BEGIN:VCALENDAR VERSION:2.0 PRODID:-//SciLifeLab - ECPv6.15.20//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-WR-CALNAME:SciLifeLab X-ORIGINAL-URL:https://www.scilifelab.se X-WR-CALDESC:Events for SciLifeLab REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/Stockholm BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20221030T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20230326T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20231029T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20240331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20241027T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20250330T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20251026T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230306T140000 DTEND;TZID=Europe/Stockholm:20230306T160000 DTSTAMP:20260503T183041 CREATED:20230213T125155Z LAST-MODIFIED:20230303T090629Z UID:10000808-1678111200-1678118400@www.scilifelab.se SUMMARY:Networking Meeting Between the Wallenberg Programs WASP-HS and Data-Driven Life Science (DDLS) DESCRIPTION:The purpose of this on-line meeting is to explore opportunities for joint and multidisciplinary research ventures between researchers working within data-driven life science and researchers from the humanities and social sciences working on Artificial Intelligence and Autonomous Systems. The meeting is divided in two parts\, one with focus on information\, where an upcoming call for seed-money for cross-program research collaborations will be announced and one part with focus on networking. \n\n\n\n \n\n\n\nAGENDA \n\n\n\n \n\n\n\n14:00-15:00 Information \n\n\n\n\n Presentation of WASP-HS\, Bodil Formark (Program Coordinator WASP-HS) and DDLS\, Erik Kristiansson (DDLS Steering Group)\n\n\n\n Information about the new call for seed-money\, Erik Kristiansson (DDLS Steering Group)\n\n\n\n Presentation of previous call\, Francis Lee (WASP-HS Management Team)\n\n\n\n Q/A\n\n\n\n\n15:00-15.30 Networking \n\n\n\nPossibilites to interact with researchers within the fields of WASP-HS and DDLS Heidi Howard (ELSI-expert DDLS) \n\n\n\n \n\n\n\nRegister here URL:https://www.scilifelab.se/event/networking-meeting-between-the-wallenberg-programs-wasp-hs-and-data-driven-life-science-ddls/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230324T090000 DTEND;TZID=Europe/Stockholm:20230324T130000 DTSTAMP:20260503T183041 CREATED:20230110T140542Z LAST-MODIFIED:20230316T094354Z UID:10000782-1679648400-1679662800@www.scilifelab.se SUMMARY:Data-driven life science and the RDA: Leveraging global data communities in regional initiatives and cross-border infrastructures DESCRIPTION:This workshop will showcase how to leverage the Research Data Alliance (RDA) to support life science research today and what role the RDA and international data infrastructures can play in the transition to an increasingly data-driven research practice. It is organised by ELIXIR\, NBIS and the Science for Life Laboratory (SciLifeLab) and includes speakers on life science data & interoperability\, stakeholder engagement\, and liaison strategies with the RDA. \n\n\n\nThe workshop aims to promote and refine strategies for liaising with global communities and in particular the RDA to develop and adopt solutions for data-driven life science research. The intended audience is research communities\, regional research infrastructures and cross-border infrastructure collaborations. However\, registration is open to everyone who is involved in furthering shared principles and standards for life science research data. To accommodate a dynamic and diverse group of participants\, the workshop is hosted as a hybrid event\, accepting participants on-site in Gothenburg\, Sweden or online via Zoom. \n\n\n\nThe event schedule is organised into two parts where invited speakers will present their experiences leading into discussions focused on finding effective liaison strategies and forming new collaborations across communities and infrastructures. Part 1 focuses on showcasing examples of how to leverage activities and outputs of the RDA to converge on shared principles and practices. Part 2 focuses on networking to outline and refine some elements of realistic and effective liaison strategies that could be implemented across the organisations\, initiatives and communities that the participants represent. \n\n\n\nRegistration is free for both on-site and virtual attendance. The number of spaces for on-site attendance is limited by the size of the room and some spaces will be reserved for speakers to promote wide representation across communities and infrastructures. \n\n\n\nContact: wolmar.n.akerstrom@uu.se \n\n\n\nRegistration\n\n\n\nPart 1: Showcase on leveraging the RDA for life science data\n\n\n\n09:00–11:00 CET | Presentations by invited speakers \n\n\n\n\nLife science data communities and infrastructures\n\n\n\nRegional resources with national and cross-border data sharing initiatives\n\n\n\nLeveraging and promoting RDA outputs and activities\n\n\n\nPanel discussion\n\n\n\n\nPart 2: Liaison strategies across communities & infrastructure\n\n\n\n11:00–12:00 CET | Guided discussions among participants \n\n\n\n\nWork towards realistic and effective liaison strategies\n\n\n\nPotential collaborations and steps going forward\n\n\n\n\n12:00–13:00 CET | Networking lunch for on-site participants URL:https://www.scilifelab.se/event/ddls_rda2023/ LOCATION:Lindholmen Conference Center\, Lindholmspiren 5\, Göteborg\, 417 56\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230515T080000 DTEND;TZID=Europe/Stockholm:20230516T170000 DTSTAMP:20260503T183041 CREATED:20220926T143527Z LAST-MODIFIED:20230514T190911Z UID:10000691-1684137600-1684256400@www.scilifelab.se SUMMARY:EMBL-SciLifeLab Data Science workshop DESCRIPTION:We would like to cordially invite members of the SciLifeLab and EMBL Communities to this workshop! This event will bring together researchers\, scientific and technical staff at the EMBL and SciLifeLab\, to make new acquaintances and collaborations and to learn and be inspired by each other. \n\n\n\nThe workshop program starts at 09:00 on May 15 and ends after lunch on May 16. \n\n\n\nThe workshop will be a hybrid event enabling participation to the wider community at all EMBL and SciLifeLab sites. \n\n\n\nLooking forward to meeting you in Uppsala in May! \n\n\n\nSessions\n\n\n\n\nInternal and external training and support\n\n\n\nProvision of public data services – computational tools\n\n\n\nArtificial intelligence\n\n\n\nIntegrated data management and Scientific workflow sharing\n\n\n\nTechnical infrastructure – computational solutions\n\n\n\nBiological theme – Imaging\n\n\n\nBiological theme – Human data\n\n\n\n\nParticipation by invitation only. Target audience: SciLifeLab and EMBL staff. \n\n\n\nScientific committee\n\n\n\n\nJohan Rung\, SciLifeLab\n\n\n\nCarolina Wählby\, SciLifeLab\n\n\n\nJan Korbel\, EMBL\n\n\n\nRupert Lueck\, EMBL\n\n\n\nRolf Apweiler\, EMBL\n\n\n\n\n\n\n\n\n\n\n\n\nProgram\n\n\n\nMonday May 15\nTime slotMonday\, May 1509:00Welcome and introductionOlli Kallioniemi\, SciLifeLab and DDLS Director\, and Jan Korbel\, Head of Data Science\, EMBL09:15Session 1: Internal and external training and supportThemes: what is training at EMBL\, Data Science training work stream -SciLifeLab training hub -Areas for synergiesModerator: Cath Brooksbank\, Head of Training\, EMBL-EBIEMBL Data Science Training: the story so farLisanna Paladin\, Bioinformatics Community Project Manager\, EMBLSciLifeLab Training Hub: the story starts now – what are the goals?Nina Norgren\, Training manager\, SciLifeLabPanel discussion and questions on stimulating exchange and collaboration10:20Coffee breakMounting of posters10:50Session 2: Provision of public data services – computational toolsModerator: Johanna McEntyre\, Associate Director for Service\, EMBL-EBISuccessfully managing a portfolio of data servicesJohanna McEntyre\, Associate Director for Service\, EMBL-EBIIntroductions to:Metabolic atlas Mihail Anton\, NBIS expert\, SciLifeLabProtein DatabaseSameer Velankar (PDB Europe)\, Team Leader\, EMBL-EBIPanel discussion: the future challenges and opportunities for public data servicesMihail Anton (Metabolic Atlas)Matthew Hartley (BioImage Archive)Cecilia Lindskog (Human Protein Atlas)Fergal Martin (Ensembl)Sameer Velankar (PDB Europe)11:55LunchPoster session13:15Session 3: Artificial IntelligenceModerator: Carolina Wählby\, Scientific Director of BioImage Informatics and Group Leader\, SciLifeLabAI in Image AnalysisAnna Kreshuk\, Group Leader\, EMBLAI in Cancer genomics\, prediction of treatmentIsidro Cortes-Ciriano\, Group Leader\, EMBL-EBIAI in spatial omicsCarolina Wählby\, Scientific Director of BioImage Informatics and Group Leader\, SciLifeLabServing AI modelsOla Spjuth\, Group Leader and AI coordinator\, SciLifeLabDiscussion on how to foster AI further14:20Coffee breakPoster session14:50Session 4: Integrated data management and scientific workflow sharingModerator: Henning Hermjakob\, Head of Molecular Systems\, EMBL-EBIExpression AtlasIrene Papatheodorou\, Team Leader – Gene Expression\, EMBL-EBIComplex WorkflowsMats Nilsson\, Platform Director Spatial Biology and Group Leader\, SciLifeLabDiscussion15:55Short break16:00Session 5: Technical infrastructure – computational solutionsModerator: Johan Rung\, Head of Data Centre\, SciLifeLabCloud – Beyond the hypeAndy Cafferkey\, Head of Technical Services\, EMBL-EBIThe IT role in empowering advanced research data managementRupert Lück\, Head of IT Services\, EMBLThe great datawanderung – how sensitive data is reshaping research infrastructures. Data transfer\, Compute moving to dataJohan Viklund\, NBIS Chief Technical Officer\, SciLifeLabNeeds and requirements to provide next generation of compute services (notebooks\, containerization\, GPUs\, etc) – energy\, carbon issuesOla Spjuth\, Group Leader and AI coordinator\, SciLifeLab17:05Wrap-up17:10Poster session with refreshments18:30Conference Dinner\n\n\n\n\nTuesday May 16\nTime slotTuesday\, May 1609:00Session 6: Biological theme – imagingModerator: Anna Klemm\, Head of the BioImage Informatics Facility\, SciLifeLabImage Data and Image analysisHjalmar Brismar\, Platform Scientific Director Advanced Light Microscopy unit and Group Leader\, SciLifeLabChristian Tischer\, Centre for Bioimage Analysis\, Scientist/IT Engineer\, EMBLPanel discussion: Workflows from image data generation to data analysis and finally image data publication. How are projects and data managed?Hjalmar Brismar\, SciLifeLabMatthew Hartley\, BioImage Archive Team Leader\, EMBL-EBIAnna Klemm\, SciLifeLabErik Lindahl\, Group Leader\, SciLifeLabChristian Tischer\, EMBL10:05Coffee breakPoster session10:35Session 7: Biological theme – human dataModerator: Helen Parkinson\, Team Leader SPOT\, EMBL-EBIIntegrated FEGA/FDA-components/Federated AnalysisOliver Stegle\, Associate Group Leader\, EMBLDevelopments from Human Data ServicesBengt Persson\, Platform Director NBIS\, SciLifeLabDiscussion11:40Workshop wrap-upCarolina Wählby\, Scientific Director of BioImage Informatics\, SciLifeLab and Rolf Apweiler\, Joint Director of EMBL-EBI12:00LunchAfternoon:Self-organized break-out tech workshops\, Site visits\, etc\n\n\n\n\n\n\n\n\n\n\n\n\nSessions\n\n\n\n \n\n\n\nSession 1: Internal and external training and support\nEMBL and SciLifeLab recently launched data science training initiatives. In this session we will share our approaches to developing data science training  – our plans\, our successes and our greatest challenges. An open discussion will explore areas for future collaboration and how we might work together to recognise those who dedicate their time\, usually on a volunteer basis\, to advanced scientific training. \n\n\n\n\nSession 2: Provision of public data services / computational tools of the SciLifeLab/EMBL-EBI \nExplore how to manage a portfolio of public computational tools and data services\, with real-world examples from both emerging and established resources\, and a panel discussion on the future challenges and opportunities for public data services \n\n\n\nIn this workshop: \n\n\n\n\nA keynote talk introduces key points of successfully managing a portfolio of data services\n\n\n\nOne emerging and one established data service summarize their management approach\n\n\n\nA panel discussion including other data service leads from EMBL-EBI and SciLifeLab discuss the future challenges and opportunities for public data services\n\n\n\n\n\nSession 3: Artificial intelligence\nIn this session we will focus on how to foster AI further (within EMBL-EBI and SciLifeLab) – What are the lessons learned during the last decade of incorporating learning-based methods using neural networks in biomedical research? Where lies the power\, and what are the limitations? How do we handle bottle-necks such as lack of reliably annotated training data\, and how do we avoid biases introduced by factors such as sample preparation and data collection? How can we include ‘the human in the loop’\, and how can we share models? \n\n\n\n\nSession 4: Integrated data management & Scientific workflow sharing\nModern\, data-intensive science requires complex and ideally reproducible workflows. Based on two opening presentations\, one from a complex “research” workflow background\, one from a repeatable “service” background\, and a subsequent panel discussion\, we want to explore \n\n\n\n\nWhat are the scientific demands and requirements for computational workflows?\n\n\n\nHow to strike the right balance between reproducibility and flexibility?\n\n\n\nWhat is the current status and future aspirations for technical support of computational workflows?\n\n\n\nWhat are the opportunities for coordination / integration of internal /external workflows between SciLifeLab and EMBL?\n\n\n\n\n\nSession 5: Technical infrastructure – computational solutions\nThe technical infrastructures and computational solutions provided by teams across EMBL and SciLifeLab are at the heart and the critical foundation of data science activities in both institutions. In this session\, we aim to initiate a cross-organizational dialogue and to set the stage for further networking among interested stakeholders to explore key IT and technical challenges and learn more about potential solutions being explored on both sides. \n\n\n\nThe session will start with four short presentations to stimulate the open discussion that will follow. Our input from the presentations will cover a wide range of technical topics and challenges: \n\n\n\ni) key aspects of using cloud services\, \n\n\n\nii) opportunities to improve scientific data management via dedicated IT solutions\, \n\n\n\niii) the challenges associated with shared analysis and transfer of (sensitive) data across centres\, and \n\n\n\niv) exploring the needs for next-gen computational\, data analytics\, and management services for data science in the life sciences. \n\n\n\n\nSession 6: Biological theme – imaging\nIn the imaging session we will discuss workflows from image data generation to data analysis and finally publication. Which paths does microscopy data take at EMBL and SciLifeLab? How can data analysis and data management be integrated early on in the project discussions? The session will also give an insight to which kind of imaging projects are handled at both EMBL and SciLifeLab\, since imaging data can have a broad range of characteristics and comes with different analysis and data management needs. \n\n\n\n\nSession 7: Biological theme – human data\nThe Human Data session will focus on challenges working with federated and multidimensional human data\, interfacing with national data \, e.g. Genomics Data Infrastructure (GDI; Persson) enabling realisation of the European 1+ Million Genome project\, and the experience of working at the interface of clinical research with industrial partners\, including the Mannheim alliance (Stegle) and precompetitive industrial collaborations\, e.g.OpenTargets (https://www.opentargets.org/). The session will have two presentations (Stegle\, Persson) followed by a panel discussion. It aims to define the skills set\, mindset\, technical solutions to address shared problems of human research data.  URL:https://www.scilifelab.se/event/embl-scilifelab-data-science-workshop/ LOCATION:Eva von Bahr\, Ångström Laboratory\, Uppsala University\, Uppsala\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230526T110000 DTEND;TZID=Europe/Stockholm:20230526T120000 DTSTAMP:20260503T183041 CREATED:20230414T123346Z LAST-MODIFIED:20230522T120452Z UID:10000861-1685098800-1685102400@www.scilifelab.se SUMMARY:SciLifeLab Data Platform Launch DESCRIPTION:Join SciLifeLab Data Centre for the official launch of the SciLifeLab Data Platform. At this launch event\, we will demonstrate how the data platform supports DDLS\, the services we offer\, and how you can get access to hosting resources. In addition\, a number of our users will present their user cases\, followed by a summary. \n\n\n\nDate: May 26th at 11-12 CEST \n\n\n\nThe SciLifeLab Data Platform is a technical environment offering data-centric tools and databases as well as an overarching website with the goal to support and accelerate data-driven life science research in Sweden. \n\n\n\nThe services hosted on the Platform are available to all life science researchers in Sweden. The platform is maintained by the SciLifeLab Data Centre.The services hosted on the SciLifeLab Data Platform adhere to the values of open science\, transparent research\, and FAIR as well as good data management practises throughout the data life cycle. \n\n\n\nRegister to join the event\n\n\n\nLaunch event \n\n\n\n11.00-11.15 Welcome and introduction to the SciLifeLab Data Platform\, Johan Rung\, Head of SciLifeLab Data Centre \n\n\n\n11.15-11.35 Platform services\, and how to access to hosting resources\, Liane Hughes\, SciLifeLab Data Centre \n\n\n\n11.35-11.50 Flash talks by Platform users Elin Kronander\, NBIS\, Wesley Schaal\, Uppsala University/ SciLifeLab\, and Oliver Billker\, Umeå University/ SciLifeLab) \n\n\n\n11.50-12.00 Summary \n\n\n\n \n\n\n\nWelcome \n\n\n\nRegistration open till Friday May 26 12.00 CEST \n\n\n\nThis event will be recorded and available on data.scilifelab.se \n\n\n\nFor more information please contact SciLifeLab Data Centre at datacentre@scilifelab.se URL:https://www.scilifelab.se/event/scilifelab-data-platform-launch/ LOCATION:Online event via Zoom CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/04/SciLifeLab-Data-Platform-Launch-event.png ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230605T080000 DTEND;TZID=Europe/Stockholm:20230609T170000 DTSTAMP:20260503T183041 CREATED:20230317T095301Z LAST-MODIFIED:20230317T150114Z UID:10000839-1685952000-1686330000@www.scilifelab.se SUMMARY:Hackathon on Web and Cloud Infrastructure for AI-Powered BioImage Analysis DESCRIPTION:We are proud to announce the upcoming hackathon (a.k.a. codefest) event\, “Web and Cloud Infrastructure for AI-Powered BioImage Analysis” on June 5th-9th\, 2023\, at SciLifeLab\, Solna. As leading partners in the AI4Life consortium\, which is funded through the Horizon Europe Research Infrastructure Grant\, SciLifeLab and KTH are organizing this event to bring together the computational and life science communities\, shaping the future of Data-Driven Life Sciences! \n\n\n\nIn the AI4Life consortium\, we focus on building web and cloud infrastructure aimed at addressing the challenges of building and deploying AI tools for bioimage analysis and making them more scalable and easily accessible from the BioImage Model Zoo.  \n\n\n\nFor the hackathon\, we are inviting international experts and hackers on AI-based image analysis and web & cloud infrastructure to lead discussions and form interest groups to hack on related topics. It will feature discussions on our current status and plans in building web and cloud infrastructure for running models in the BioImage Model Zoo\, as well as the opportunity to form interest groups to hack on related topics in breakout sessions during the week. \n\n\n\nIf you are interested in participating\, please RSVP by April 15th\, 2023\, and let us know through this form: \n\n\n\nregistration\n\n\n\nPlease also note that the participants’ number of the event is limited to 15\, and in case of overbooking\, we will select based on the relevance of your current work and give priority to international participants outside Sweden. \n\n\n\nThe event is organized by Wei Ouyang\, a Data-Driven Life Science fellow who is leading the AICell Lab (https://aicell.io) and the development of the cloud-based AI infrastructure in the AI4Life consortium. \n\n\n\nWe are proud to have the support of Global BioImaging\, an international network of imaging infrastructures and communities. Together\, we are committed to generating new synergies in the community and to collecting feedback from users and experts in the field. \n\n\n\nContact at SciLifeLab: \n\n\n\nWei OuyangKTHDDLS FELLOWwei.ouyang@scilifelab.se +46762867366 URL:https://www.scilifelab.se/event/hackathon-on-cloud-based-and-ai-powered-bioimage-analysis/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/Ai-for-life.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230906T090000 DTEND;TZID=Europe/Stockholm:20230906T170000 DTSTAMP:20260503T183041 CREATED:20230320T105854Z LAST-MODIFIED:20230901T113534Z UID:10000842-1693990800-1694019600@www.scilifelab.se SUMMARY:Emerging data-driven approaches to cancer DESCRIPTION:Welcome to the second in-person symposium in data-driven precision medicine and diagnostics (PMD) research area. Listen to leading experts in this area\, including Data-Driven Life Science (DDLS)\, and expand your network with international and national colleagues. \n\n\n\nThis meeting brings together the community in precision medicine and diagnostics and researchers who implemented artificial intelligence and machine learning applications in their research in PMD to improve human health and diagnostics\, introduces newly appointed DDLS fellows in the PMD research area\, and provides opportunities for networking across the research community and the SciLifeLab infrastructures. Thematically\, this meeting will focus on emerging approaches to cancer research\, ranging from both cutting-edge basic science to promising translational developments of AI. \n\n\n\nWe are excited to host international keynote speakers and welcome the community to join us. Hopefully\, this event will inspire you on the potentials of data-driven precision medicine and diagnostics in Sweden. \n\n\n\nTarget group: We welcome all researchers interested in the DDLS program and data-driven precision medicine and diagnostics. This is an onsite event only. The event will not be recorded as the speakers might share their unpublished results. \n\n\n\nDeadline for registration to guarantee fika and lunch: August 30. Note; to minimize food waste\, we ask you kindly to cancel your participation before August 30\, if you can´t participate. \n\n\n\nSpeakers\n\n\n\n\nAbhishek Niroula\, DDLS Fellow\, University of Gothenburg\n\n\n\nAvlant Nilsson\, DDLS Fellow\, Karolinska Institutet\n\n\n\nBeatrice Melin\, Umeå University\n\n\n\nBjörn Nilsson\, Lund University\n\n\n\nFredrik Strand\, Karolinska Institutet\n\n\n\nIda Larsson\, Uppsala University\n\n\n\nHannah Muti\, University Hospital RWTH Aachen\n\n\n\nKarin Forsberg Nilsson\, Uppsala University\n\n\n\nMichael Mints\, Weizmann Institute of Science\n\n\n\nNina Linder\, Uppsala University\n\n\n\nOlli Kallioniemi\, Director SciLifeLab and DDLS\n\n\n\nVeronica Rendo\, Uppsala University\n\n\n\n\n\n\n\n\nRegister here\n\n\n\nWhen the event is fully booked\, add yourself to the waiting list. You will be notified by email if a place becomes available. We kindly ask participants to cancel if they can´t come so the seat can become available to someone else. Thank you! \n\n\n\n\n\n\n\nProgram\n\n\n\nH:son Holmdahlsalen\, Ing 100/101\, 2 tr. Akademiska sjukhuset\, Uppsala. \n\n\n\n08:45Registration 08:45 – Please be seated at 09:1509:15Welcome and Introduction to Precision Medicine and Diagnostics Research AreaBasic science 1: Tumor heterogenetity and dynamics. Moderator: Sven Nelander\, SciLifeLab\, Uppsala University09:30Data-Driven Hallmarks (DDHMs) for Cancer Diagnostics and Precision Therapy\, Olli Kallioniemi\, SciLifeLab\, KI09:50Precision Medicine in Head and Neck Cancer Powered through Single-cell RNA Sequencing\, Michael Mints\, Weizmann Institute of Science\, Israel10:15Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers\, Ida Larsson\, Uppsala University10:35Coffee breakBasic science 2: Pushing the envelope on cancer genetics. Moderator Janne Lehtiö\, SciLifeLab\, KI10:55Genetic variation exposes regulators of hematopoietic stem and progenitor cells in vivo in humans\, Björn Nilsson\, Lund University11:15Using Evolutionary Constraint to Define Novel Candidate genes in Brain Tumors\, Karin Forsberg Nilsson\, Uppsala University11:35Understanding brain tumors; machine learning meets epidemiology\, Beatrice Melin\, Umeå University11:55Identification and exploration of toxic genes in human cancer\, Veronica Rendo\, Uppsala University12:15Lunch and network13:15DDLS Precision Medicine and Data Science Node\, Janne Lehtiö\, SciLifeLab\, KI13:25Panel discussion with all the speakers. Moderator: Janne Lehtiö\, SciLifeLab\, KIAI\, cancer\, and precision medicine. Moderator: Päivi Östling\, SciLifeLab\, KI14:05Artificial intelligence cervical cancer diagnostics at the point-of-care\, Nina Linder\, Uppsala University14:25AI for Breast Cancer Risk Prediction\, Fredrik Strand\, KI14:45The use of artificial intelligence in gastrointestinal oncology – past\, present and future\, Hannah Sophie Muti\, University Hospital Dresden\, Germany and EKFZ Institute for Digital Health\, Technical University Dresden\, Germany15:10Coffee breakDDLS Fellows session. Moderator: Åsa Johansson\, SciLifeLab\, Uppsala University15:30Pre-malignant clonal hematopoiesis stratifies risk of hematologic cancers\, Abhishek Niroula\, DDLS Fellow\, University of Gothenburg15:50A deep learning model of cellular networks\, Avlant Nilsson\, DDLS Fellow\, KI16:10Closing\, Sven Nelander\, Uppsala University 16:15The symposium ends\n\n\n\n\n\n\n\nFind your way to the Venue! \n\n\n\nEvent coordinator: Fulya Taylan\, DDLS RA coordination and Erika Erkstam\, Operations office\, SciLifeLab. \n\n\n\n\n\n\n\nMembers of The Data-driven Precision Medicine & Diagnostics expert group:\n\n\n\nGunnar Cedersund\, Linköping UniversitySven Nelander\, Uppsala UniversityLars Klareskog\, Karolinska InstitutetJohan Trygg\, Umeå UniversityPatrik Georgii-Hemming\, Karolinska InstitutetPäivi Östling\, KI (adj. SciLifeLab Precision Medicine Capability lead)Francis Lee (adj. WASP-HS representative in DDLS)David Gisselsson Nord (adjunct as GMS representant)Janne Lehtiö\, chair (DDLS SG member) \n\n\n\nAbstracts\n\n\n\nKarin Forsberg Nilsson Using Evolutionary Constraint to Define Novel Candidate Genes in Brain Tumors\nCurrent knowledge of cancer genomics remains biased against non-coding mutations. To systematically search for regulatory non-coding mutations\, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end\, we use whole-genome sequencing data from the International Cancer Genome Consortium (ICGC) and combined it with evolutionary constraint inferred from 240 mammals\, to identify genes enriched in non-coding constraint mutations (NCCMs)\, mutations likely to be regulatory in nature. We compare medulloblastoma (MB)\, which is malignant\, to pilocytic astrocytoma (PA)\, a primarily benign tumor\, and find highly different NCCM frequencies between the two\, in agreement with the fact that malignant cancers tend to have more mutations. In PA\, a high NCCM frequency only affects the BRAF locus\, which is the most commonly mutated gene in PA. In contrast\, in MB\, >500 genes have high levels of NCCMs. Intriguingly\, several loci with NCCMs in MB are associated with different age of onset\, such as the HOXB cluster in young MB patients. NCCMs in this locus were found to alter expression of HOXB2\, HOXB5 and HOXB9 in MB cells. In adult patients\, NCCMs occurred in e.g. the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR\, and augmented responsiveness of MB cells to dasatinib\, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver genes may aid in patient stratification in MB\, and could be valuable for future selection of personalized treatment options. \n\n\n\nKarin Forsberg Nilsson is Professor of Stem Cell Research at the Department of Immunology\, Genetics and Pathology\, Uppsala\, and Dean of the Faculty of Medicine\, University. She is SciLifeLab Faculty\, and has a position as Guest Professor at the University of Nottingham\, UK. Karin Forsberg Nilsson obtained her PhD in 1992 from Uppsala University and did a postdoc 1994-1996 at the National Institutes of Health\, MD\, USA. She has held leadership positions in both pharmaceutical industry and academia. The focus of her lab is brain tumor biology and genetics. \n\n\n\n\nOlli Kallioniemi Data-Driven Hallmarks (DDHMs) for Cancer Diagnostics and Precision Therapy\nTranslating complex multi-level molecular profiling data into actionable insights for cancer diagnosis and therapy poses a formidable challenge. We propose here a paradigm for analyzing and interpreting in-depth multi-omics and functional drug response data derived from acute myeloid leukemia (AML)\, aiming at practical applications in precision clinical oncology. Our approach is based on Data-Driven Hallmarks (DDHMs)\, drawing inspiration from the Weinberg-Hanahan cancer hallmark concept (Hanahan\, 2022). While the original cancer hallmark concept provides a useful theoretical framework for understanding cancer\, it is not applicable for processing\, interpreting\, and translating molecular profiling data for precision diagnostics and therapy in individual patients. \n\n\n\nWe first acquired and integrated genomics\, transcriptomics\, epigenetics\, and proteomics data alongside ex-vivo drug response data for over 500 drugs across 150 AML samples\, resulting in nearly 100 million data points (Erkers et al.\, 2023). Subsequently\, we identified 11 dimensions of variability across the entire dataset\, referred here as DDHMs of AML. DDHMs intertwine specific multi-omics molecular features (potential diagnostic biomarkers) with distinct vulnerabilities to individual drugs (potential cancer treatments). DDHMs show proficiency in predicting high-risk AML and determining the effective drugs for each AML sample. The strategy of assembling drugs targeting active hallmarks in each patient offers a promising avenue for tailoring effective drug combinations. \n\n\n\nIn summary\, we showcase the conversion of millions of complex multi-omics research data into a manageable set of DDHMs\, which are based on specific biomarkers and linked drug vulnerabilities and provide an opportunity for tailoring drug treatments and drug combinations for individual patients. This approach aligns well with current practices and guidelines in translational\, clinical\, regulatory\, and industrial setting and could expedite bringing the benefits of data-driven precision medicine research to cancer patients. \n\n\n\nReferences: \n\n\n\n\nHanahan\, D. (2022). Hallmarks of Cancer: New Dimensions. Cancer Discov 12\, 31-46.\n\n\n\nErkers T\, Struyf N\, James T…. Orre L\, Jafari R\, Pawitan Y\, Seashore-Ludlow B\, Lehtiö J\, Lehmann S\, Östling P\, Kallioniemi O. Data-driven hallmarks of acute myeloid leukemia\, submitted\, 2023.\n\n\n\n\nOlli Kallioniemi\, M.D.\, Ph.D. is director of the Science for Life Laboratory (www.SciLifeLab.se)\, a national infrastructure for life sciences in Sweden and also a professor in Molecular Precision Medicine at the Karolinska Institutet (2015-present). He also directs the national SciLifeLab program on Data-Driven Life Science (DDLS). Olli Kallioniemi was previously the founding director of FIMM – the Institute for Molecular Medicine Finland at the University of Helsinki\, as part of the Nordic EMBL partnership in Molecular Medicine (2007-2015) Olli Kallioniemi is a member of European Molecular Biology Organization (EMBO)\, European Academy of Cancer Sciences\, the Nobel Assembly at the Karolinska Institutet and the Royal Swedish Academy of Sciences. \n\n\n\n\nIda Larsson Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers\nNervous system cancers contain a large spectrum of transcriptional cell states\, reflecting processes active during normal development\, injury response and growth. However\, we lack a good understanding of these states’ regulation and pharmacological importance. Here\, we describe the integrated reconstruction of such cellular regulatory programs and their therapeutic targets from extensive collections of single-cell RNA sequencing data (scRNA-seq) from both tumors and developing tissues. Our method\, termed single-cell Regulatory-driven Clustering (scRegClust)\, predicts essential kinases and transcription factors in little computational time thanks to a new efficient optimization strategy. Using this method\, we analyze scRNA-seq data from both adult and childhood brain cancers to identify transcription factors and kinases that regulate distinct tumor cell states. In adult glioblastoma\, our model predicts that blocking the activity of PDGFRA\, DDR1\, ERBB3 or SOX6\, or increasing YBX1 -activity\, would potentiate temozolomide treatment. We further perform an integrative study of scRNA-seq data from both cancer and the developing brain to uncover the regulation of emerging meta-modules. We find a meta-module regulated by the transcription factors SPI1 and IRF8 and link it to an immune-mediated mesenchymal-like state. Our algorithm is available as an easy-to-use R package and companion visualization tool that help uncover the regulatory programs underlying cell plasticity in cancer and other diseases. \n\n\n\nIda Larsson studied medical biotechnology at the Royal Institute of Technology in Stockholm and received her MScEng in 2018. She then continued as a PhD student in computational systems biology at Uppsala University\, where her research has focused on the brain tumor glioblastoma and developing methods for analyzing single-cell RNA sequencing data. She defended her PhD in 2023 and is now starting as a postdoctoral fellow at Dana-Farber Cancer Institute in Boston. Her research interests revolve around intratumoral heterogeneity and plasticity in neural cancers. \n\n\n\n\nNina Linder Artificial intelligence cervical cancer diagnostics at the point-of-care\nOur research group has developed and conducted proof-of-concept studies of a novel method that combines artificial intelligence (AI) and mobile digital microscopy for cell-based cervical cancer screening in resource-limited settings. The mobile microscopes are wirelessly connected via mobile networks for AI-based analysis and provide access to diagnostics where there is a lack of medical experts. We are now assessing the use of the new diagnostic method in the form of a validation studies in Kenya and Tanzania with the aim of detecting premalignant changes for the purpose of cervical cancer prevention. Cervical smears are collected at the point-of-care and digitized with mobile microscope scanners and premalignant cells detected with an AI-algorithm. Suspected abnormal cells are verified by a pathologist and treated. The method’s diagnostic accuracy\, technical feasibility\, cost and time per test\, and acceptance of the AI method is evaluated and compared to conventional diagnostics. Throughout the project\, opportunities for larger scale implementation of the diagnostic platform in East Africa are evaluated\, with the ultimate goal of achieving sustainable solutions for low-resource settings.The methods have great potential to improve equitable and sustainable access to high-quality diagnostics for cervical cancer screening among women residing in low- and middle income countries\, carrying the highest cervical cancer burden globally. \n\n\n\nNina Linder is a physician by