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DTSTART;TZID=Europe/Stockholm:20261126T083000
DTEND;TZID=Europe/Stockholm:20261126T170000
DTSTAMP:20261026T110042Z
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SUMMARY:Mechanistic Modelling in Pharmacology\, Physiology\, and Neuroscience
DESCRIPTION:Understanding complex biological systems requires more than data\, it demands mechanistic insight. This conference highlights how mechanistic models can integrate clinical and experimental data with computational approaches. \n\n\n\n\n\n\n\nThe volume and complexity of life science data are growing at an unprecedented pace. While computational tools are increasingly used to structure and analyze these data\, there remains a critical gap in our ability to understand the data in a mechanistic and physically realistic way. Bridging this gap is essential for uncovering the fundamental principles that govern the function of molecules\, cells\, organs\, and entire organisms. \n\n\n\nMechanistic models play a central role in this effort and are key to advancing applications such as the development of new pharmaceuticals and improved clinical interventions. However\, progress is often hindered by the lack of a shared language between experimental scientists\, clinicians\, and computational researchers. \n\n\n\nThis conference will bring together experts from these fields to explore state-of-the-art tools and methodologies\, discuss how they can be effectively applied\, and foster stronger integration across disciplines. By promoting collaboration and mutual understanding\, the meeting aims to accelerate progress in pharmacology\, physiology\, and neuroscience. \n\n\n\n\nRegistration closed\n\n\n\n\nRegistration deadline October 25 \n\n\n\nProgram\n\n\n\n8:30 Registration opens \n\n\n\n9:00-12:15 Morning session: Molecules and Cells \n\n\n\nOpening – Fredrik Elinder \n\n\n\n \n\n\n\nJan Ellenberg – Imaging the molecular processes of cell division across scales\nProfessor\, Director of SciLifeLab \n\n\n\nThe rapid development of new imaging technologies allows unprecedented insights into the molecular machinery inside living cells and organisms. For the first time\, light and electron microscopy have molecular sensitivity and resolving power in situ\, and\, if used together\, can connect structural detail with molecular dynamics of the whole cell. Aided by machine learning driven image analysis powered by open sharing of image data\, this provides unprecedented opportunities for new insights into the molecular mechanisms that drive life’s core functions at the scale of the cell. \n\n\n\nI will present the progress we have made to study one of life’s most fundamental functions\, cell division\, by mapping the dynamic protein network\, assembly of individual protein complexes and genome re-folding that drive it. Our work has studied cell division in human cancer cells and early mammalian embryos using advanced cross-scale imaging methods\, including light-sheet\, quantitative fluorescence correlation spectroscopy (FCS)-calibrated\, super-resolution and correlative light and electron microscopy. The quantitative integrated molecular data that these new technologies deliver\, allow us to better understand how the molecular machinery functions in space and time to ensure faithful cell division and prevent the errors that underlie congenital disease\, infertility and cancer. \n\n\n\n\nLucie Delemotte – Common evolutionary mechanism of activation of class A GPCRs\nSciLifeLab fellow\, KTH Royal Institute of Technology \n\n\n\nCells communicate with their environment by integrating signals\, often chemical in nature\, triggered by specific molecules binding to specific membrane-bound receptors\, resulting in a downstream signaling cascade. Arguably\, G-protein-coupled receptors (GPCRs) constitute the most pharmacologically important family of such receptors\, binding small molecules\, peptides\, lipids\, and hormones with high specificity.However\, despite a highly conserved fold and sequence similarity\, GPCRs are still mostly studied on a case-by-case basis. Here\, we infer a general\, evolutionarily conserved mechanism of class A GPCR activation. By