molecular motions to be visualized with more flexibility than other methods. However\, this is highly dependent on the sample and conditions\, and the wide range of use cases and application details creates a necessity for data processing to be adaptive. Historically\, this has relied on expert users to inject reasonable bias into the processing pipeline\, using deep technical knowledge and elaborate specialized pipelines. Here I will present an overview of how we aim to provide more adaptive control of the data processing\, through construction of natural features that decrease bias with increased meaningful regularization. This also requires a new framework for evaluating performance and better synthetic data for legitimate ground-truth evaluation of current methods of data processing. \n\n\n\nAffiliation: Linköping University \n\n\n\n\nAbishek Niroula\nTitle: Leveraging population genomic data to understand clonal hematopoiesis and blood cancer risk \n\n\n\nBio: Abhishek Niroula is a DDLS Fellow and Assistant Professor at the University of Gothenburg. He received his PhD from Lund University\, where he studied the impact of genetic variation on human health. During his first postdoctoral appointment\, he worked in computational functional genomics to understand the functional impact of genetic variants identified through genome-wide association studies. He subsequently joined the Broad Institute\, where his postdoctoral research focused on pre-cancerous somatic mutations and the development of models to predict an individual’s risk of developing blood cancer. His laboratory at the University of Gothenburg now investigates the biology of pre-cancerous clones\, the mechanisms that regulate their expansion\, and how these clones contribute to human diseases\, including cancer and cardiovascular disease. \n\n\n\nAbstract: Cancer develops through the gradual accumulation of somatic genetic alterations and clonal evolution\, often over many years. Large-scale genomic and health datasets provide new opportunities to detect these changes at an early stage and identify individuals at increased risk of disease. Our lab studies clonal hematopoiesis\, an age-associated expansion of blood cell clones carrying somatic genetic mutations. Clonal hematopoiesis is associated with an elevated risk of blood cancers as well as non-malignant conditions\, including cardiovascular disease. Using genomic data from large population-based cohorts\, we characterize clonal hematopoiesis in individuals without blood cancer and investigate the genetic drivers and regulators of clonal expansion. By integrating genomic information with demographic\, clinical\, and longitudinal health data\, we investigate the factors that influence malignant transformation and develop models for predicting future blood cancer risk. Ultimately\, our work seeks to improve our understanding of the earliest stages of cancer evolution and provide a foundation for identifying individuals who may benefit from closer monitoring or early intervention. \n\n\n\nAffiliation: Department of Medical Biochemistry and Cell Biology\, Institute of Biomedicine\, Sahlgrenska Academy\, University of Gothenburg\, Gothenburg\, Sweden Science for Life Laboratory\, University of Gothenburg\, Gothenburg\, Sweden \n\n\n\n\nNicholas Pearce\nTitle: Steering AlphaFold through the distogram \n\n\n\nBio: Nicholas Pearce is a DDLS Fellow at Uppsala University working on method development within structural biology\, particularly for the identification of weak and dynamic signals in X-ray crystallography and Cryo-EM data. \n\n\n\nAbstract: Since its publication in 2021\, the networks within AlphaFold2/3 have been prodded and probed to understand how to steer the predicted structures to contain desirable features. We now have several methods that allow the imposition of external restraints on the structure predictions\, whether geometric priors or experimental data. However\, existing methods either use a sample-and-prune approach or else the restraint is a weak prior and can be ignored during structure prediction. We present a method for directly optimizing the pair representation within AlphaFold-like structure predictors to produce desirable features in the distogram\, which can be intuitively linked to different kinds of structural restraint. We demonstrate this “resTrain” method in a variety of applications including conformer