training and received her MD and PhD from the University of Helsinki\, Finland and is an Associate Professor at Uppsala University\, Sweden as well the Institute for Molecular Medicine\, University of Helsinki\, Finland. Nina Linder’s current research involves the development of novel artificial intelligence-based solutions for cancer and infectious disease diagnostics. Linder is co-heading projects developing artificial intelligence-based tools for point-of-care diagnostics in a global setting. The overall goal of Linder’s research is to promote the implementation of innovative decision-support solutions for precision medicine to improve the translation from basic medical research to the doctor and patient at the clinic. \n\n\n\n\nBeatrice Melin Understanding brain tumors; machine learning meets epidemiology\nThe causes of glioma\, the most malignant brain tumor\, is in most cases unknown. Common environmental factors such as alcohol and smoking has not been linked to brain tumors. High doses of ionizing radiation are associated with increased risk\, but it explains very few cases. Therefore\, one assumption could be\, that glioma is an endogenous disease that is caused by a stochastic effect initiated by a complex inheritance and subsequent biological cascades leading to tumor development. To discover which biological parameters that are associated with glioma risk\, several factors need to be taken in consideration. Taking glioma as an example\, important factors when collecting data and samples and biostatistical considerations will be presented\, giving corner stones for how we have been able to harvest and find true association through data driven analyses. \n\n\n\nBeatrice Melin is MD\, PHD and Professor of Oncology at Umeå University and Director of Research Development and Innovation at Region Västerbotten. Professor Melin has worked in the field of brain tumor research for 25 years and published on both cohort\, blood tumor and registry studies. \n\n\n\n\nMichael Mints Precision Medicine in Head and Neck Cancer Powered through Single-cell RNA Sequencing\nHead and neck cancer (HNC) can be divided into two biologically distinct entities based on human papillomavirus (HPV) status. In HPV-negative HNC\, the main challenge remains finding treatments to improve survival rates and decrease recurrence\, while HPV-positive patients need better stratification methods to avoid morbidity from overtreatment. Intra-tumour heterogeneity (ITH) is a major feature in both types of HNC and a barrier to successful patient stratification and treatment. Despite its significance\, ITH remains poorly understood. \n\n\n\nWe posit that HNC tumours consist of a vast\, diverse ecosystem of cell types with different roles. In order to improve patient-tailored treatment\, our goal is to\, through single-cell RNA sequencing\, characterize these populations\, their biological and clinical significance and their roles in responses to various treatments. \n\n\n\nWe report firstly\, the identification of a novel population of cancer cells with undetectable HPV expression in HPV+ tumours. These cells are less proliferative\, more invasive and respond poorly to treatment. Validating these findings through TCGA\, we found that decreased HPV expression levels are linked to poor prognosis in HPV-positive oropharyngeal cancer. \n\n\n\nSecondly\, we show that malignant cells in HPV- oral cavity cancer express antigen-presentation genes\, and that expression of these genes together with an interferon signal across multiple cell types strongly predicts response to neoadjuvant PD-1 inhibition. \n\n\n\nFinally\, through collecting a dataset comprising > 120 HNC patients and one million cells\, we were able to find diverse recurrent cancer cell states and microenvironmental co-expression patterns. Notably\, we found a rare subset of cancer cells that undergo a full\, rather than partial epithelial-mesenchymal transition (EMT). These cells are linked to depletion of CD8+ T-cells and increased numbers of fibroblasts and macrophages in the microenvironment\, as well as poor outcomes. \n\n\n\nIn summary\, we have created a comprehensive atlas of the HNC ecosystem at previously unseen scale and resolution. We identify rare cell populations responsible for cancer hallmarks such as senescence\, proliferation and metastasis and show how subpopulations change in response to HPV infection\, radiotherapy and immunotherapy. This knowledge will greatly advance personalised treatment of head and neck cancer through guiding patient stratification\, drug development and treatment selection. \n\n\n\nMichael Mints studied medicine at Karolinska Institutet through the clinician-scientist training programme. He received his MD in 2013 and his PhD in 2015 at the Department of Oncology-Pathology. After clinical work in Umeå and a physician-researcher internship in Östersund he started a postdoc in Itay Tirosh’s lab at the Weizmann Institute in 2019. There\, his work focuses on leveraging single-cell RNA sequencing and computational methods in order to understand head and neck cancer heterogeneity with the goal of personalizing head and neck cancer treatment. \n\n\n\n\nHannah Sophie Muti The use of artificial intelligence in gastrointestinal oncology – past\, present and future\nArtificial intelligence (AI) can infer information from data in a way that exceeds human capacity to do so. Especially in clinical oncology\, scientists use AI to generate biomarkers\, find correlations or extract prognostic or predictive information. This talk will give you an idea of how it started\, how it’s going and what the future might hold for cancer researchers in an era of paradigm-shifting technological advances. \n\n\n\nHannah Muti is a Clinician/Scientist with interests in precision medicine in gastrointestinal oncology and visceral surgery. Her research covers the use of artificial intelligence to investigate gastrointestinal cancers in the context of precision oncology. She simultaneously works in the Department for Visceral\, Thoracic and Vascular Surgery at the University Hospital Dresden to obtain her specialization in visceral surgery.  \n\n\n\n\nAvlant Nilsson A deep learning model of cellular networks\nThe activity of human cells depends on interactions between molecules in molecular networks. Disruptions to these networks are common in disease\, e.g. it can drive unrestricted growth in cancer cells. Simulations of these processes could predict disease mechanisms and identify suitable drug targets. However\, these networks consist of thousands of different molecules with tens of thousands of interactions\, and it has been challenging to parametrize systems-wide models using traditional approaches. We have developed recurrent neural network models of the networks that use molecules as hidden nodes with connections constrained to known molecular interactions. These models predict unseen test-data from living cells\, e.g. we predict gene expression in macrophages in response to different ligands and we use the models to infer causative signaling cascades. Currently\, we are expanding the framework to integrate signaling\, metabolism\, and gene regulation for a more complete mechanistic description of cellular activities. \n\n\n\nAvlant Nilsson is a computational biologist and assistant professor in precision medicine at Karolinska Institutet\, Stockholm. He holds a MSc (2009-2014)\, and a PhD (2014-2019) degree in biological engineering from Chalmers University of Technology\, where his thesis focused on the metabolism of growing cells. In his postdoctoral work at Massachusetts Institute of Technology (2019-2023)\, he developed artificial neural network models to simulate signal transduction in immune cells. His new lab at Karolinska will be using these techniques to simulate cellular processes in cancer\, aiming at identifying effective drug combinations\, predicting resistance mechanisms\, and understanding cell-cell interactions in the tumor microenvironment. \n\n\n\n\nBjörn Nilsson Genetic variation exposes regulators of hematopoietic stem and progenitor cells in vivo in humans\nStem cell transplantation is a cornerstone in the treatment of blood malignancies. The most common method to harvest stem cells for transplantation is by leukapheresis\, requiring mobilization of CD34+ hematopoietic stem and progenitor cells (HSPCs) from the bone marrow into the blood. Identifying the genetic factors that control blood CD34+ cell levels could reveal new drug targets for HSPC mobilization. Here we report the first large-scale\, genome-wide association study on blood CD34+ cell levels. Across 13 167 individuals\, we identify 9 significant and 2 suggestive associations\, accounted for by 8 loci (PPM1H\, CXCR4\, ENO1-RERE\, ITGA9\, ARHGAP45\, CEBPA\, TERT\, and MYC). Notably\, 4 of the identified associations map to CXCR4\, showing that bona fide regulators of blood CD34+ cell levels can be identified through genetic variation. Further\, the most significant association maps to PPM1H\, encoding a serine/threonine phosphatase never previously implicated in HSPC biology. PPM1H is expressed in HSPCs\, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. Through functional fine-mapping\, we find that this downregulation is caused by the variant rs772557-A\, which abrogates an MYB transcription factor-binding site in PPM1H intron 1 that is active in specific HSPC subpopulations\, including hematopoietic stem cells\, and interacts with the promoter by chromatin looping. Furthermore\, PPM1H knockdown increases the proportion of CD34+ and CD34+90+ cells in cord blood assays. Our results provide the first large-scale analysis of the genetic architecture of blood CD34+ cell levels and warrant further investigation of PPM1H as a potential inhibition target for stem cell mobilization. \n\n\n\n\nAbhishek Niroula Pre-malignant clonal hematopoiesis stratifies risk of hematologic cancers\nClonal hematopoiesis (CH) is a pre-malignant condition characterized by the expansion of genetically distinct blood cell clones in healthy individuals. CH with cancer driver variations is common in the elderly population and is associated with a 10-fold higher risk of blood cancer. A number of genes recurrently mutated in CH are known (e.g.\, DNMT3A\, TET2\, and ASXL1); however\, these gene variants only account for <30% of CH clones in elderly individuals. To identify new genetic drivers of CH\, we analyzed exome sequencing data from peripheral blood samples of >50\,000 individuals. We identified CH with genetic variants in several genes previously not linked to CH. Further\, we grouped CH into myeloid and lymphoid based on the mutated genes\, which stratified the risk of incident myeloid and lymphoid malignancies. Integrating the genetic data with clinical measurements allowed identification of individuals at high risk of developing hematologic malignancies. Currently\, we are developing methods to analyze somatic variants across the whole genome to characterize CH and identify new genetic regulators of CH. \n\n\n\nI am a DDLS Fellow in precision medicine and diagnostics at the University of Gothenburg. I obtained my PhD from Lund University and did a postdoc at the Broad Institute\, Cambridge MA. My research background is on bioinformatics and human genomics\, focusing on the effects of genetic variants in human diseases including cancer. As a DDLS Fellow\, my research focuses on the study of clonal hematopoiesis (CH)\, a pre-cancer of blood. We utilize large-scale genomic data from population cohorts to understand the origin and evolution of CH and its malignant transformation. \n\n\n\n\nVeronica Rendo Identification and exploration of toxic genes in human cancer\nChromosomal gains are one of the most common somatic genetic alterations found in cancer. While the impact of sustained oncogene expression has been extensively studied\, the effects of copy number gains on “bystander” genes\, which are collaterally amplified\, remain less understood in terms of cellular fitness. To shed light on this\, we integrated the expression and copy number profiles of over 8\,000 TCGA tumors and CCLE cell lines\, along with the viability effect of gene overexpression from 17 human cancer ORF screens. Through this comprehensive and data-driven analysis\, we identified a group of genes termed ‘Amplification-Related Gain Of Sensitivity’ (ARGOS) genes. ARGOS genes are situated in frequently amplified regions of the genome\, and their expression level is reduced compared to their copy number status. However\, when overexpressed upon gain\, they prove to be toxic to the cell. Our compensation and toxicity analyses revealed five frequently amplified ARGOS genes. Notably\, one candidate showed a mechanism of toxicity involving altered DNA damage and innate immune signaling responses upon gene overexpression. This study represents a significant effort to better understand the toxicity effects associated with gene overexpression in human cancers. \n\n\n\nVeronica studied Biology at Simon Bolivar University in Venezuela\, and then moved to Sweden to pursue a PhD at Uppsala University. During this time\, she worked under the mentorship of Prof. Tobias Sjoblom and studied how genomic losses occurring in colorectal cancer can be exploited for therapy. In 2019\, she moved to Boston (USA) to pursue a postdoc in Dr. Rameen Beroukhim’s lab at Dana-Farber Cancer Institute\, affiliated with Harvard Medical School and the Broad Instititute of MIT and Harvard. Veronica’s research focused on studying therapeutic vulnerabilities associated with aneuploidy\, including predictors of resistance to clinically relevant p53 reactivation strategies in brain tumors and negative selection against amplifications in cancer. In 2023\, Veronica left the Beroukhim lab to start her own laboratory at the Department of Immunology\, Genetics and Pathology at Uppsala University. Here\, she combines descriptive and functional genomic approaches to understand how brain tumors respond and evolve during treatment. This includes continued exploration of how aneuploidy creates vulnerabilities that can be therapeutically exploited. \n\n\n\n\nFredrik Strand AI for Breast Cancer Risk Prediction\nAmong women attending screening\, 30% of their cancer is missed by current mammography-based screening. We have trained AI models to assess specific aspects of the mammography images to measure when a negative exam is less reliable. After retrospective validation we are conducting a randomized clinical trial selecting around 7% of women from screening to be offered MRI. \n\n\n\nFredrik Strand is a Swedish breast radiologist and associate professor at Karolinska Institutet\, Stockholm. He holds an MD\, PhD and MSc degrees\, and has prior experience as a strategy consultant and leading a start-up company. Fredrik is head of the research and education committee at the Swedish society of breast imaging. His academic research evolves around exploring AI for breast imaging. He and his team are involved in retrospective validation of AI algorithms\, prospective clinical trials\, and in developing new machine-learning algorithms for breast cancer detection and supplemental MRI imaging. URL:https://www.scilifelab.se/event/ddls-pmd-minisymposium-2023/ LOCATION:Martin H:son Holmdahlsalen\, Dag Hammarskjöldsväg 8\, Entrance 100\, Akademiska sjukhuset\, Uppsala CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/PMD_Icon.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230908T110000 DTEND;TZID=Europe/Stockholm:20230908T120000 DTSTAMP:20260503T183041 CREATED:20230808T131008Z LAST-MODIFIED:20230829T082636Z UID:10000943-1694170800-1694174400@www.scilifelab.se SUMMARY:Overview of compute and storage resources in data-driven life science DESCRIPTION:Compute and storage resources available to the life science field in Sweden are provided by several different organisations. SciLifeLab and the DDLS program are in various ways providing access to infrastructure\, new data services\, and support to existing ones. We work towards improved coordination and accessibility. \n\n\n\nAt this event on September 8\, representatives for SciLifeLab Data Centre\, National Bioinformatics Infrastructure Sweden (NBIS)\, National Academic Infrastructure for Super­computing in Sweden (NAISS) and National Supercomputer Centre at Linköping University (NSC) will give an overview of who does what and how to access different services\, and how to interact regarding input\, feedback or suggested new services. There will also be time for a Q & A. \n\n\n\nAgenda \n\n\n\n11:00-11.05  Introduction\, Johan Rung \n\n\n\n11:05-11:15 Overview of SciLifeLab resources\, Jonas Svensson\, Liane Hughes\, Konstantin Dossis \n\n\n\n11:15-11:25 Overview of NAISS resources\, Johan Raber \n\n\n\n11:25-11:35 Overview of NSC resources (Berzelius)  Soumi Chaki\, Xuan Gu \n\n\n\n11:35-11:45 Overview of NBIS & UPPMAX resources\, Marcus Lundberg \n\n\n\n11.45.