leveraging coevolution and machine learning methods applied to all class A GPCRs structures\, we derive a mathematical description (a so-called collective variable – CV) of the receptor’s activation state which is independent of its sequence. Then\, we bias molecular dynamics simulations along this CV to obtain transitions between activation states of a diverse set of class A GPCR family members. To demonstrate that our model generalizes beyond GPCRs in our training set\, we obtain conformational transitions of an orphan receptor\, GPR183. Finally\, we show that we can model ligand effect on the receptors by converging Free Energy Surfaces of activation of the β2-adrenergic receptor within this common mechanism framework. These results\, to ourknowledge\, prove for the first time the existence of a mechanism uniting all class A GPCRs. Our approach thus facilitates direct comparisons between receptors and opens up the possibility of structural and dynamical studies of many orphan and understudied GPCRs. It also serves as a blueprint for inferring family-wide protein mechanisms. \n\n\n\n\nBjörn Forsberg – Direct estimation of cryo-EM fields to control estimation of biological function\nDDLS Fellow\, Linköping University \n\n\n\nLearning molecular variability from cryo-EM data relies on strict manual control of correlated variables\, or the use of general ML frameworks that have to learn the correlative variation in addition to estimating it. This presents a complexity trade-off that is prone to bias in either modality\, preventing maximal use of current datasets. Here we present an approach that seeks to parameterize 3D cryo-EM reconstructions in maximally interpretable ways\, based on general causative mechanisms\, that can then be recast to provide explicit learning objectives through an explicit model. This seeks to minimize the bias incurred by specifying ad-hoc mechanistic models\, and efficiently regularize general learning frameworks. \n\n\n\n\n10:15-10:45 Coffee \n\n\n\nErik Lindahl – Title TBA\nProfessor Stockholm University\, Linköping University and KTH Royal Institute of Technology\, Director of National Academic Infrastructure for Super­computing in Sweden (NAISS) \n\n\n\nFocus TBA \n\n\n\n\nFredrik Heintz – From Language to Knowledge and Back Again\nProfessor\, Linköping University\, WASP Graduate School Director \n\n\n\nFocus TBA \n\n\n\n\nJuliette Griffie – From Black Box to Biological Insight: Generative AI for Life Science and Microscopy\nDDLS fellow\, The Computational Microscopy for Cell Biology (CMCB) laboratory\, Stockholm University \n\n\n\nThe life sciences are entering a transformative era\, with generative AI emerging as a powerful engine for discovery. This talk will explore how these technologies can move beyond prediction towards interpretability\, while being tailored to the realities of biological research\, where datasets are often small and models must be designed to answer very specific biological questions. \n\n\n\n\nPanel Debate\nModerator – Per Petersson \n\n\n\n\n12:15-13:30 Lunch \n\n\n\n13:30-16:45 Afternoon Session – System Biology \n\n\n\n \n\n\n\nPetra Ritter – Trustworthy Digital Brain Twins\nProfessor\, Charité University Medicine Berlin \n\n\n\nThis talk explores the integration of mechanistic modeling\, multiscale physiological data\, and artificial intelligence to construct personalized “Digital Brain Twins” for neuroscientific research and clinical applications. It addresses the computational\, methodological\, and ethical challenges in ensuring these virtual replicas remain dynamic\, precise\, and robustly validated across spatial and temporal scales. Ultimately\, the presentation highlights frameworks for building trustworthy in silico models capable of predicting disease progression\, evaluating targeted pharmacological interventions\, and advancing personalized medicine in neurology and neuroscience. \n\n\n\n\nGunnar Cedersund – M4-HEALTH – hybrid mechanistic and machine learning digital twin models as a basis for a new ecosystem for health\nAssociate Professor\, Linköping University \n\n\n\nFocus TBA \n\n\n\n\nHenrik Jörntell – How brain circuitry operation emerges from nested closed loop interactions