generation\, docking\, and NMR structure determination. \n\n\n\nAffiliation: Department of Cell and Molecular Biology\, Uppsala University \n\n\n\n\nJosé Cerca\nTitle: \n\n\n\nBio:  \n\n\n\nAbstract: \n\n\n\nAffiliation:   \n\n\n\n\nJennifer James\nTitle: Predictors of genome-wide variation in the effects of new mutations \n\n\n\nBio: As a researcher\, I’m fascinated by new mutations; these provide the vital raw material necessary for evolution and adaptation. New mutations occur regularly\, generating genetic diversity- new heritable variation among individuals. However\, how many of these new mutations generate variation in the traits of the individuals that carry them? And\, most importantly for evolution by natural selection\, how do new mutations impact fitness\, the ability of individuals to survive and reproduce? My work seeks to address these important questions\, using a combination of population genetics and proteomics. \n\n\n\nAbstract: In our recent work\, we assessed how predictive gene features (such as local recombination rate\, level of organisation within gene gene networks\, and gene length) are to the level of selective constraint genes experience\, and assessed how this impacts the effects that new mutations have on such genes. We used data from the full genomes of Mus musculus castaneus (mouse)\, Drosophila melanogaster (fruit fly) and Saccharomyces cerevisiae (yeast)\, and a combination of population genetics and machine learning inference methods. We found that genes with higher connectivity in gene interaction networks and higher levels of expression were under greater selective constraint\, and new mutations in such genes had the strongest deleterious effects.  Our results highlight the value of using gene features collectively to link the genomic architecture\, fitness landscapes\, and patterns of molecular evolution. We also found that genes with the highest proportion of fixed beneficial mutations and therefore the highest rates of adaptive evolution tended to be those that have intermediate levels of selective constraint- i.e.\, not those genes that are under extremely strong negative selection but also not the genes under low levels of selective constraint. These are perhaps the genes in a ‘happy middle ground’- mutations in these genes are able to effect moderate phenotypic change when adaptive evolution is required\, but not so much change that they risk disrupting many systems at once. \n\n\n\nAffiliation: DDLS fellow Uppsala University \n\n\n\n\nRegistration\n\n\n\nRegister here\n\n\n\nDeadline: 21/10-26 \n\n\n\nDDLS Annual Poster Prize\n\n\n\nThe DDLS Poster Prize encourages PhD students and postdoctoral researchers to present high-quality work in data-driven life science. The award\, decided by a Scientific Committee jury\, includes a certificate and a travel grant of up to 5\,000 SEK. Conditions apply. If you present a poster\, please ensure you stay for the Poster Award Ceremony at 12:00 by the end of the Conference. \n\n\n\nDDLS Annual Conference Workshops 2026\n\n\n\nDuring the second day of the DDLS Annual Conference\, participants will have an opportunity to attend one of two workshops. The workshops are designed for researchers in data-driven life sciences at all career stages. \n\n\n\nEach workshop has a limited number of seats on a first-come\, first-served basis. Those registered after the limit is reached will be placed on a waiting list. The workshops will take place in various rooms at the Aula Magna. All workshops start at 13:30 and end 15:30. Coffee/tea and fika will be served during the workshops. \n\n\n\nFeel free to email datacentre@scilifelab.se with any questions about the workshops. \n\n\n\n \n\n\n\nRead more & register\n\n\n\nWorkshop 1. How to use LLMs to present results from your research project as a web application \n\n\n\nWorkshop 2. Public hosting of Shiny apps: hands-on workshop
URL:https://www.scilifelab.se/event/ddls-annual-conference-2026/
LOCATION:Aula Magna\, Frescativägen 6\, Stockholm\, 114 18 Stockholm\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2026/03/DDLS-pressmeddelande-2026-03-25_bild-scaled.jpg
ORGANIZER;CN="SciLifeLab Event":MAILTO:events@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261110T133000
DTEND;TZID=Europe/Stockholm:20261110T153000
DTSTAMP:20260825T100549Z
CREATED:20260825T091248Z
LAST-MODIFIED:20260825T100549Z
UID:10001880-1794317400-1794324600@www.scilifelab.se