-11:50 Summary \n\n\n\n11:50-12:00 Q & A- ways of working \n\n\n\n \n\n\n\n12:00-12.30 For follow-up questions in four breakout rooms: SciLifeLab\, NBIS-UPPMAX\, NAISS\, or NSC. \n\n\n\nDate: Sept 8\, 11:00-12:00 CEST on Zoom\, followed by 30 min break-out rooms for additional questions to the respresentatives from SciLifeLab\, NBIS-UPPMAX\, NAISS\, and NSC. \n\n\n\nTarget group: Researchers\, research staff and others interested in compute and storage resources in life science. \n\n\n\n\nRegister here\n\n\n\n\nWelcome! \n\n\n\nFor questions about the event please contact SciLifeLab Data Centre on email datacentre@scilifelab.se For more information about services for data-driven life science research see SciLifeLab Data Platform URL:https://www.scilifelab.se/event/overview-of-compute-and-storage-resources-in-data-driven-life-science/ CATEGORIES:Event ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230918T151500 DTEND;TZID=Europe/Stockholm:20230918T161500 DTSTAMP:20260503T183041 CREATED:20230831T123817Z LAST-MODIFIED:20230904T061932Z UID:10000963-1695050100-1695053700@www.scilifelab.se SUMMARY:[The Svedberg seminar] - Female sex hormones and the human microbiome DESCRIPTION:Luisa Hugerth \n\n\n\nAssistant ProfessorDDLS FellowDepartment of Medical Biochemistry and Microbiology\, UU \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\n\n\n\n\nLuisa Hugerth has a background in molecular biology and biomedicine\, but got her PhD in 2016 at KTH Royal Institute of Technology with an analysis of microbial community time-series in the Baltic Sea. After that\, Dr. Hugerth spent 6 years at the Centre for Translational Microbiome Research in Karolinska Institutet\, where she studied the human microbiome in functional bowel disorders\, before becoming deeply involved in research on the microbiome of pregnant and non-pregnant women. Since 2022\, she is a DDLS fellow in epidemiology and biology of infection at Uppsala University’s Department of Medical Biochemistry and Microbiology\, Imbim \n\n\n\n \n\n\n\nFemale sex hormones and the human microbiome\n\n\n\nEstrogen and progesterone have pleitropic effects throughout the body. This includes mucosal surfaces and the diverse microbial communities that inhabit them. Microbiota can enhance or dampen these effects\, thereby acting as risk mediating factors for various diseases\, most notably gynecologic and periodontal inflammation. The vaginal microbiota has been epidemiologically linked to various outcomes\, from STI acquisition to preterm birth. The oral microbiota has also been causally linked to as disparate outcomes as preterm birth and newly onset depression. Here\, I will present ongoing work on the interplay between endogenous and exhogenous hormones on the oral\, vaginal and gut microbiome\, in women with a regular menstrual cycle as well as pregnant women. Additionally\, since both sex hormones and the gut microbiome are implicated in mood disorders\, I will touch upon the gut-brain axis in relation to pregnancy nausea and perinatal depression. \n\n\n\n\n\n\n\n\n\n\n\nHost: Mikael Sellin mikael.sellin@imbim.uu.se\, UU URL:https://www.scilifelab.se/event/the-svedberg-seminar-luisa-hugerth/ LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20230921T090000 DTEND;TZID=Europe/Stockholm:20230921T170000 DTSTAMP:20260503T183041 CREATED:20230426T155028Z LAST-MODIFIED:20230922T130208Z UID:10000871-1695286800-1695315600@www.scilifelab.se SUMMARY:Computational Methods in Evolution and Biodiversity DESCRIPTION:This symposium and workshop will showcase the latest computational methods for analysing big data in evolution and biodiversity and provide an opportunity for participants to gain hands-on experience in these methods. Two keynote speakers will discuss a) new advances in using image recognition to analyse biodiversity and b) population genomics approaches to understand the effects of climate adaptation on genetic diversity. In addition\, there will be three parallel computer workshops focused on the application of computational and machine learning methods to genome variation and biodiversity data. Participants should bring their own computers to join these workshops. This symposium is organised by the DDLS Evolution and Biodiversity expert group in conjunction with the SciLifeLab summit on Genomics of Biodiversity and Evolution. \n\n\n\nPost-symposium material from the Workshops\n\n\n\nWe have the workshop leaders’ permission to share links to the material for the workshops in the DDLS symposium Computational Methods in Evolution and Biodiversity. Feel free to do tutorials from the other workshops than the one you attended. \n\n\n\nTobias Andermann’s workshop (slides\, tutorial\, and data): https://github.com/tandermann/ai_workshop \n\n\n\nPer Unneberg’s workshop: https://percyfal.github.io/workshop-biodiversity-summit/lab/index.html \n\n\n\nMarcin Kierczak’s workshop: https://github.com/mkierczak/autoencoders_workshop \n\n\n\n\n\n\n\n\n\n\n\nProgram\n\n\n\n09:00Welcome and introduction09:10Challenges in Fine-Grained Image Analysis. Keynote speaker: Serge Belongie\, Pioneer Center for AI\, Denmark09:50Computational methods give insight into paradigms and paradoxes in landscape genomics. Keynote speaker: Katie E. Lotterhos Northeastern University\, USA10:30CoffeeIntroduction to Workshop x 311:00Looking at population structure from a machine learning perspective\, Marcin Kierczak11:25Neural Networks for biodiversity research: challenges and opportunities\, Tobias Andermann11:50Inference of ancestral recombination graphs for population genomics\, Per Unneberg12:15Lunch13:30Workshop x 3; parallel sessions:Room P232\, P224\, P216. (Guidance on site)From PCA to Generative Deep Learning Models for better understanding population structure\, Marcin KierczakBuilding your own customized neural network model (bring your own data if you want)\, Tobias AndermannIntroduction to whole genome tree sequence inference with tsinfer\, Per Unneberg17:00End of DayVenue: Vivi Täckholmsalen (Q-salen)\, NPQ-huset\, Svante Arrhenius väg 20\, Stockholm University\n\n\n\n\n\n\n\nAbstract Serge Belongie\, Pioneer Center for AI\, Denmark\nChallenges in Fine-Grained Image Analysis\n\n\n\nFine-grained image analysis (FGIA) is a longstanding and fundamental problem in computer vision and pattern recognition\, and underpins a diverse set of real-world applications. The task of FGIA is concerned with visual objects from subordinate categories\, e.g.\, species of birds or models of cars. The small inter-class and large intra-class variation inherent to fine-grained image analysis makes it a challenging problem. Capitalizing on advances in deep learning\, in recent years we have witnessed remarkable progress in deep learning powered FGIA. In this talk we review representative examples in the context of recognition\, retrieval\, and generation/synthesis. In addition\, we also review other key issues of FGIA\, such as publicly available benchmark datasets\, related domain-specific applications\, and connections with other modalities including text and audio. We conclude by highlighting several research directions and open problems. \n\n\n\n\nAbstract Katie E. Lotterhos\, Northeastern University\, USA\nComputational methods give insight into paradigms and paradoxes in landscape genomics \n\n\n\nPredicting organisms’ vulnerabilities to rapid and multivariate climate change is a major scientific challenge. A hurdle to addressing this challenge arises from evolution in multivariate environments. This talk will highlight how adaptation in multivariate environments can lead to unexpected patterns at the alleles under selection\, which has implications for the inference of the genetic basis of adaptation and for predicting vulnerability to environmental change.  \n\n\n\n\n\n\n\n\nWorkshop\n\n\n\nFrom PCA to Generative Deep Learning Models for better understanding population structure\, Marcin Kierczak \n\n\n\nThe workshop will focus on looking at different ways of modelling and visualising population structure based on genomic kinship. Starting from more traditional approaches like PCs or MDS as a benchmark\, we will build more complex deep learning-based models and discuss when such approach can be beneficial. Finally\, we will see how deep learning can potentially be used to augment original input data with some artificially-generated individuals with desired pre-defined kinship relations. Throughout this workshop\, we will be using Python and keras interface to Tensorflow. \n\n\n\nBuilding your own customized neural network model (bring your own data if you want)\, Tobias Andermann \n\n\n\nIn this workshop we will cover some computational and data processing tools that will come in handy when working with neural network models. The workshop is focused on implementing your own custom-built neural network model for a chosen task. The provided examples will be from the field of biodiversity research\, but you can apply the tools we cover during the workshop to problems in other research fields. In general this is an easy to follow and hands-on introduction to using neural network models. The workshop requires very basic familiarity with Python\, as the model will be implemented using the Python tensorflow library. \n\n\n\nIntroduction to whole genome tree sequence inference with tsinfer\, Per Unneberg \n\n\n\nIn this workshop\, we will introduce tree sequence (a.k.a. ARG) inference using the tsinfer library. We will build tree sequences from input variation data and look at some applications and analyses using the resulting tree sequences. As the exercises will be performed in jupyter notebooks in Python\, basic familiarity with Python is required. \n\n\n\n \n\n\n\n\n\n\n\nScientific Committee\n\n\n\n\nFredrik Ronquist\, NRM\n\n\n\nTanja Slotte\, SU\n\n\n\nMatthew Webster\, UU\n\n\n\n\n\n\nData-driven Evolution and biodiversity\n\n\n\nThe DDLS subject area concerns research that takes advantage of the massive data streams offered by techniques such as high-throughput sequencing of genomes and biomes\, continuous recording of video and audio in the wild\, high-throughput imaging of biological specimens\, and large-scale remote monitoring of organisms or habitats. This research subject area aims to lead the development or application of novel methods relying on machine learning\, artificial intelligence\, or other computational techniques to analyze these data and take advantage of such methods in addressing major scientific questions in evolution and biodiversity. \n\n\n\nThe research area Expert Group arranges symposia and workshops and welcomes interested to join the activities. More information about the research area Evolution and Biodiversity here. URL:https://www.scilifelab.se/event/computational-methods-in-evolution-and-biodiversity/ LOCATION:Vivi Täckholmsalen (Q-salen)\, NPQ-huset\, Stockholm University\, Svante Arrhenius väg 20\, Stockholm\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/EB_Icon.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231106T090000 DTEND;TZID=Europe/Stockholm:20231110T170000 DTSTAMP:20260503T183041 CREATED:20230818T135627Z LAST-MODIFIED:20230915T130032Z UID:10000955-1699261200-1699635600@www.scilifelab.se SUMMARY:DDLS Population genomics in practice DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of hands-on and practical skills for the analyses of population genomics data. \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-08-17 \n\n\n\nApplication closes: 2023-09-30 \n\n\n\nConfirmation to accepted students: 2023-10-10 \n\n\n\nCourse Leader and teachers: Per Unneberg (CL)\, Nikolay Oskolkov\, Jason Hill\, André Soares \n\n\n\nIn case you miss information on any of the above dates\, please contact: edu.population-genomics-in-practice@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an introduction to commonly used methods in population genomics. As the focus of the course is on hands-on work\, the topics have been designed to cover the fundamental analyses that are common in many population genomics studies. The course consists of lectures and exercises\, with a focus on the practical aspects of analyses. Whereas lectures introduce some background theory\, their primary aim is to set the stage for accompanying exercises. \n\n\n\nTopics covered will include: \n\n\n\n\nFoundations of population genetics\n\n\n\nIntroduction to simulation and the coalescent\n\n\n\nBasics of variant calling\n\n\n\nVariant filtering and sequence masks\n\n\n\nCharacterization and interpretation of DNA sequence variation\n\n\n\nCalculation and interpretation of summary statistics from variation data\n\n\n\nInvestigating population structure with admixture modelling and principal component analyses\n\n\n\nDemographic modelling using sequentially Markovian coalescent models and linkage disequilibrium\n\n\n\nSelection scans\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ndescribe the different forces of evolution and how they influence genetic variation\n\n\n\nunderstand and interpret genealogical trees and how they relate to genetic variation data\n\n\n\ndescribe the basics of the coalescent\n\n\n\nperform simple coalescent simulations with msprime\n\n\n\nrun simple SLiM forward simulation models\n\n\n\ndescribe and run the steps of a variant calling pipeline\, including quality control of raw reads\, read mapping\, and variant calling\n\n\n\nknow how and when to filter raw variant calls using manual coverage filters\n\n\n\ndescribe and calculate nucleotide diversity from variation data\n\n\n\nanalyse population structure with admixture modelling and dimensionality reduction methods\n\n\n\nperform demographic modelling with sequential Markovian coalescent models\n\n\n\ndescribe methods that identify regions undergoing adaptation and selection\n\n\n\nrun selection scans\, score identified regions and interpret findings in the context of genome annotations\n\n\n\n\n\n\n\n\n\n\nEntry Requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge in R or Python\n\n\n\nBasic knowledge of variant calling\, or the equivalent of NBIS course “Introduction to Bioinformatics using NGS data”\n\n\n\nBasic knowledge of population genetics\n\n\n\nBasic understanding of frequentist statistics\n\n\n\nA computer\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with analysis of NGS and other omic data\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance. URL:https://www.scilifelab.se/event/population-genomics-in-practice/ LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231115T123000 DTEND;TZID=Europe/Stockholm:20231116T123000 DTSTAMP:20260503T183041 CREATED:20230119T182051Z LAST-MODIFIED:20231114T233510Z UID:10000792-1700051400-1700137800@www.scilifelab.se SUMMARY:DDLS Annual Conference 2023; The emerging role of AI in data-driven life science DESCRIPTION:Image generated with DALL-E 3\n \n\n\n\n\n\n\n\n\nThis DDLS Annual Conference brings together the data-driven community in Life Science\, introduces newly appointed DDLS fellows\, and provides opportunities for networking across the research community and SciLifeLab infrastructures. The theme for 2023 is “the emerging role of AI in data-driven life science”\, and we are excited to welcome Prof. Dr. Fabian Theis\, Director of the Computational Health Center and Director of the Institute for Computational Biology and Rocio Mercado\, WASP Fellow\, Chalmers University of Technology as Keynote speakers. There will be presentations from DDLS fellows\, and invited speakers on how they use AI in their research and their future visions. The conference also features two pre-conference introductory lectures on AI for imaging and natural language processing and a post-conference workshop on AI model serving. \n\n\n\nTarget group: All scientists interested in data-driven research are welcome to join the 2-day lunch-to-lunch Conference in Stockholm. \n\n\n\nRegistration\n\n\n\nThe onsite event has reached total capacity. Please register as a Zoom participant to get access to the Zoom link. Feel free to add yourself to the waiting list\, and you will be notified by email if a place becomes available. \n\n\n\nRegistration for zoom link\n\n\n\n\n\n\n\nPoster session\n\n\n\nPoster session\, Flash Talk & Best Poster Award (click to open)\nPoster list \n\n\n\nPoster-List-DDLS-Annual-conference-2023Download\n\n\n\nPoster booklet\, including abstracts \n\n\n\nPoster-Booklet-DDLS-Annual-conference-2023Download\n\n\n\nThe DDLS Annual Conference Best Poster Award\, encourages the submission and exhibition of high-quality posters carried out by young scientists\, including Ph.D. students\, post-doctoral researchers\, etc. The poster should be on a topic related to data-driven life science. The Prize\, which is based upon the decision of a Scientific Committee-appointed Jury\, consists of a certificate and a travel grant of up to 5 000 SEK. The travel must be booked and ordered through the DDLS Support team and follow regular University travel policy. The trip should be completed before 2024-12-31. \n\n\n\nThe Best Poster Award winner for 2022 was Adelina Rabenius\, KTH\, and we are proud to support her attendance at an EMBO conference this summer. \n\n\n\nOrganizer: SciLifeLab\, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science\, on behalf of the DDLS Steering group. \n\n\n\n\nPre-conference introductory lectures \n\n\n\nIn the morning of the first conference day\, there will be two introductory lectures; one on AI within image analysis (by Anna Klemm from Bioimage Informatics Facility\, SciLifeLab) and one on large-language models (by Magnus Sahlgren from AI Sweden). The purpose of these lectures is to cover the basics and emerging role of AI within these two active fields. No prior knowledge of the fields is required. \n\n\n\nPost-conference activities\n\n\n\nNote! The Post-conference workshop and different DDLS stakeholder meetings will be handled separately and require separate registrations. \n\n\n\nWorkshop\n\n\n\nBuilding and sharing machine learning demo applications within life sciences: a practical tutorial. This event is now full\, you can register for the wait list only (in case we receive a cancellation). November 16\, at 13:30 – 15:30. SciLifeLab Campus Solna\, Tomtebodavägen 23. Meet-up in the Lobby. Room Gamma 2 Lunchroom. Participant list here \n\n\n\nStakeholder meetings\n\n\n\nDDLS Fellows meeting (DDLS Fellows only). November 16\, at 13:30 – 15:30. Biomedicum\, Solnavägen 9. Room B0317. Participant list here \n\n\n\nDDLS Fellows PhD & Postdocs meeting (for the PhD and Postdoc members of the DDLS Fellows research groups). November 16\, at 13:30 – 15:30. Biomedicum\, Solnavägen 9. Room B0313. Participant list here \n\n\n\nDDLS Cell and Molecular Biology Expert group meeting (for the CMB Expert group and the CMB Data Science Node). November 16\, at 15:30 – 17:30. SciLifeLab Campus Solna\, Tomtebodavägen 23. Room Earth \n\n\n\n\nDDLS Research area Cell and Molecular Biology Symposium\, Nov 17\n\n\n\nThe DDLS research area\, Cell and molecular biology\, invites you to the first in-person symposium on November 17 from 9 to 14. The day will be an introduction to the research area Fellows and Expert