through the body\nProfessor\, Lund University \n\n\n\nOne of the hottest scientific topics today is how does the brain actually work and\, in the era of artificial intelligence perhaps even more\, what is ‘intelligence’ really? Here we will address these questions to illustrate the path towards arriving at a general conceptualization of the brain circuitry operation that emerges from the fundamental dynamics of neuron interactions\, i.e. from neurophysiological observations. In this ambition\, there is also a need to explain the resulting roles fulfilled by the different structural subsystems of the nervous system. Fundamental differences with current AI systems is one outcome. Consequences relative to the wider literature are; (i) the function of any one neuron alter depending on context; (ii) in this mode of operation predictive neural activity emerges as a trivial by-product without any assumptions of architectural specializations. This underscores the need for integrated neurophysiological work\, as the broader field is still far away from understanding the physiological infrastructure that underlies the emerging computational architecture of the brain. \n\n\n\n\n14:30-15:00 Coffee \n\n\n\nMorten Grunnet – Neuroscience Drug discovery and AI – Opportunities and limitations\nVice President and Head of Neuroscience at Lundbeck & Affiliate Professor at University of Copenhagen \n\n\n\nHow AI and data-driven approaches are currently being integrated into neuroscience drug discovery\, and how these approaches can be combined with mechanistic understanding across different biological scales – from molecular and cellular mechanisms to circuits\, systems and ultimately clinical phenotypes. A perspective on where the main opportunities\, but also the current limitations\, of AI and mechanistic modeling in pharmaceutical research. \n\n\n\n\nEduard Kerkhoven – From pathway maps to predictive models: Human-GEM and human metabolism\nSenior Researcher\, Chalmers University of Technology \n\n\n\nMetabolic pathway maps are familiar\, but they cannot tell you what happens when a gene is lost or a nutrient runs short. Genome-scale metabolic models turn the same biochemistry into something computable and testable against real perturbations. I will introduce Human-GEM\, the community model of human metabolism\, show a few applications across tissues\, organs and disease\, and suggest that models of this kind become more valuable as omics data accumulate\, by giving those measurements a mechanistic structure to be interpreted against. \n\n\n\n\nJeanette Hellgren-Kotaleski – Simulating the Basal Ganglia in Health and Disease using a Biophysically Detailed Approach\nProfessor\, KTH Royal Institute of Technology \n\n\n\nTo understand any part of the brain\, it is necessary to integrate data from the molecular level up to the systems level. For this effort\, data-driven and mechanistic modelling provides an important tool for synthesizing the diverse experimental data into in silico models. Simulation experiments can then generate new predictions which give rise to novel questions. In our lab\, the microcircuit level is one important starting point when bridging biological scales. Our biophysically detailed neuron and network modelling pipeline integrates data on cellular morphologies\, electrophysiology\, synaptic properties\, and also takes transcriptomics data on e.g. ion channels into account. In my talk I will exemplify insights gained when we apply our modelling pipeline to investigate the structural and functional alterations seen in the diseased striatal microcircuit. \n\n\n\n\nPanel Debate\nModerator: Johan Wessberg \n\n\n\n\nConcluding Remarks – Per Petersson & Johan Wessberg \n\n\n\nConfirmed Panelists \n\n\n\nSiv Andersson\, Professor\, Uppsala University\, Knut and Alice Wallenberg Foundation \n\n\n\nGunnar Schulte\, Professor\, Karolinska Institutet\, The Swedish Research Council \n\n\n\nPartners \n\n\n\nSciLifeLab & the National Committee for Pharmacology\, Physiology and Neuroscience of the Royal Academy of Sciences \n\n\n\nOrganizing committee \n\n\n\nFredrik Elinder\, Professor of Molecular Neurobiology\, Electrophysiologist\, Linköping University \n\n\n\nJohan Wessberg\, Professor and Principal Investigator Department of Physiology / Neurophysiology\, Gothenburg University \n\n\n\nPer Petersson\, Professor in the field of Neurophysiology\, Umeå University