SUMMARY:DDLS Annual Conference 2026 workshops
DESCRIPTION:During the second day of the DDLS Annual Conference 2026 held at Aula Magna at Stockholm University participants will have an opportunity to attend one of the workshops. The workshops are directed at researchers in data-driven life science in all career stages. \n\n\n\nPlease note that each workshop has a limited number of seats\, on the first come first served basis. Those registered after the limit is reached will be placed on a waiting list (and get invited to register if a spot becomes available). The workshops will take place in various rooms of the main venue of the conference – Aula Magna at Stockholm University. The workshops start at 13:30 and last for up to 2 hours. Coffee/tea and fika will be served during the workshops. \n\n\n\nFeel free to email datacentre@scilifelab.se with any questions about the workshops. \n\n\n\nWorkshops\n\n\n\nWorkshop 1. How to use LLMs to present results from your research project as a web application\n\n\n\nHeld by: team members at SciLifeLab Data Centre\, TBA \n\n\n\nWhere and when: November 10\, 2026 at 13:30-15:30\, room Spelbomskan (Frescativägen 6 Stockholm) \n\n\n\nParticipants: max 30 \n\n\n\n\nRegistration\n\n\n\n\nDescription: In case of many research projects\, there is a need to present results not only as a traditional conference or journal paper but also as an interactive web-based tool that can be used by the readers or collaborators to e.g.\, explore the project data as interactive dashboards\, test out performance of a machine learning model\, input own arbitrary parameters in a simulation tool\, etc. Building such web applications for research projects has become rather easy with the help of large language model based tools such as ChatGPT\, Mistral\, Claude\, etc. This means that researchers can build and share web applications for their research projects without learning Python for web in depth (i.e. only using scientific Python knowledge). In this workshop\, we will demonstrate a few examples of where a web-based application can be built to present the results. Subsequently\, we will show how to package the resulting application and make it available to collaborators or general public through a URL using a SciLifeLab hosting service. Participants can follow along on their own laptops and either use our examples or build web-based applications for their own research projects during the workshop. We will be using a SciLifeLab hosted LLM tool during this workshop so that no data is shared with commercial companies. \n\n\n\nParticipants will need to bring a laptop to this workshop to be able to fully participate. \n\n\n\nWorkshop 2. Public hosting of Shiny apps: hands-on workshop\n\n\n\nHeld by: Arnold Kochari (SciLifeLab Data Centre) \n\n\n\nWhere and when: November 10\, 2026 at 13:30-15:30\, room Polstjärnan (Frescativägen 6 Stockholm) \n\n\n\nParticipants: max 30 \n\n\n\n\nRegistration\n\n\n\n\nDescription: Researchers often create R Shiny applications as part of their projects and want to publish them as research output – as analysis tools with a graphical interface\, as supplementary materials for publications\, in order to make annotation easier\, etc. In order to make Shiny apps available to the collaborators or general public\, they need to be hosted somewhere and have a URL. We will start this workshop by giving an overview of what it means to create and publish Shiny apps as researcher in terms of institutional and funder requirements. We will then take a look at different hosting options for Shiny apps. During the hands-on part\, we will focus on packaging Shiny apps for hosting as Docker images. Together with the participants\, we will step-by-step package and publish an example Shiny app or the participants’ own Shiny app. If you are a researcher with an existing Shiny app you’d like to host\, or if you plan to build a Shiny app in the future\, this workshop is for you. If you already have a Shiny app you would like to host\, bring it\, and we will help you with it. \n\n\n\nExpected outcomes: After this workshop\, the participants will both have an understanding of working with Shiny apps within research projects in a Swedish university context and have practical knowledge about public hosting of Shiny apps. \n\n\n\nParticipants will need to bring a laptop to this workshop to be able to fully participate.