Group. \n\n\n\nMore information here\n\n\n\n\nProgram\n\n\n\nNovember 15\n\n\n\n09:30Venue: Jacob Berzeliussalen\, Berzelius väg 3\, SolnaRegistration is open from 09:30. Hang your poster from 09:30 to 12:30.10:00Pre-conference introductory lecture: AI in bioimage analysisAnna Klemm\, Uppsala University10:45Pre-conference introductory lecture: Large Language ModelsMagnus Sahlgren\, AI Sweden11:30Lunch12:30WelcomeOla Spjuth\, chair of Scientific Committee DDLS Annual ConferenceModerator: Ola Spjuth\, Uppsala University12:35Data-driven Life ScienceOlli Kallioniemi\, Director SciLifeLab13:00Blood proteome is a powerful tool to monitor human health and diseaseWen Zhong\, DDLS Fellow\, Linköping University 13:20Artificial intelligence-based computational pathology for precision diagnostics in breast cancerMattias Rantalainen\, KI13:40Coffee break 14:10Keynote: Generative AI for modeling single-cell state and responseFabian J. Theis\, Helmholtz Munich\, Technical University of Munich15:00Short breakModerator: Fredrik Johansson\, Chalmers15:155 x Flash Talks à 5 min per selected poster1. Gonzalo Uribarr2. Melisa Maidana Capitan3. Marcel Tarbier4. Sheng Joevenller5. Philipp Rentzsch 15:45Poster session with snacks and drinks17:30End of Day 117:30Speakers Dinner. Invited only. Speakers\, DDLS Steering Group\, DDLS Fellows\, Organizing committee\n\n\n\nNovember 16\n\n\n\n08:30CoffeeModerator: Laura Carroll\, Umeå University09:00From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processesJuliette Griffé\, DDLS Fellow\, Stockholm University09:20Multi-omics data integration with robust penalized regression identifies context-dependent signaling networksCemal Erdem\, DDLS Fellow\, Umeå University09:40AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell ModelingWei Ouyang\, DDLS Fellow\, KTH10:00Data Centre – capabilities and collaborationsJohan Rung\, SciLifeLab Data centre10:20Coffee break10:45Announcement of Best Poster Award10:50Keynote: Transforming Biomolecular Engineering Through AIRocio Mercado\, WASP Fellow\, Chalmers University of Technology Moderator: Johan Bengtsson-Palme\, Chalmers11:45Panel discussion about the emerging role of AI in DDLS12:30Lunch and end of DDLS Annual Conference13:30Post-Conference activities (separate registration)Building and sharing machine learning demo applications within life sciences: a practical tutorial. The event is fully booked.SciLifeLab Campus Solna\, Tomtebodavägen 23A. Room Gamma lunch room.DDLS Fellows meetingBiomedicum\, Solnavägen 9. Room B0317.DDLS Fellows PhD & Postdoc meetingBiomedicum\, Solnavägen 9. Room B0313.15:30End of Post-Conference activities15:30DDLS Cell and Molecular Biology Expert group meetingSciLifeLab Campus Solna\, Tomtebodavägen 23A. Room Earth.\n\n\n\nAbstracts\n\n\n\nPre-Conference Lectures\n\n\n\nAnna Klemm – AI in bioimage analysis\nIn this introductory lecture I will present how AI is used in bioimage analysis. The lecture will start with examples of “classical” image analysis to then explain the concepts of machine learning and AI-techniques in bioimage analysis. In the lecture I will give examples of life science projects in which we have trained convolutional neural networks to segment and classify structures of interest in the images\, or encode entire images. I will explain why we chose AI-based methods over classical image analysis and will also point to resources of the growing landscape of workflows\, pre-trained networks\, and repositories of freely available bioimage data + their annotations. \n\n\n\n\n\n\n\nExample of using a CNN for image segmentation on H&E-stained sections of mouse salivary glands. Segmentation starting from manually generated ground-truth\, using a Xception network model. Source: https://biifsweden.github.io/projects/2023/08/07/EduardoVillablanca2023-1/\, Xenia Tolstoy\, Christophe Avenel (BIIF) \n\n\n\n\nMagnus Sahlgren – Large Language Models\nThis presentation gives an introduction to and overview of the currently dominating trend in AI with Large Language Models (LLMs). We cover the theoretical background\, basic architectures\, training methodologies\, and capabilities of LLMs\, spotlighting models like the GPT series\, as well as Sweden’s national initiative GPT-SW3. We will touch upon diverse applications of LLMs in both the public and private sectors\, and address various considerations and challenges related to LLMs\, including biases\, transparency\, and societal implications. \n\n\n\n\nConference\n\n\n\nMartin Eklund – Prediction models and artificial intelligence for improving prostate cancer diagnostics and treatment\nProstate cancer diagnostics and treatment suffer from inefficient use of information for clinical decision making\, leading to high rates of overdiagnosis and overtreatment of indolent disease at the same time as prostate cancer is the leading cause of cancer death among men. We will in our presentation discuss how we are systematically trying to develop and clinically implement prediction models and artificial intelligence (AI) systems to address these inefficiencies. We will for example discuss the combination of the Stockholm3 test with MRI to improve prostate cancer diagnostics (Eklund et al. NEJM\, 2021; Nordström et al. Lancet Oncology\, 2021)\, and show results from the development of an AI-system for diagnosis and grading of prostate cancer in biopsies (Ström et al. Lancet Oncology\, 2020; Bulten et al. Nature Medicine\, 2022; Olsson et al. Nature Communications 2022)\, which we have demonstrated can performs on par with internationally leading uro-pathologist. We will also discuss the link between AI and clinical trials and how clinical trials can be transformed into continuous learning systems\, which we will exemplify with the ongoing ProBio trial for improving treatment for men with metastatic prostate cancer (Crippa et al. Trials\, 2020; De Laere et al. European Urology Focus\, 2022). \n\n\n\n\nCemal Erdem – Multi-omics data integration with robust penalized regression identifies context-dependent signaling networks\nCells integrate signals from different external stimuli to decide their fate\, such as growth or death. The “context” of a cell -the extracellular and intracellular environments- dictates the structure of signaling networks that determine such cellular responses. Identifying context-specific edges is vital for predicting and understanding cell decision-making logic. However\, robust identification of context-dependent network structures remains a broadly unsolved problem. Here\, I will talk about a pipeline we built previously to integrate multi-omics datasets using machine learning algorithms in a central-dogmatic view. Applying this pipeline to publicly available datasets\, we showed that it could pinpoint differentially activated pathways: (i) in response to two highly similar sister cytokines in breast epithelial cells and (ii) in breast tumor subtypes. I will conclude my talk with a vignette showing how such knowledge can further be utilized to explore new gene regulatory mechanisms. \n\n\n\n\nJuliette Griffié – From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processes\nSingle Molecule Localisation Microscopy (SMLM) is a fluorescence super-resolution microscopy technique which allows to image fluorophores in cells with unprecedented resolution (typically 10-30nm). It produces lists of localisations from which fundamental information about key cellular processes can be extracted. We will focus here on how SMLM data sets can be used as input to design dynamic models on cellular membrane biophysics. We will apply these data-driven models to reliably recapitulate and predict the nanoscale requirements for immune cells activation as well as to control and modify cellular signalling in the context of diseases. \n\n\n\n\nRocío Mercado – Transforming Biomolecular Engineering Through AI\nAI’s lightning-paced advancements are ushering in a new era of scientific research\, and the realm of molecular engineering stands as a prime beneficiary of this transformation. This talk explores the growing integration of AI in the life sciences\, with a primary emphasis on therapeutic discovery\, shedding light on the current state-of-the-art for molecular discovery and future prospects. We delve into the evolution of deep generative models and their practical applications in molecular engineering\, giving a few key examples of reinforcement learning and synthesizability-constrained design in this domain. Moreover\, we share recent progress in challenging application areas\, such as targeted protein degradation and synthesis prediction. With adaptive AI models\, capable of learning from vast datasets in real time\, we can streamline computational and experimental resources\, improving efficiency as we search through the complex chemical space. The talk will conclude with an overview of leading developments in AI which have yet to see widespread application in the life sciences\, offering new horizons for scientists exploring data-driven life science research. These innovative methodologies hold the potential to reshape conventional practices and bridge the gap between scientific exploration and AI-driven innovation. \n\n\n\n\nWei Ouyang – AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell Modeling\nAs part of the Data-Driven Life Science fellows program at SciLifeLab\, AICell Lab is actively laying the groundwork for a future powered by AI in cellular and molecular biology. With a focus on long-term strategic planning\, the lab is investing in state-of-the-art automated imaging farms\, complete with advanced microscopes\, robotic arms\, liquid handlers\, and automatic incubators. \n\n\n\nIn addition\, AICell Lab is developing specialized AI software to augment real-time microscopic imaging\, enable smart acquisition\, facilitate robotic control\, integrate multi-omics data\, and power AI-driven cell simulators\, among other functionalities. These preparatory steps align with the lab’s long-term vision to build large-scale\, comprehensive models of human cells\, utilizing both existing multi-omics datasets and new data generated in-house. \n\n\n\nThrough this focused preparation and investment\, AICell Lab aims to redefine in-silico cellular research and drug discovery\, contributing to a unified and systematic understanding of human cellular biology. \n\n\n\n\nFabian J. Theis – Generative AI for modeling single-cell state and response\nAdvances in single cell genomics nowadays allow the large scale construction of organ atlases. These can be used to study perturbations such as signaling\, drugs or diseases\, with large-scale access to state changes on the multi-omic and spatial level. This provides an ideal application area for machine learning methods to understand cellular response. With generative AI revolutionizing many fields of science by allowing researchers to explore uncharted territories\, generate novel hypotheses\, and simulate complex phenomena\, we ask how it has been enabling modeling single cell variation\, potentially towards a single cell foundation model. \n\n\n\nAfter reviewing deep generative representation learning approaches to identify the gene expression manifold\, I will shortly outline some applications on cell atlas building. Then I will discuss interpretable modeling of perturbations on this manifold\, in particular effect of drug responses as well as multiscale readouts such as disease state across patients\, and how to learn organism-wide cell type predictors. I will finish with extensions towards temporal and spatial observations. \n\n\n\n\nWen Zhong – Blood proteome is a powerful tool to monitor human health and disease\nThe rise of high throughput molecular technologies has shed lights on the development of next-generation molecular diagnostics and biomarkers for patient stratifications in the precision medicine era. There is an urgent need to develop new systematic tools to combine multi-omics data and link genotype to phenotype to expand our knowledge of complex traits of human diseases. Our research group mainly focuses on the integration of multi-omics\, the interplay between genetics and phenotypes\, and the development of data-driven strategies/tools for precision medicine. The aim is to investigate the molecular biomarkers for the estimation of disease risks\, early diagnosis of disease\, stratification of drug treatment response\, disease progression monitoring and the stratification of patients.  \n\n\n\n\nWorkshop \n\n\n\nBuilding and sharing machine learning demo applications within life sciences: a practical tutorial\nIt is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application\, prepare it for deployment\, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable within a couple of hours. \n\n\n\nThe workshop will last for 2 hours with a break in the middle. We have room to accept 30 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nNote that registration for the workshops is separate from the registration for the conference. Please see the workshop page for information on registration. \n\n\n\n \n\n\n\n\nScientific Committee\n\n\n\n\nChair: Ola Spjuth\, Uppsala University\n\n\n\nJohan Bengtsson-Palme\, Chalmers\n\n\n\nLaura Carroll\, Umeå University\n\n\n\nFredrik Johansson\, WASP\, Chalmers\n\n\n\n\nProject leader\n\n\n\n\nErika Erkstam\, Operations office URL:https://www.scilifelab.se/event/ddls-annual-conference-2023/ LOCATION:Jacob Berzelius salen\, KI\, Berzelius väg 3\, Solna\, 171 65\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/DDLS_cropped-Liten.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231116T133000 DTEND;TZID=Europe/Stockholm:20231116T153000 DTSTAMP:20260503T183041 CREATED:20231017T130803Z LAST-MODIFIED:20231101T115949Z UID:10001003-1700141400-1700148600@www.scilifelab.se SUMMARY:Building and sharing machine learning demo applications within life sciences: a practical tutorial DESCRIPTION:This workshop is part of the DDLS Annual Conference 2023: The emerging role of AI in data-driven life science. This event is also part of Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre. \n\n\n\nTitle: Building and sharing machine learning demo applications within life sciences: a practical tutorial \n\n\n\nOrganizer: AI Data Engineers from the SciLifeLab Serve team. \n\n\n\nWhere and when: November 16\, 2023 at 13:30-15:30 at SciLifeLab Solna (Tomtebodavägen 23A\, Solna) \n\n\n\nAbstract: It is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application\, prepare it for deployment\, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable in under an hour. \n\n\n\nThe workshop will last for 2 hours with a break in the middle. We have room to accept 30 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nSince there is a limited number of spots in this workshop please sign up only if you intend to attend. \n\n\n\nThis event is now full\, you can register for the waiting list only (in case we received a cancellation). We will organize similar workshops in the future\, it will be announced in the same event series. \n\n\n\nRegister to join the event\n\n\n\nMore about the event series: \n\n\n\nTools for AI/ML research in life sciences is an event series by the SciLifeLab Data Centre aimed at life science researchers who use machine learning methods in their work. The goal of the events in this series is to provide introductions to different tools for ML research but also to foster discussions around our practices and how they can be improved. The events takes place virtually (over Zoom) and are open to researchers in Sweden and beyond. Each event is scheduled for 60 minutes\, consisting of a talk and an extended discussion. Follow the page of the event series to learn about future seminars. \n\n\n\nFor questions about the events please contact the organizing team by emailing serve@scilifelab.se \n\n\n\n \n\n\n\nScientific lead: Prof. Ola Spjuth\, SciLifeLab Data Centre and Uppsala University \n\n\n\nContact information: serve@scilifelab.se URL:https://www.scilifelab.se/event/building-and-sharing-machine-learning-demo-applications-within-life-sciences-a-practical-tutorial/ LOCATION:SciLifeLab Campus Solna\, Tomtebodavägen 23 A\, Solna\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231117T090000 DTEND;TZID=Europe/Stockholm:20231117T141000 DTSTAMP:20260503T183041 CREATED:20230830T210018Z LAST-MODIFIED:20231112T090520Z UID:10000962-1700211600-1700230200@www.scilifelab.se SUMMARY:Cell and Molecular Biology Symposium DESCRIPTION:The DDLS research area\, Cell and molecular biology\, invites you to the first in-person symposium. The day will be an introduction to the research area Fellows and Expert Group. \n\n\n\nRegistration\n\n\n\nWe have a limited number of seats (52p). All participants must register (including the speakers i.e.\, DDLS Fellows and research area Expert group). Participant list here If you register after Nov 7\, we offer fika and lunch but can’t accommodate food preferences. \n\n\n\nRegistration\n\n\n\nAgenda\n\n\n\n08:45Registration\, check-in and Coffee09:00Introduction to Data-driven Life Science program and the Cell and molecular biology research areaMargit Mahlapuu\, Chair of the DDLS CMB Expert groupPresentations of fellows\, Expert group members\, and Data science node09:15Title TBAJuliette Griffie\, DDLS Fellow09:40Making it work in reality – bridging the gap between curated proof of concept tests and real world deployment of biomedical image based deep learningIda-Maria Sintorn\, DDLS Expert group 09:55AICell Lab: Towards AI-powered Data-driven Whole-cell ModelingWei Ouyang\, DDLS Fellow10:20Title TBAErik Lindahl\, DDLS Expert group10:35Coffee break 10:50Time-resolved structural studies of photoactive proteinsSebastian Westenhoff\, DDLS Expert group11:05From model systems to global surveillance programs for infectious diseases: Some challenges and the road aheadJohan Bengtsson-Palme\, DDLS Fellow11:30The DDLS Data Science Node – status report towards supporting the national CMB research communityThomas Svensson\, Sverker Holmgren\, Data Science node12:00RNA insights from extinct animals and single cellsMarc Friedländer\, DDLS Expert group12:15Understanding intestinal diseases with spatial transcriptomicEduardo Villablanca\, DDLS Expert group12:30Lunch13:15“Weak\, noisy and uninteresting”: subtle features of macromolecular structuresNicholas Pearce\, DDLS Fellow13:40Metabolic Liver Disease: Molecular Mechanisms and Novel TargetsMargit Mahlapuu\, DDLS Expert group13:55Wrap-up and Action item summaryMargit Mahlapuu14:10End of the day URL:https://www.scilifelab.se/event/cell-and-molecular-biology-symposium/ LOCATION:Biomedicum\, room Peter Reichard\, Solnavägen 9\, Stockholm\, 171 65 CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/CMB_Icon-1.