URL:https://www.scilifelab.se/event/mechanistic-modelling-in-pharmacology-physiology-and-neuroscience/
LOCATION:Royal Swedish Academy of Sciences\, Lilla Frescativägen 4A\, Stockholm\, 114 18\, Sweden
CATEGORIES:Event
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ORGANIZER;CN="SciLifeLab Link%C3%B6ping":MAILTO:linkoping@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261201T090000
DTEND;TZID=Europe/Stockholm:20261201T190000
DTSTAMP:20261016T151029Z
CREATED:20261015T082050Z
LAST-MODIFIED:20261016T151029Z
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SUMMARY:Hackathon: AI agents transforming life sciences\, medicine\, and healthcare
DESCRIPTION:Join us on 1 December 2026 for a hackathon focused on developing AI agents for applications in life sciences\, medicine and healthcare. There is a lot happening in the agentic AI sphere right now\, and many people have great ideas or knowledge that can be exchanged. We hope that during this event we can build interesting things together\, share knowledge with each other\, and network. \n\n\n\nThe hackathon is open to members of the SciLifeLab\, DDLS and WASP communities and is jointly organised by SciLifeLab\, the WASP Research Arena for Medicine (WARA Medicine)\, and the DDLS research areas of Cell and Molecular Biology and Precision Medicine and Diagnostics. \n\n\n\nEveryone is welcome to join\, whether you have a specific idea for something to build or you simply want to join and build together with others. In the registration form we will ask you to share interests or propose ideas for a project\, and we will do our best to create teams based on the ideas and interests. If you have already formed a team with which you will work\, you can indicate this in the registration form. There will also be opportunities to form or adjust teams at the beginning of the day.  \n\n\n\nDuring the hackathon\, participants will get API keys to access Claude and open weight models hosted by SciLifeLab. We will also facilitate hosting of your tools on the SciLifeLab Kubernetes cluster if needed.We will start the day with breakfast and pitches of various ideas (pre-submitted or spontaneous). We will end the day with pizza for everyone. We can accept up to 70 participants. If you have questions or suggestions\, get in touch with us: datacentre@scilifelab.se \n\n\n\nRegistration\n\n\n\nRegistration is open to members of the SciLifeLab\, DDLS and WASP communities. Participation is free of charge\, and places are limited to 70 participants. \n\n\n\nRegister here\n\n\n\nCancellation\n\n\n\nTo help us minimise empty seats and food waste\, please cancel your registration if you are no longer able to attend the event. If a waiting list is active\, this will allow us to offer your place to another participant. Timely cancellations also help us avoid unnecessary costs for refreshments and lunch. \n\n\n\nIf you have questions or suggestions\, please get in touch with us: datacentre@scilifelab.se \n\n\n\nSamuelssonsalen
URL:https://www.scilifelab.se/event/hackathon-ai-agents-transforming-life-sciences-medicine-and-healthcare/
LOCATION:Samuelssonsalen\, Tomtebodavägen 6\, Stockholm\, 17165\, Sweden
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20261202T130000
DTEND;TZID=Europe/Stockholm:20261202T150000
DTSTAMP:20261102T135045Z
CREATED:20261102T124353Z
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SUMMARY:Workshop:  Accessing and Analysing Clinical and Patient Data: Learning from Swedish Peers