URL:https://www.scilifelab.se/event/ddls-annual-conference-2026-workshops/
LOCATION:Aula Magna\, Frescativägen 6\, Stockholm\, 114 18 Stockholm\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261204T101500
DTEND;TZID=Europe/Stockholm:20261204T163000
DTSTAMP:20261014T150556Z
CREATED:20261013T183155Z
LAST-MODIFIED:20261014T150556Z
UID:10001900-1796379300-1796401800@www.scilifelab.se
SUMMARY:Research Data Management in Life Science - Lund
DESCRIPTION:Location: Forum Medicum\, Rådslaget seminar room\, Lund. On-site event co-arranged by SciLifeLab Data Centre\, NBIS & SciLifeLab Lund \n\n\n\nMake the most of your research data \n\n\n\nHow can you effectively manage\, share and safeguard your research data while following current requirements and best practices? \n\n\n\nJoin SciLifeLab Data Centre\, National Bioinformatics Infrastructure Sweden (NBIS) and SciLifeLab Lund for an interactive event on research data management in the life sciences. Local and national experts will provide practical guidance and discuss available support for research data handling\, GDPR\, FAIR principles and Open Science. \n\n\n\nThe event is aimed at life-science researchers and research infrastructure staff in the Lund area who want to strengthen their data management practices and learn more about available support. \n\n\n\nThe format will be informal and interactive\, with plenty of opportunities to ask questions\, share experiences and join the discussion. \n\n\n\nWelcome to join us! \n\n\n\n\nRegister here\n\n\n\n\nRegistration deadline: 27 November\, 2026 \n\n\n\nPROGRAM\n\n\n\nNote: It is important to bring a laptop to actively participate in the workshops.  \n\n\n\n10.00-10.15: Welcome coffee/tea\nEveryone is welcome for the coffee/tea. You can just walk in between 10.00-10.15. \n\n\n\n\n10.15-10.30: Introduction\nIntroduction of the program.   \n\n\n\n\n10.30-12.00: Handling personal data in Life Science – Navigating GDPR and Swedish legislation \nAre you confident in how your research project documents and processes personal data? This seminar guides you through the legal landscape\, from the GDPR to specific Swedish national laws. Using a practical research scenario\, we will clarify essential roles and terms\, including: \n\n\n\n\nResearch principal (forskningshuvudman): Understanding the role and responsibilities of the organisation hosting the research.\n\n\n\nData controllers vs. processors: Identifying who is responsible for each stage of data processing.\n\n\n\nSensitive data: Best practices for securely sharing biomedical research data in FEGA Sweden while remaining compliant.\n\n\n\n\n \n\n\n\n \n\n\n\n\n12.00-13.00: Lunch break\nLunch is not included in this event. At Forum Medicum and the surrounding area you will find several options for lunch. \n\n\n\n\n13.00-13.45: Writing a strong Data Management Plan (DMP) – Improving the lifecycle of your research data\nManaging research data involves a complex web of decisions. How do you ensure nothing falls through the cracks and that your data remains FAIR? The answer is a Data Management Plan (DMP). \n\n\n\nThis hands-on workshop emphasises data management planning at all project phases to keep your data secure and organised. Participants will gain direct access to the Data Stewardship Wizard (DSW) tool to begin drafting a customised DMP tailored to life science research projects. \n\n\n\n\n13.45-14.30: Marketplace: an interactive exhibition – including fika for registered participants\nVisit the Interactive Marketplace to explore local and national research data management services in an engaging and informal setting. Meet experts\, discover practical support and tools\, join interactive discussions\, and learn how different services can support your research.Interested in contributing to the Marketplace and showcasing your data management support services? Please contact: sophie.hellstrand@scilifelab.se \n\n\n\n\n14.30-15.30: Open source software for research – Sharing code the right way\nResearch depends on code\, but without open and FAIR practices\, code can be difficult to understand\, reproduce\, and reuse. Open-source refers to code that is not only available\, but also licensed for free use\, modification\, and sharing. This workshop provides an overview of open and FAIR practices for research code\, and provides practical resources at three