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231122T141500 DTEND;TZID=Europe/Stockholm:20231122T150000 DTSTAMP:20260503T183041 CREATED:20231115T101836Z LAST-MODIFIED:20231115T150503Z UID:10001028-1700662500-1700665200@www.scilifelab.se SUMMARY:Launch of calls for DDLS PhD projects DESCRIPTION:The SciLifeLab & Wallenberg National Program for Data-Driven Life Science announces calls for PhD projects within academia and industry. The calls will be open for researchers in Sweden who are interested to act as supervisor for a PhD student. The aim is to fund 20 projects for academic PhD students and 7 for industrial. Join this online event for detailed information about the calls and the possibility to ask questions. \n\n\n\nAGENDA \n\n\n\nInformation about calls – Olli Kallioniemi\, DDLS director \n\n\n\nQ & A session \n\n\n\n\nRegister here\n\n\n\n\nWebpage: https://www.scilifelab.se/data-driven/ddls-research-school/ URL:https://www.scilifelab.se/event/call-for-ddls-phd-projects/ LOCATION:Online event via Zoom CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/11/Academy_call.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231206T080000 DTEND;TZID=Europe/Stockholm:20231208T170000 DTSTAMP:20260503T183041 CREATED:20231002T115541Z LAST-MODIFIED:20231002T115646Z UID:10000980-1701849600-1702054800@www.scilifelab.se SUMMARY:DDLS Biomarker Discovery: from theory to real world examples DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of understanding biomarker research and methods. \n\n\n\nWorkshop location:  SciLifeLab\, Tomtebodavägen 23A\, Solna \n\n\n\nVenue:  Air&Fire (G2690) and Milky Way (A2631) \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-10-01 \n\n\n\nApplication closes: 2023-10-30 \n\n\n\nConfirmation to accepted students: 2023-11-15 \n\n\n\n \n\n\n\nCourse Leaders and teachers: Animesh Acharjee\, Clemens Wittenbecher\, Markus Mayrhofer\, Mun-Gwan Hong\, Paul Pyl\, Prasoon Agarwal \n\n\n\nplease contact edu.biomarkers@nbis.se for course-specific questions \n\n\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\nWorkshop fee\n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunch and coffee. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nWorkshop content\n\n\n\nThe main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research\, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery. \n\n\n\nTopics covered will include: \n\n\n\n\nBiomarker study design for “context of use”\n\n\n\nTypes of biomarkers\, diagnostic\, prognostic\, and wellness\n\n\n\nBiomarkers are in use for various diseases such as cancer\, cardiovascular diseases\n\n\n\nBiomarker discovery from various omics data including proteome\, microbiome\n\n\n\nBiomarker and multi-omics data integration\n\n\n\nMachine learning methods\, lasso logistic regression and random forest\, to identify biomarkers\n\n\n\nPerformance indicators\, e.g. sensitivity and specificity\n\n\n\nInternal/external validation\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required to be able to follow the workshop and complete the exercises: \n\n\n\n\nAbility to bring your own laptop with R installed for the practical exercises\n\n\n\nBasic Programming/scripting experience in R\n\n\n\nor took an R course NBIS prepared.\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nSome basic knowledge of biostatistics\n\n\n\nPrevious experience in biomarker-related studies\n\n\n\n\nDue to limited space\, the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance. URL:https://www.scilifelab.se/event/ddls-biomarker-discovery-from-theory-to-real-world-examples/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240112T130000 DTEND;TZID=Europe/Stockholm:20240112T140000 DTSTAMP:20260503T183041 CREATED:20231220T101638Z LAST-MODIFIED:20240112T114300Z UID:10001072-1705064400-1705068000@www.scilifelab.se SUMMARY:DDLS Data Science Node information DESCRIPTION:Welcome to a brief update on the status of the Data Science Node (DSN) for Cell and Molecular Biology (CMB) and information about a community survey that will open after this meeting. Data Science Node management\, Sverker Holmgren and Thomas Svensson will describe the survey and answer questions. The event is open to everyone. Please register to get the Zoom link in your mailbox. You can pre-send input or questions regarding the DSN in CMB to Sverker and Thomas in the registration form. \n\n\n\n\n\n\n\n\n \n\n\n\nRegistration\n\n\n\n\n\nSurvey\n\n\n\nLink to Survey\n\n\n\n\nRead more about DDLS Data Science Nodes URL:https://www.scilifelab.se/event/ddls-data-science-node-information/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/CMB_web.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240119T100000 DTEND;TZID=Europe/Stockholm:20240119T110000 DTSTAMP:20260503T183041 CREATED:20240115T114456Z LAST-MODIFIED:20240116T094413Z UID:10001107-1705658400-1705662000@www.scilifelab.se SUMMARY:AICell Lab -- Building AI Systems for Human Cell Modeling and Simulation DESCRIPTION:NBIS\, Scilifelab’s Bioinformatics platform\, arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms\, typically between 10 and 11 am\, with ca. 45 min long presentation and 15 min discussion. \n\n\n\nFor further info\, please see this website. \n\n\n\n \n\n\n\n\n\n\n\nAICell Lab — Building AI Systems for Human Cell Modeling and Simulation\n\n\n\nWei Ouyang\, DDLS fellow\, Royal Institute of Technology\, KTH \n\n\n\nThe AICell Lab is a newly founded group by the Data-Driven Life Science fellows program at the department of applied physics at KTH. The lab is dedicated to building artificial intelligence (AI) systems for cell and molecular biology\, with the ultimate goal of modeling the human cell and building human cell simulators using powerful AI models. The lab’s approach to this grand challenge involves not only innovations in data analysis and modeling\, but also in data generation\, specifically the creation of an automated imaging farm equipped with multiple microscopes\, robotic arms\, liquid handling robots\, and automatic incubators. The lab’s AI software infrastructure enables real-time augmentation of microscopy views\, generating artificial labels and annotations\, and optimizing experimental conditions to capture rare events in live cells. The long-term goal of the AICell Lab is to create large-scale whole human cell models trained on existing multi-omics datasets and new data generated by the imaging farm\, which have the potential to revolutionize in-silico cell experimentation and drug discovery while contributing to a holistic and systematic understanding of the human cell. \n\n\n\nClick here to join zoom conference URL:https://www.scilifelab.se/event/ai-approach-to-cell-and-molecular-biology/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240202T100000 DTEND;TZID=Europe/Stockholm:20240202T110000 DTSTAMP:20260503T183041 CREATED:20231207T150409Z LAST-MODIFIED:20240122T160625Z UID:10001063-1706868000-1706871600@www.scilifelab.se SUMMARY:Practical intro to GPU programming in Python and Julia DESCRIPTION:This event is part of the Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre. This webinar is organized in collaboration with the EuroHPC National Competence Centre Sweden (ENCCS) as well as the National Supercomputer Centre\, LiU. \n\n\n\nTitle: Practical intro to GPU programming in Python & Julia \n\n\n\nSpeaker: Yonglei Wang\, PhD\, Research Software Engineer and HPC application expert\, ENCCS \n\n\n\nWhere and when: February 2\, 2024 at 10:00-11:00 Stockholm time\, online. Registration is open till February 2 at 9:00. \n\n\n\nAbstract: Availability of Graphics Processing Units (GPUs) has transformed the way we work with machine learning and data science challenges in life sciences. The parallel processing capabilities of GPUs have allowed training of ever more complex models\, allowing researchers to analyze large biological datasets with unprecedented efficiency. However\, in order to make use of the potential that GPUs offer we need be able to write fitting machine learning model code and analysis pipelines. In this webinar ENCCS will present some practical tips about what to keep in mind and how to optimize your code when running analyses on GPU hardware. This webinar will be most useful to researchers who already work with large datasets and would like to improve their understanding of how to work with GPUs. At the end\, the participants will also be given an overview of online materials and in-person courses where researchers can learn about this topic in depth. \n\n\n\nRegister to join the event\n\n\n\nMore about the event series: \n\n\n\nTools for AI/ML research in life sciences is an event series by the SciLifeLab Data Centre aimed at life science researchers who use machine learning methods in their work. The goal of the events in this series is to provide introductions to different tools for ML research but also to foster discussions around our practices and how they can be improved. The events takes place virtually (over Zoom) and are open to researchers in Sweden and beyond. Each event is scheduled for 60 minutes\, consisting of a talk and an extended discussion. Follow the page of the event series to learn about future seminars. \n\n\n\nFor questions about the events please contact the organizing team by emailing serve@scilifelab.se \n\n\n\n \n\n\n\nScientific lead: Prof. Ola Spjuth\, SciLifeLab Data Centre and Uppsala University and DDLS \n\n\n\nContact information: serve@scilifelab.se URL:https://www.scilifelab.se/event/practical-intro-to-gpu-programming-in-python-and-julia/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240207T080000 DTEND;TZID=Europe/Stockholm:20240209T170000 DTSTAMP:20260503T183041 CREATED:20230516T145922Z LAST-MODIFIED:20240206T113507Z UID:10000893-1707292800-1707498000@www.scilifelab.se SUMMARY:SciLifeLab International Advisory Board site visit DESCRIPTION:SciLifeLab International Advisory Board will visit SciLifeLab to evaluate the operations and advise on how we can develop even further. \n\n\n\nThe International Advisory Board (IAB) is an advisory body to the Board of SciLifeLab and consists of expert members operating outside of Sweden. The SciLifeLab Board appoints the IAB Chair and members. The IAB shall mainly contribute to SciLifeLabs’ strategic development regarding research infrastructure and scientific direction and meets every two years to report to the SciLifeLab Board. \n\n\n\nSciLifeLab biannually produces reports for the IAB visit. The reports from 2021 and 2019 can be found here. The report for 2024 has been distributed as a printed report and a digital file for the IAB members. The participants at the IAB site visit have been invited to the Nextcloud folder\, where the written material (report) and the Program can be found. The report to the IAB will be published on the SciLifeLab website after the site visit. \n\n\n\nThe IAB evaluation is reported to the SciLifeLab Board. \n\n\n\nFor questions or more information about the IAB site visit\, don’t hesitate to get in touch with Project leader Erika Bergqvist Erkstam\, erika.erkstam@SciLifeLab.uu.se or 070-425 03 87. \n\n\n\n\n\n\n\nDownload Program\n\n\n\nIAB-visit-2024-program_ver1.2Download\n\n\n\nShort program\n\n\n\nFeb 6\n\n\n\nArrival in Uppsala\, Sweden \n\n\n\n18:45 Internal IAB Preparation Meeting \n\n\n\n19:15 IAB Preparation Meeting with SciLifeLab Directors \n\n\n\nFeb 7\n\n\n\n08:00Transport from the hotel08:30SciLifeLab Recent Developments and Ongoing PlansSession 1: Provide excellent and impactful life science infrastructure10:35Infrastructure: Future Strategies and Organization11:30Lunch12:15Flash talks: Infrastructure PlatformsSession 2: Facilitate the transformation of life science data into knowledge14:30Data-Driven Life Science programSession 3: Attract scientific excellence and provide advanced training16:30SciLifeLab Research Community17:45Closed session with the Board19:15Dinner with the SciLifeLab Board\, Uppsala University Main Building\n\n\n\nFeb 8\n\n\n\n08:30Transport from the hotelCont. Session 3: Attract scientific excellence and provide advanced training09:00Training Hub and strategy09:45IAB SciLifeLab Fellows meeting11:15IAB DDLS Fellows meeting12:30LunchSession 4: Strengthen capabilities\, research communities and global partnerships13:30Capabilities15:00SciLifeLab National Sites16:30SciLifeLab Campus Solna17:15Genomic Medicine Sweden17:45IAB internal discussion19:00Dinner\n\n\n\nFeb 9\n\n\n\n08:00Transport from the hotelSession 5: Support innovation and bridge-building for the benefit of society08:30Innovation\, Collaboration and Partnerships09:30National organization and support functions11:00Future perspectives and opportunities12:00General discussion time 12:30Working closed lunch\, followed by writing and discussion14:00Initial feedback and questions14:30Additional writing session15:00End of IAB site visit updated: 2023-12-11\n\n\n\nIAB members\n\n\n\nRuedi Aebersold\, ETH Zürich\, Switzerland\nRuedi Aebersold is a Swiss/Canadian scientist trained at the Biocenter\, University of Basel\, Switzerland. After postdoctoral research at Caltech he was on the faculties of the University of British Columbia in Vancouver and the University of Washington in Seattle and co-founded\, with Lee Hood and Alan Aderem\, the Institute for Systems Biology in Seattle. In 2004 he joined ETH Zürich to establish the Institute of Molecular Systems Biology. He has co-founded several companies and holds multiple public service appointments. The group’s work was recognized with numerous awards including the Biemann medal of ASMS\, the Paracelsus prize of the SCS\, the Otto Naegeli Prize\, the Thomson medal of IMSF and the HUPO achievement award and the Marcel Benoist Swiss Science Prize\, the most prestigious science award in Switzerland. The group’s publications have been cited more than 132.000 times and reached an h-factor of 174 (WoS) and 203.000 times with h-factor 218 in Google Scholar (Oct 2023). \n\n\n\nThe research focus of the Aebersold group was the proteome. The group pioneered several widely used techniques and generated a range of open access/open source software and statistical tools that have contributed to making proteomic research results more transparent\, reproducible and accurate. \n\n\n\nRuedi Aebersold entered emeritus status in 2021 and now serves as a member of the board of trustees of several foundations that support basic and translational life science research.  \n\n\n\n\nSøren Brunak\, Novo Nordisk Foundation Center for Protein Research\, University of Copenhagen\, Denmark\nSøren Brunak\, Ph.D.\, is professor of Disease Systems Biology and Research Director at the University of Copenhagen. He is a pioneer in the application of machine learning techniques to the analysis of biological sequences. His group combines molecular level systems biology data with analysis of healthcare sector phenotypic data (electronic patient records\, registry information and biobank questionnaires) to understand multimorbidities and treatment related disease correlations as temporal disease trajectories. This stratifies patients not only from their genotype\, but also from the clinical descriptions in their medical records and is particularly relevant in the context of the precision medicine agenda. \n\n\n\n\nJo Bury\, VIB\, Belgium\nJo Bury is founder and director-emeritus of VIB\, the Flanders Institute for Biotechnology. He was managing director of VIB in the period November 1995-March 2022. VIB is a life science research institute where 1.800 scientists and technicians study the molecular mechanisms of growth and development of different organisms (human beings\, plants\, micro-organisms) in normal (health) vs abnormal (disease\, stress) conditions. The focus is strategic basic research with potential applications (in the long term) in molecular medicine and molecular farming. VIB is a multisite institution\, integrated within the campuses of the universities of Ghent\, Leuven\, Brussels\, Antwerp and Hasselt\, based on a joint venture agreement of VIB with these 5 partner universities. Through the performance of its scientists\, VIB has become a center of excellence in life science research in Europe. \n\n\n\nJo Bury has a Master’s degree in Pharmacy and is PhD in Pharmaceutical Sciences (University of Gent). He obtained an MBA degree at the Vlerick School for Management in Gent. After performing scientific research in the field of atherosclerosis during several years\, he has made a career in science policy. He previously held the post of Operational Director of VLAB (Flanders’ Action Programme on Biotechnology) and science advisor at federal and regional granting bodies (IWONL-IRSIA\, IWT). \n\n\n\nOutside VIB Jo Bury has been a board member of different research intensive companies (Seghers Genetics and Nutrition NV\, Vitamex NV\, Oystershell NV)\, research institutions (Temasek Life Sciences Laboratories (Singapore)\, ITG)\, and granting bodies (Hercules\, EIC\, FWO). He served / serves on SABs of different research centers in life sciences s.a. IIMCB (Warsaw)\, HCEMM (Budapest)\, IGC (Lisbon)\, MDC (Berlin)\, CRG (Barcelona)\, SciLife (Stockholm) and DRI (London). \n\n\n\n\nJanet K. Jansson\, Pacific Northwest National Laboratory\, USA\nJanet K. Jansson is a Chief Scientist (Emeritus) and a Laboratory Fellow at the Pacific Northwest National Laboratory (PNNL). Her research uses molecular tools “omics” to study microorganisms in a variety of habitats – ranging from soil to the human gut to outer space. Jansson is a Fellow of the American Academy of Microbiology\, the Washington State Academy of Science and the American Association for the Advancement of Science. She also has an Honorary Doctorate from the University of Helsinki\, Finland. She has authored more than 250 publications and is one of the most highly cited researchers in the world. \n\n\n\n\nSirpa Jalkanen\, University of Turku\, Finland\nAcademician Sirpa Jalkanen\, MD\, PhD is Professor at the Medical Faculty\, University of Turku and Director of a National Flagship\, InFLAMES. She has published more than 380 peer-reviewed papers and has more than 10 patents on different discoveries in the fields of inflammation and cancer. She is a member of EMBO and Academia Europaea and has received several prizes/honours such as Datta Medal (from FEBS)\, major medical prizes: Anders Jahre\, and Äyräpää\, innovator prizes: 2nd European Women Innovator and the Finnish Pharma Industry Prizes. She has several positions of trust. She is a member/vice chair/chair of the boards in three big Finnish Foundations financing research and a board member of the Association of Finnish Foundations. In addition\, she is a co-founder of BioTie Therapies and Faron Pharmaceuticals. \n\n\n\n\nIain Mattaj\, Human Technopole Foundation \, Italy\nProfessor Iain Mattaj was born in St. Andrews\, Scotland. He attended Edinburgh University\, Scotland and after completing his undergraduate degree in Biochemistry (honors)\, he obtained his Ph.D. degree from the University of Leeds\, England. Following his Ph.D.