DESCRIPTION:A virtual workshop organized within the SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS)\, aimed at bringing together DDLS fellows and researchers with hands-on experience in working with clinical and patient data.  \n\n\n\nThe focus is on sharing practical insights\, challenges\, and opportunities related to accessing\, managing\, and analyzing clinical and patient data for data-driven research.  \n\n\n\nTopics include data sources\, data access processes\, ethical and legal considerations\, technical challenges\, data storage and movement\, and computational approaches. The workshop also aims to foster networking and potential collaborations between experienced researchers and DDLS fellows. \n\n\n\nRegister here\n\n\n\nProgram\n\n\n\n13:00Introduction Carolina Wählby\, DDLS co-directorJanne Lehtiö\, PMD RA leader13:10Real world examples15 min + 10 min Q&AJohan Sundström\, Professor of MolecularEpidemiology at Department of MedicalSciences; Uppsala UniversityTove Fall\, Professor of MolecularEpidemiology at Department of MedicalSciences; Uppsala UniversityEric Herlenius\, Professor of Pediatrics atDepartment of Women’s and Children’sHealth Karolinska Institutet14:25-15:00Open discussion: how to promote data access for Swedish data driven clinical and translational research.All participants\n\n\n\nContact: Xenia Villalobos (xenia.villalobos.alberu@ki.se)
URL:https://www.scilifelab.se/event/workshop-accessing-and-analysing-clinical-and-patient-data-learning-from-swedish-peers/
LOCATION:Online event via Zoom
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20261209T090000
DTEND;TZID=Europe/Stockholm:20261209T163000
DTSTAMP:20261027T133311Z
CREATED:20251124T130114Z
LAST-MODIFIED:20261027T133311Z
UID:10001673-1796806800-1796833800@www.scilifelab.se
SUMMARY:Heart 360° - Harnessing AI for Cardiovascular Research\, Diagnosis\, Therapy & Prevention
DESCRIPTION:Join us for an inspiring day at the forefront of cardiovascular research\, where AI helps to advance precision medicine.\n\n\n\n \n\n\n\nHeart 360° is a focused seminar exploring the transformative role of artificial intelligence (AI) across the cardiovascular disease spectrum\, from early discovery to prevention. As cardiovascular disease remains a leading global health burden\, the integration of AI into research\, clinical care\, drug development\, and public health offers new opportunities to enhance understanding\, precision\, and outcomes. \n\n\n\nThe seminar is structured into four sessions: Discovery\, Diagnosis\, Drug Development\, and Prevention\, bringing together experts from academia\, healthcare\, and industry. Each session will highlight how AI-driven tools are reshaping translational research\, enabling earlier and more accurate diagnoses\, accelerating therapeutic innovation\, and supporting data-driven prevention strategies. \n\n\n\nBy fostering interdisciplinary dialogue\, Heart 360° aims to showcase cutting-edge applications of AI\, identify key challenges\, and inspire collaborative efforts to drive the future of cardiovascular science and care. \n\n\n\nRegistration\n\n\n\n\nRegister here\n\n\n\n\nRegistration deadline: 11 November  \n\n\n\nConfirmed speakers\n\n\n\n\n\n\n\n\n\nSøren BrunakUniversity of Copenhagen \n\n\n\n\n\n\n\n\n\n\n\n\n\nCharlotta LjungmanSahlgrenska University Hospital \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nMarcus SchindlerScientific and Strategic Advisor Former CSO\, Novo Nordisk \n\n\n\n\n\n\n\n\n\nAraz RawshaniSahlgrenska University Hospital \n\n\n\n\n\nCall for Presentations!\n\n\n\nAre you a PhD student\, postdoc\, or working at a start-up company in the field of AI and cardiovascular disease (CVD) research? \n\n\n\nShowcase your work in a short talk or poster! Simply indicate your preference in the registration form. \n\n\n\nAgenda\n\n\n\nPowered By EmbedPress \n\n\n\nOrganized by\n\n\n\nMuhammad Arif\, DDLS Fellow\, Computational Multi-Omics Lab\, University of Gothenburg \n\n\n\nSponsors
URL:https://www.scilifelab.se/event/heart-360-harnessing-ai-for-cardiovascular-research-diagnosis-therapy-prevention/
LOCATION:Conference Centre Wallenberg\, Medicinaregatan 20A\, Gothenburg\, 413 90\, Sweden
CATEGORIES:Event
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ORGANIZER;CN="SciLifeLab Gothenburg":MAILTO:gothenburg@scilifelab.se
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DTSTART;TZID=Europe/Stockholm:20270406T120000
DTEND;TZID=Europe/Stockholm:20270408T160000
DTSTAMP:20260929T180124Z
CREATED:20260902T125845Z
LAST-MODIFIED:20260929T180124Z
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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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