different levels; beginner\, intermediate and advanced. Participants will apply these principles in a hands-on tutorial to improve the openness\, transparency\, and reusability of their research code. \n\n\n\n\n15.30-15.45: Wrap up\nWrap up of the workshops. \n\n\n\n\n15.45-16.30: Hands on / hackathon\n \n\n\n\n\n \n\n\n\nMore information on Research Data Management and Open Science\n\n\n\nResearch Data Management (RDM) concerns the organization\, storage\, preservation\, and sharing of data that is collected and analyzed during a research project. Proper planning and management of research data will make project management easier and more efficient while projects are being performed. It also facilitates sharing and allows others to validate as well as reuse the data. \n\n\n\nOpen Science is a set of principles and practices that aim to make scientific research from all fields accessible to everyone for the benefits of scientists and society as a whole. Open science is about making sure not only that scientific knowledge is accessible but also that the production of that knowledge itself is inclusive\, equitable and sustainable. \n\n\n\nContact information: NBIS\, SciLifeLab Data Centre – Data Management\, and SciLifeLab Lund. For questions\, please contact: sophie.hellstrand@scilifelab.se
URL:https://www.scilifelab.se/event/research-data-management-in-life-science-lund/
LOCATION:Forum Medicum\, Sölvegatan 19\, Lund\, 223 62\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2025/05/OpenScience-scaled.jpeg
ORGANIZER;CN="SciLifeLab Lund":MAILTO:lund@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20270406T120000
DTEND;TZID=Europe/Stockholm:20270408T160000
DTSTAMP:20260929T180124Z
CREATED:20260902T125845Z
LAST-MODIFIED:20260929T180124Z
UID:10001883-1807012800-1807200000@www.scilifelab.se
SUMMARY:DDLS Cell & Molecular Biology 2027 theme workshop: Toward a national imaging informatics strategy
DESCRIPTION:Please save the day for the 2027 workshop on the theme “Toward a national imaging informatics strategy” – hosted by DDLS Cell & Molecular Biology. \n\n\n\nMicroscopy is facing ever-increasing challenges: Datasets are reaching terabyte sizes\, computing requires software designed for GPUs\, and there is an increased demand for smart microscopy (“AI in the loop”).  \n\n\n\nVision & Aim: \n\n\n\nFind a way to make microscopes and image data AI-ready – particular focus on large images and image collections \n\n\n\nSolution: \n\n\n\n1. Bring all developers in Sweden together\, produce a solution that matches user needs and is deployable on Swedish HPC infrastructure \n\n\n\n2. Make HPC infrastructure image-ready (S3!) \n\n\n\n3. Form long-term collaborations among the top scientific software developers \n\n\n\nStakeholders: \n\n\n\nSciLifeLab AI strategy \n\n\n\nBIIF (BioImage Informatics Facility) \n\n\n\nNAISS\, local HPC facilities & AI factory \n\n\n\nSciLifeLab Serve / Data Centre \n\n\n\nTarget Group: This event aims to gather stakeholders (power users\, software developers\, HPC and core facility managers) in identifying present and future challenges (first day)\, followed by a 2-day hands-on hackathon and/or focus sessions to begin tackling the most pressing issues. \n\n\n\n\n\n\n\nConfirmed Speakers\n\n\n\nJoel Luhti (BioVisionCenter\, U. Zurich) \n\n\n\nAubrey Weigel (AlphaCell) \n\n\n\nArco Bast (HHMI Janelia Farm) \n\n\n\nPreliminary Program\n\n\n\nTuesday\, April 6\, 2027 \n\n\n\n12:00Registration and LunchSession I:Compute & store of big image dataSession II:Smart microscopyMingle dinner withgames and activities\n\n\n\nWednesday\, April 7\, 2027 \n\n\n\n08:30Session III:AI-ready microscopySession IV:A Swedish nationalimaging strategy15:00End of main program;Start of hackathon\n\n\n\nThursday April 8\, 2027 \n\n\n\n08:30Hackathon\, focus sessions TBA16:00End of hackathon\n\n\n\n\n\n\n\nRegistration\n\n\n\nParticipation fee of 1000 SEK/pp. Includes dinner & activities. \n\n\n\nRegistration will open <date>\, limited seats available\, in-person attendance only. Travel and accommodation will be paid by participants.  \n\n\n\nFor questions\, please contact johan.henriksson@umu.se
URL:https://www.scilifelab.se/event/ddls-cell-molecular-biology-2027-theme-workshop-toward-a-national-imaging-informatics-strategy/
CATEGORIES:Event
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END:VCALENDAR