\, Iain carried out postdoctoral research out at the Friedrich Miescher Institute\, Switzerland\, then at the Biocentre\, University of Basel\, Switzerland.  In 1985\, he joined EMBL as a Group Leader at the Heidelberg laboratory. He became Coordinator of the Gene Expression Unit at EMBL in 1990 before being promoted to the position of Scientific Director in 1999. Iain was appointed Director General of EMBL in May 2005 and remained in post till the end of 2018. He then moved to Italy to launch the Human Technopole Foundation (HT)\, a government-funded foundation focusing on research on human health and wellbeing. He grew the organization from 14 staff to 390 including 273 researchers in just over four years. This included construction and refurbishment of 20\,000 m2 of lab and office space\, organized and mainly carried out during the COVID pandemic. HT is now producing high-quality research. \n\n\n\nIn addition to his leadership success at EMBL and HT\, Iain’s own research achievements have been considerable and varied. His early work centered on a group of ribonucleoprotein (RNP) particles that function in the processing of messenger RNA precursors. His analyses of these RNPs spanned a variety of topics including transcription of the RNA components\, RNA-protein interactions\, function of the RNPs in messenger RNA production and assembly of the RNPs from their component parts in vivo. This work led to numerous studies of transport of RNA and proteins between the cell nucleus and cytoplasm. Iain’s group identified numerous factors and mechanisms involved in this important process. Iain’s more recent work has demonstrated the critical role of the Ran GTPase in regulating mitotic events including spindle assembly\, nuclear pore complex formation and nuclear envelope assembly. \n\n\n\nHis prominent standing in the field was underlined by his election as President of the RNA Society and his award of the prestigious Louis-Jeantet Prize for Medicine in 2001.In addition\, he has received numerous other awards and honorary lectureships\, including the FEBS Anniversary Prize\, Caledonian Research Foundation – Royal Society of Edinburgh Award\, Italian Chemical Society Award\, Feldberg Foundation Prize. He is Honorary Professor of the Faculty of Bio-Sciences of the Ruprecht-Karls-Universität Heidelberg\, and Honorary Doctor of the Universities of Edinburgh\, Dundee\, Umea and Leeds.His scientific contributions have also been recognized by his election as a Fellow of the Royal Society (London)\, Foreign Associate of the National Academy of Sciences (USA)\, Foreign Member of the Royal Swedish Academy of Science\, Fellow of the Royal Society of Edinburgh\, Member of Academia Europea\, Foreign Honorary Member of the American Academy of Arts and Science\, Member of the Deutsche Akademie der Naturforscher (Leopoldina)\, appointed Trustee of the Darwin Trust\, appointed Curator of the Lautenschläger Research Prize\, appointed Member of the Life Sciences Search Committee for the Körber Prize\, and appointed Member of the Search Committee for the Louis-Jeantet Prize for Medicine. He was awarded the German Cross of Merit (Bundesverdienstkreuz) in 2021. \n\n\n\nHe is a member of many national and international scientific advisory boards and panels\, including periods as chair of EIROforum (European Intergovernmental Research Organisations)\, the Senior Awards Advisory Board of the Wellcome Trust\, Senior Review Board of the HHMI\, Chair of the ISTA executive Board\, Chair of the Institut Curie ISAB\, Chair of the Darwin Trust of Edinburgh Board of Trustees\, etc. etc. He is a member of the European Molecular Biology Organization (EMBO) and helped make The EMBO Journal a highly successful international scientific journal\, acting as Executive Editor from 1990 to 2004. \n\n\n\n\nSvante Pääbo\, Max Planck Institute for Evolutionary Anthropology\, Germany\nSvante Pääbo has developed techniques that allow DNA sequences from archaeological and paleontological remains to be determined. His research group has determined high-quality genome sequences from Neanderthals and discovered Denisovans\, a previously unknown hominin group in Asian. They have shown that both Neanderthals and Denisovans contributed DNA to present-day humans and that these contributions have physiological and medical consequences today. Pääbo also works on the comparative and functional genomics of modern and archaic humans and apes. \n\n\n\nHe is a Director at the Max-Planck Institute for Evolutionary Anthropology in Leipzig\, Germany\, and an Adjunct Professor at the Okinawa Institute of Science and Technology\, Japan. \n\n\n\n\nKjetil Tasken\, Univ. of Oslo\, Oslo University Hospital\, Norway\nProfessor Kjetil Taskén has been key in building Norway’s national cancer precision medicine initiative and now coordinates the Cancer Mission PRIME-ROSE project for DRUP-like clinical trials across Europe. He authors >300 publications and is an inventor of >20 patents (h-index =65). He won the King Olav V’s Prize for Cancer Research in 2016\, and the University of Oslo Innovation Prize in 2023 and is Vice-President of the Norwegian Academy of Science and Letters. Current research is in tumor immune evasion mechanisms and functional precision medicine for different solid and blood cancers. \n\n\n\n\nSarah A. Teichmann\, Wellcome Sanger Institute\, University of Cambridge\, UK\nSarah did her PhD at the MRC Laboratory of Molecular Biology\, Cambridge\, UK and was a Beit Memorial Fellow at University College London. She started her group at the MRC Laboratory of Molecular Biology in 2001. In 2013\, she moved to the Wellcome Genome Campus where her group was joint between the EMBL-European Bioinformatics Institute and the Wellcome Sanger Institute\, and in 2016 was appointed Head of the Cellular Genetics programme at the Sanger. Sarah’s laboratory develops and applies cell atlas technologies to decipher human tissue architecture\, with a particular focus on how cellular diversity is generated in the immune system and through development. Sarah is co-founder and co-leader of the international Human Cell Atlas consortium which aims to create reference maps for cells across all human tissues and has grown to include over two thousand members across the world. Sarah is also co-director of the CIFAR Research Programme ‘The Multiscale Human’. Her work has been recognised by numerous awards\, including the EMBO Gold Medal\, Genetics Society Mary Lyons Award\, Biochemical Society GlaxoSmithKline Award\, the FEBS|EMBO Women in Science Award among others. She is an EMBO Member\, ISCB Fellow\, and Fellow of the Academy of Medical Sciences and Royal Society. URL:https://www.scilifelab.se/event/scilifelab-international-advisory-board-site-visit/ CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/06/Navet-fasad-innegård-scaled.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240213T094500 DTEND;TZID=Europe/Stockholm:20240213T153000 DTSTAMP:20260503T183041 CREATED:20240205T094820Z LAST-MODIFIED:20240212T154340Z UID:10001142-1707817500-1707838200@www.scilifelab.se SUMMARY:Karolinska Institutet DDLS Fellows – Public research seminars with candidates DESCRIPTION:Welcome to attend research seminars presented by candidates for the following positions:1. DDLS Fellow in Data-Driven Epidemiology and Biology of Infection2. DDLS Fellow in Data-Driven Precision Medicine and Diagnostics \n\n\n\nPart 1. 13 February 2024: DDLS Fellow in Data-Driven Epidemiology and Biology of Infection\n\n\n\nNAMECURRENT AFFILIATIONTIMESupriya KhedkarNA10:00-10:20Andreas LuttensMassachusetts Institute of Technology10:20-10:40Shilpa RayKarolinska Institutet10:40-11:00\n\n\n\nPart 2. 13 February 2024: DDLS Fellow in Data-Driven Precision Medicine and Diagnostics\n\n\n\nNAMECURRENT AFFILIATIONTIMEKimmo KartasaloKarolinska Institutet13:00-13:20David MarleviMassachusetts Institute of Technology and Karolinska Institutet13:20-13:40Amirata Saei DibavarUniversity of Basel and Karolinska Institutet13:40-14:00Alexa McIntyreUniversity of Zurich14:30-14:50Antônio Horta RibeiroUppsala University14:50-15:10Daniel HageyKarolinska Institutet15:10-15:30 URL:https://www.scilifelab.se/event/karolinska-institutet-ddls-fellows-public-research-seminars-with-candidates/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240221T130000 DTEND;TZID=Europe/Stockholm:20240221T163000 DTSTAMP:20260503T183041 CREATED:20240205T092304Z LAST-MODIFIED:20240207T115231Z UID:10001139-1708520400-1708533000@www.scilifelab.se SUMMARY:DDLS Fellow candidates seminar at the Swedish Museum of Natural History (NRM) DESCRIPTION:The Swedish Museum of Natural History (NRM) is hiring a tenure-track researcher in Data-Driven Life Science (DDLS)\, within the field of biodiversity and evolution. \n\n\n\nThe research position is funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS)\, which is a 12-year initiative funded with a total of 3.1 billion SEK from the Knut and Alice Wallenberg Foundation (for more details\, see www.scilifelab.se/data-driven). The DDLS Fellows will be recruited as independent group leaders at the respective host institution\, and will have the opportunity to link up with other local research groups as well as the within the national DDLS programme. \n\n\n\nAs a part of the recruitment process\, the top-ranked candidates for the NRM position will give digital seminars that are open for the general public.  \n\n\n\nFebruary 21 2024\, 13:00 – 16:30 \n\n\n\nSchedule of presentations: \n\n\n\n13.00-13.30Allison HsiangTeaching an old foram new tricks: Illuminating biodiversity patterns and morphological evolution in deep time using artificial intelligence13.30-14.00Moritz LürigHow AI-based computer vision can inform us about the diversity and evolution of organisms14.00-14.30Viktor SenderovHarnessing Human Intelligence for Biodiversity Informatics15.00-15.30Mariana Pires-BragaBiotic interactions: teasing apart evolutionary processes from data biases15.30-16.00Jose CercaEvolution of genetic diversity in insular lineages: A genomics data-driven approach16.00-16.30Mette LillieBiodiversity conservation in the face of host-pathogen evolutionary dynamics\n\n\n\nOrganizers: NRM DDLS Recruitment Committee URL:https://www.scilifelab.se/event/ddls-fellow-candidates-seminar-at-the-swedish-museum-of-natural-history-nrm-2/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240226T151500 DTEND;TZID=Europe/Stockholm:20240226T161500 DTSTAMP:20260503T183041 CREATED:20240207T162516Z LAST-MODIFIED:20240207T162519Z UID:10001149-1708960500-1708964100@www.scilifelab.se SUMMARY:[The Svedberg seminar] - Spatial biodiversity modeling with remote sensing and AI DESCRIPTION:Tobias Andermann \n\n\n\nAssistant Professor\, DDLS fellowUppsala University \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\nTobias Andermann is a biodiversity researcher dedicated to providing data and computatio- nal tools for combating the global biodiversity crisis. His group\, the Biodiversity Data Lab\, is working on the intersection of molecular biology\, spatial ecology\, and machine learning\, with the mission to provide a more comprehensive view on the distribution of biodiversity\, including hidden diversity of inconspicuous and even undescribed species through the use of environmental DNA. \n\n\n\n \n\n\n\nSpatial biodiversity modeling with remote sensing and AI\n\n\n\nThere is an ever-increasing need for developing standardized ways of quantifying the biodiversity value of a site. This need arises from international and local policies (e.g. the COP15 UN Biodiversity agreement) as well as from the independent investments of companies world-wide in developing biodiversity-positive profiles\, motivated by their public perception. This momentum provides an unprecedented opportunity to efficiently protect biodiversity on a large scale to turn around the alarmingly negative biodiversity trends of the recent decades and centuries. While individual biodiversity assessments for specific sites can be done through targeted inventories\, either through taxonomic experts or increasingly through the use of environmental DNA\, we also need ways of scaling up such biodiversity evaluations to larger scales\, covering entire regions or countries. AI models provide a unique tool to leverage complex biodiversity and remote sensing data to make predictions of biodiversity on large spatial scales\, while at the same time providing high spatial resolution. In this talk I will present some of these models from my ongoing research and discuss their utility\, as well as their current shortcomings and limitations. \n\n\n\n \n\n\n\n\n\n\n\nHost: Joëlle Rüegg joelle.ruegg@ebc.uu.se\, UU URL:https://www.scilifelab.se/event/the-svedberg-seminar-tobias-andermann/ LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240312T080000 DTEND;TZID=Europe/Stockholm:20240315T170000 DTSTAMP:20260503T183041 CREATED:20231215T124733Z LAST-MODIFIED:20240304T133407Z UID:10001071-1710230400-1710522000@www.scilifelab.se SUMMARY:Nordic Oikos 2024 - New perspectives in ecological and evolutionary research DESCRIPTION:The Planetary Biology Capability is organizing a session on “Exploring and understanding biodiversity” that will count on the participation of Prof. Davis Wardle (Umeå University)\, Prof. Katherine McMahon (University of Wisconsin-Madison) and Prof. Mark Blaxter (Sanger Institute). The DDLS research area\, Evolution\, and Biodiversity\, is organizing a session on the importance of data-driven life science in ecology and evolution. The DDLS Fellow Kelly Swarts is one of the Plenary speakers. \n\n\n\nSciLifeLab related sessions:\n\n\n\n\nPlanetary Biology pre-conference session: Towards the efficient use of molecular approaches and infrastructure to accelerate research in the field of Planetary Biology\n\n\n\n\nThis session aims to enhance connections between SciLifeLab\, the Planetary Biology Capability\, and the PB research community in Lund. Discussions will address challenges and opportunities for the efficient use of SciLifeLab’s services to support and accelerate research in the field of Planetary Biology.  \n\n\n\n12th March from 15:00 to 17:00. Venue: Room Heden G110\, Ecology Building\, Sölvegatan 37\, Lund. \n\n\n\nProgram for the session \n\n\n\n15:00-15:20:     Introduction to the PB concept and capability leads. \n\n\n\n15:20-15:40:    Overview of PB research in Lund. Bengt Hansson\, Lund University \n\n\n\n15:40 – 15:50:   Presentation of SciLifeLab Lund and facilities. \n\n\n\n15:50 – 16:00:   Break \n\n\n\n16:00 – 17:00:   Presentation of SciLifeLab Platforms and PB-related projects. Discussion on needs and challenges for using SciLifeLab services. \n\n\n\nRegister\n\n\n\n\nPlanetary biology: exploring and understanding biodiversity (S1)\n\n\n\n\nBiodiversity at local to global scales is a key feature that constrains and controls ecosystem function and key biogeochemical processes. In this session\, we welcome contributions addressing various aspects of biodiversity\, including how to assess it\, key drivers affecting biodiversity\, and the consequences of change (and loss) of biodiversity. We particularly encourage presentations that emphasize large-scale patterns and processes that move beyond the local scale. \n\n\n\n\nDDLS: the importance of data-driven life science in ecology and evolution (S13)\n\n\n\n\nThe importance of data-driven science in Ecology and Evolution” will spotlight innovative research methodologies and findings utilizing computational techniques and massive data streams to explore ecological dynamics. This session could encompass presentations on leveraging high-throughput sequencing\, remote sensing\, machine learning\, and AI to investigate biodiversity patterns\, ecosystem functioning\, species interactions\, and the impact of environmental changes on ecosystems\, fostering discussions on cutting-edge approaches shaping the future of ecological and evolution research within the Nordic scientific community and beyond. \n\n\n\n\n\n\n\nWe are delighted to invite you to the upcoming biennial meeting of the Nordic Society Oikos​ 12-15th of March 2024 with the theme New perspectives in ecological and evolutionary research. The meeting will be jointly organised by the Nordic Society Oikos and the European Ecological Federation​ (EEF). The conference will be held at AF Borgen​ in the picturesque area Lundagård​ in Lund\, southern Sweden. \n\n\n\nThe meeting provides a platform for researchers engaged in all aspects of ecology and evolutionary biology. We have a broad set of session themes covering a diverse range of topics in basic and applied research\, and we warmly welcome submissions for both oral- and poster presentations exploring these themes. Data Driven Life Science​\, Planetary Biology​\, Biodiversity and Ecosystem services in a Changing Climate​ (BECC) will be organizing theme sessions ensuring the representation of a diverse set of perspectives. Registration and abstract submission will open October 17th. Registration will close February 1\, 2024 at 00:00 \n\n\n\nRegister\n\n\n\nAt the Nordic Society 2024 meeting\, you can anticipate: \n\n\n\n\nEngaging plenary speakers and thematic sessions\, delivering insightful perspectives\n\n\n\nTwo dedicated poster sessions\n\n\n\nVibrant discussions and ample opportunities for social interaction throughout the meeting\n\n\n\nSocial events\, conference dinner and excursion to foster inspiration and facilitate networking with fellow participants\n\n\n\n\nWe hope you join us in Lund to exchange knowledge\, forge new connections\, and explore new frontiers in ecological and evolutionary biology. \n\n\n\nWe are looking forward to welcome you in Lund! \n\n\n\nLocal organizing committee:\n\n\n\nLund University \n\n\n\nAnna Runemark – Biodiversity \n\n\n\nCaroline Isaksson – Evolutionary Ecology \n\n\n\nSusana Garcia Dominguez – Evolutionary Ecology \n\n\n\nRichard Walters – Centre for Environmental and Climate Science \n\n\n\nPetronella Wessman – Biodiversity \n\n\n\nMargot Knapen – Physical Geography and Ecosystem Science \n\n\n\nSwedish University of Agricultural Sciences\, Alnarp \n\n\n\nÅsa Lankinen – Integrated Plant Protection \n\n\n\nKristina Karlsson Green – Chemical Ecology Agriculture \n\n\n\nNordic Society Oikos \n\n\n\nJohan Nilsson  \n\n\n\nÅsa Langefors \n\n\n\nMichael Tobler URL:https://www.scilifelab.se/event/nordic-oikos-2024-new-perspectives-in-ecological-and-evolutionary-research/ LOCATION:AF Borgen\, Sandgatan 2\, Lund\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240408T130000 DTEND;TZID=Europe/Stockholm:20240409T153000 DTSTAMP:20260503T183041 CREATED:20240402T125022Z LAST-MODIFIED:20240402T153433Z UID:10001224-1712581200-1712676600@www.scilifelab.se SUMMARY:Data Driven Life Science Seminars: "Data driven research in evolution and biodiversity" DESCRIPTION:Data Driven Life Science Seminars. On the topic of “Data driven research in evolution and biodiversity “. \n\n\n\nWelcome to attend the open\, digital seminars as part of the recruitment process given by the top candidates for the group leader position in data driven life science (DDLS). \n\n\n\nLink to join the webinar\, password: 526883 \n\n\n\nRead more on the event website \n\n\n\nApril 8th\n\n\n\n13.00-14.00: Malin Olofsson\, Swedish University of Agricultural Sciences\, SLU. Combining multiple data to enhance understanding of phytoplankton evolution and biodiversity \n\n\n\n14.30-15.30: Mariana Pires Braga\, Swedish University of Agricultural Sciences\, SLU. Biotic interactions: teasing apart evolutionary processes from data biases \n\n\n\nApril 9th\n\n\n\n13.00-14.00: Harith Farooq\, University of Copenhagen\, Denmark. Biodiversity Data to guide Macroecology and Conservation \n\n\n\n14.30-15.30: Pooja Choksi\, University of Minnesota\, USA. tbd URL:https://www.scilifelab.se/event/data-driven-life-science-seminars-data-driven-research-in-evolution-and-biodiversity/ LOCATION:Loftets bankettsal\, Ultuna\, Duhrevägen 8\, Uppsala CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240418T100000 DTEND;TZID=Europe/Stockholm:20240418T110000 DTSTAMP:20260503T183041 CREATED:20240328T075011Z LAST-MODIFIED:20240404T101946Z UID:10001214-1713434400-1713438000@www.scilifelab.se SUMMARY:Leveraging supercomputers for data-driven life science research: examples from Berzelius DESCRIPTION:This event is part of the Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre. This webinar is organized in collaboration with the National Supercomputer Centre\, LiU as well as the EuroHPC National Competence Centre Sweden (ENCCS). \n\n\n\nTitle: Leveraging supercomputers for data-driven life science research: examples of use cases and introduction to Berzelius \n\n\n\nSpeaker: Soumi Chaki and Xuan Gu (National Supercomputer Centre\, Linköping University)\, Kimmo Kartasalo (Karolinska Institute)\, Claudio Mirabello (Linköping University). \n\n\n\nWhere and when: April 18\, 2024 at 10:00-11:00 Stockholm time\, online. Registration is open till April 18 at 9:00. \n\n\n\nAbstract: \n\n\n\nAgenda:10:00-10:05 – Introduction to supercomputers and Berzelius10:05-10:20 – Developing computational pathology AI models for improved prostate cancer diagnostics and prognostics using Berzelius (Kimmo Kartasalo\, Post-doctoral researcher\, Karolinska Institute)10:20-10:35 – Modelling large protein complexes on Berzelius (Claudio Mirabello\, Principal Research Engineer\, Docent\, Linköping University)10:35-10:50 – Resource allocation procedure and user support available on Berzelius10:50-11:00 – Q&A session \n\n\n\nPowerful GPU supercomputers allow to carry out large-scale experiments in a fraction of time that it would otherwise take as well as pursue research projects that would otherwise not be possible. Life science researchers at Swedish universities can apply and make use of the Berzelius AI/ML cluster at the National Supercomputer Center in Linköping. In this one hour long webinar two researchers will present how they use Berzelius in their work and what research it allows them to carry out. In addition\, we will present the technical specifications of Berzelius\, the resource allocation procedure\, as well as the available user support. We will give a short demonstration on how to request GPU resources on Berzelius and run scripts/software on the allocated GPU(s). This webinar is particularly tailored for researchers interested in and working with AI/ML methods. \n\n\n\nRegister to join the event\n\n\n\nMore about the event series: \n\n\n\nTools for AI/ML research in life sciences is an event series by the SciLifeLab Data Centre aimed at life science researchers who use machine learning methods in their work. The goal of the events in this series is to provide introductions to different tools for ML research but also to foster discussions around our practices and how they can be improved. The events takes place virtually (over Zoom) and are open to researchers in Sweden and beyond. Each event is scheduled for 60 minutes\, consisting of a talk and an extended discussion. Follow the page of the event series to learn about future seminars. \n\n\n\nFor questions about the events please contact the organizing team by emailing serve@scilifelab.se \n\n\n\n \n\n\n\nScientific lead: Prof. Ola Spjuth\, SciLifeLab Data Centre and Uppsala University and DDLS \n\n\n\nContact information: serve@scilifelab.se URL:https://www.scilifelab.se/event/leveraging-supercomputers/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240419T100000 DTEND;TZID=Europe/Stockholm:20240419T110000 DTSTAMP:20260503T183041 CREATED:20240115T121853Z LAST-MODIFIED:20240115T121929Z UID:10001109-1713520800-1713524400@www.scilifelab.se SUMMARY:Model-guided ML approaches to integrative omics analyses DESCRIPTION:NBIS\, Scilifelab’s Bioinformatics platform\, arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms\, typically between 10 and 11 am\, with ca. 45 min long presentation and 15 min discussion. \n\n\n\nFor further info\, please see this website. \n\n\n\n \n\n\n\n\n\n\n\nModel-guided ML approaches to integrative omics analyses\n\n\n\nCemal Erdem\, DDLS fellow\, Umeå University \n\n\n\nClick here to join zoom conference URL:https://www.scilifelab.se/event/model-guided-ml-approaches-to-integrative-omics-analyses/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240425T113000 DTEND;TZID=Europe/Stockholm:20240426T170000 DTSTAMP:20260503T183041 CREATED:20231221T105648Z LAST-MODIFIED:20240425T193524Z UID:10001075-1714044600-1714150800@www.scilifelab.se SUMMARY:Cell and Molecular Biology - DDLS symposium DESCRIPTION:Welcome to the Cell and Molecular Biology Symposium\, starting with lunch at Restaurant Lyktan from 11:30. The conference then takes place in the Birgit Thilander Lecture Hall in Academicum. The program includes presentations from local and national experts within data driven life science research – and a keynote lecture by Prof. Edda Klipp from the Humboldt University in Berlin. \n\n\n\nDay two\, on April 26\, takes place in the AstraZeneca facilities in Mölndal. Here we will meet with the exciting BioVenture Hub and learn about how AstraZeneca works with data driven life science in a clinical setting. Bus transfer from Clarion Hotel Post leaves at 07:30 directly to Astra Zeneca. \n\n\n\n\nPractical information\n\n\n\n\n\nPublic Transport to Medicinareberget \n\n\n\nThursday\, April 27 \n\n\n\nPlease note that due to construction work\, there are disturbances in the tram operations at nearby stops Medicinaregatan and Sahlgrenska Huvudentrén. \n\n\n\nFind your best route through the Västtrafik website or app. \n\n\n\n\n\nCoach to Astra Zeneca \n\n\n\nFriday\, April 26 \n\n\n\nA chartered bus will depart from Clarion Post Hotel at 07:30\, directly to the Astra Zeneca Conference Center (PGN Entrance).  \n\n\n\n\n\nGuidelines for Self-Transport Arrivals to Astra Zeneca \n\n\n\nFriday\, April 26 \n\n\n\nWhether you’re arriving by public transport\, bike\, or car\, kindly make your way to the KC-entrance at Pepparedsleden 1. \n\n\n\nPlease be punctual at 08:00\, as you’ll be guided from the entrance to the conference area. \n\n\n\n\n\n\nProgram\n\n\n\nClick to expand and see the program \n\n\n\nThursday\, April 25\nApril 2510:30Expert Group meeting11:30LunchRestaurant Lyktan13:00Welcome WordsMargit Mahlapuu\, University of GothenburgSverker Holmgren\, ChalmersOla Engkvist\, AstraZeneca13:10Precision Glycomics: How AI and advanced mass spectrometry are changing the gameDaniel Bojar\, University of Gothenburg13:40Towards a universal molecular framework for structure prediction and designPatrick Bryant\, SciLifeLab/Stockholm University (DDLS Fellow)Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However\, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly\, given a multiple sequence alignment representation of the protein\, protein pocket information\, and a SMILES string representing the ligand.14:10Integrating single-cell transcriptomics with cellular phenotypesJoan Camuñas\, University of Gothenburg14:40Thermodynamics-informed modeling of biochemical reaction and regulation networksEdda Klipp\, Humboldt-Universität zu Berlin15:20Coffee Break15:50Tumor biology using multiomicsAnders Ståhlberg\, University of Gothenburg16:10Multiomics – state of art data generation and analysis at NGIMattias Ormestad and Franziska Bonath\, National Genomics InfrastructureMultiomics projects can span over long time frames\, sometimes years\, until all data is created. Often sequencing is an integral part and is outsourced to a core facility like NGI. For projects in which data generation is performed by different groups\, it is crucial that important information about library preparation\, sequencing and analysis is recorded and available to all other participants. Therefore\, NGI applies quality control measures and reports important metadata to ensure that our users can use our data with confidence even years after data generation.16:30Data-Driven Microscopy: the automation of end-to-end imaging workflowsElisabet Carlsohn and Rafael Camacho\, SciLifeLab/University of GothenburgBiological complexity mandates comprehensive imaging for statistically significant results. Manual operation impedes large dataset acquisition\, affecting reproducibility. Smart microscopy\, integrating image analysis and computer-controlled microscopes\, streamlines workflows. At GU’s Centre for Cellular Imaging\, we offer open-access “smart microscopy” services optimizing data management with next-gen file formats\, ome-zarr\, community-driven visualization tools\, napari\, and collaborative platforms\, webknossos. This ensures efficient resource utilization in the era of data-driven life sciences.17:00Tour to SciLifeLab units in Gothenburg Optional\, sign up in registration form18:00Dinner for CMB fellows and experts\, and speakers\n\n\n\n \n\n\n\n\nFriday\, April 26\nApril 2607:30Bus transport to Astra Zeneca Conference Centre in Mölndal08:00Visitor registration Astra Zeneca Conference Centre in Mölndal08:25IntroductionOla Engkvist\, AstraZeneca & Margit Mahlapuu\, University of Gothenburg08:30Empowering data-driven innovations in Life Sciences: A journey with GU VenturesKlementina Österberg\, GU Ventures & Carl-Peter Mattsson\, GU VenturesKlementina Österberg CEO & Carl-Peter Mattsson Investment director at GU Ventures will present their experiences and the journeys to create successful new business in collaborations with investors\, industry and the eco system. They will also show some examples of these journeys with their companies.09:15BioVentureHub – an antidote to the incubent’s curseMagnus Björsne\, AstraZeneca BioVentureHub10:00Coffee Break10:30Precision Medicine from the start – using omic data to deliver actionable insight to drug discovery and developmentDaniel Muthas\, AstraZeneca11:15Data driven life sciences in a clinical settingJesper Havsol\, AstraZeneca12:00Networking lunch12:40Tour – “The Amazing Journey the story about Astra Zeneca in Mölndal”Optional\, sign up in registration form\n\n\n\n \n\n\n\n\nSymposium Program for Download and PrintDownload\n\n\n\nData-driven Life Science\n\n\n\nThe future of life science is data-driven\, providing major new opportunities to explore and understand biology\, human health and changing ecosystems. The SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS) is set up to make use of these opportunities. URL:https://www.scilifelab.se/event/ddls-symposium-cell-and-molecular-biology/ LOCATION:Birgit Thilander Lecture Hall\, Medicinaregatan 3\, Göteborg CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240516T141500 DTEND;TZID=Europe/Stockholm:20240516T163500 DTSTAMP:20260503T183041 CREATED:20240429T090516Z LAST-MODIFIED:20240429T091240Z UID:10001246-1715868900-1715877300@www.scilifelab.se SUMMARY:Uppsala University DDLS Fellows - public seminars with candidates DESCRIPTION:Welcome to a data driven-rich afternoon of scientific presentations by 4 candidates for the DDLS program fellow position on Data-driven Precision Medicine and Diagnostics and Biträdande Universitets Lektor position at Uppsala University. \n\n\n\nMeeting details\n\n\n\nMonday\, May 6\, 2024 14:15-16:35 \n\n\n\nZoom link >>   \n\n\n\nMötes-ID: 640 7985 9903 \n\n\n\nSchedule\n\n\n\n14:15-14:50     \n\n\n\nSergi Sayols Baixeras\, Uppsala University\, Dep. of Medical Sciences\, Sweden \n\n\n\nNovel Insights fromZMetagenomics and Metabolomics on Atherosclerotic Disease \n\n\n\n14:50-15:25      \n\n\n\nQiaoli Wang\, Harvard University Medical School\, Cambridge\, USA \n\n\n\nAnticipatory Detection of Upper-Gastrointestinal Cancers: Staying One Step Ahead with a Dash of Wit \n\n\n\n15:25-16:00      \n\n\n\nMuhammad Arif\, National Institute on Alcohol Abuse and Alcoholism\, Rockville\, USA \n\n\n\nIntegrative Multi-Omics Frameworks for Understanding the Molecular Mechanism of Progressive Diseases \n\n\n\n16:00-16:35      \n\n\n\nFilipe Barata\, Centre for Digital Health Interventions\, ETH Zurich\, Switzerland & Stanford University\, Palo Alto\, USA.  \n\n\n\nAdvancing Personalized Healthcare Through Digital Biomarkers URL:https://www.scilifelab.se/event/uppsala-university-ddls-fellows-public-seminars-with-candidates/ CATEGORIES:Event ORGANIZER;CN="SciLifeLab Event":MAILTO:events@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240517T100000 DTEND;TZID=Europe/Stockholm:20240517T110000 DTSTAMP:20260503T183041 CREATED:20240311T123125Z LAST-MODIFIED:20240311T123126Z UID:10001199-1715940000-1715943600@www.scilifelab.se SUMMARY:Digital twins and integrative systems biology DESCRIPTION:NBIS\, Scilifelab’s Bioinformatics platform\, arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms\, typically between 10 and 11 am\, with ca. 45 min long presentation and 15 min discussion. \n\n\n\nFor further info\, please see this website. \n\n\n\n \n\n\n\n\n\n\n\nDigital twins and integrative systems biology\n\n\n\nGunnar Cedersund\, Linköping University \n\n\n\nClick here to join zoom conference URL:https://www.scilifelab.se/event/digital-twins-and-integrative-systems-biology/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20240521T103000 DTEND;TZID=Europe/Stockholm:20240521T120000 DTSTAMP:20260503T183041 CREATED:20240515T074909Z LAST-MODIFIED:20240515T074909Z UID:10001259-1716287400-1716292800@www.scilifelab.se SUMMARY:Uppsala University DDLS Fellows - public seminars with candidates - part II DESCRIPTION:Welcome to the second data driven-rich morning of scientific presentations by 2 candidates for the DDLS program fellow position on Data-driven Precision Medicine and Diagnostics and Biträdande Universitets Lektor position at Uppsala University. \n\n\n\nSchedule \n\n\n\nMeeting details\n\n\n\nTuesday\, May 21\, 2024 10:30-12:00 \n\n\n\nZoom link >>   \n\n\n\nMötes-ID: 663 2681 5420 \n\n\n\nSchedule\n\n\n\n10:30-11:05     \n\n\n\nMarcel Tarbier\, Karolinska Institutet\, Stockholm\, Sweden \n\n\n\nInto the Single-Verse: Inferring complex gene and cell features from gene expression – and an excursion through space and time \n\n\n\n11:05-11:40      \n\n\n\nMuhammad Arif\, National Institute on Alcohol Abuse and Alcoholism\, Rockville\, USA \n\n\n\nIntegrative Multi-Omics Frameworks for Understanding the Molecular Mechanism of Progressive Diseases URL:https://www.scilifelab.se/event/uppsala-university-ddls-fellows-public-seminars-with-candidates-part-ii/ CATEGORIES:Event ORGANIZER;CN="SciLifeLab Event":MAILTO:events@scilifelab.se END:VEVENT END:VCALENDAR