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DTSTART;TZID=Europe/Stockholm:20230515T080000
DTEND;TZID=Europe/Stockholm:20230516T170000
DTSTAMP:20260416T014932
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
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DTSTART;TZID=Europe/Stockholm:20220516T080000
DTEND;TZID=Europe/Stockholm:20220517T170000
DTSTAMP:20260416T014932
CREATED:20220309T093342Z
LAST-MODIFIED:20220512T143421Z
UID:10000548-1652688000-1652806800@www.scilifelab.se
SUMMARY:Planetary Biology Workshop
DESCRIPTION:EMBL-SciLifeLab workshop on the theme Planetary Biology \n\n\n\nThe purpose of the workshop is to enhance connectivity between researchers at both\, SciLifeLab and EMBL\, to identify new collaboration ideas\, and to promote joint technology and infrastructure resource development within Planetary Biology. \n\n\n\nThis is one of many workshops that will follow the conclusion of the MoU between SciLifeLab and EMBL in 2021. \n\n\n\nThe workshop is a hybrid event. Physical location is the EMBL Heidelberg campus\, where in-person attendance is limited. Allocation of spaces is on a first-come first-served basis.  \n\n\n\nPlease note: there are two separate registration links for on-site or virtual participation. In case you sign up for on-site participation but your availability changes\, please make sure to inform the responsible contacts. \n\n\n\nThe workshop will include talks on a broad set of themes including: \n\n\n\nBiodiversity Genomics & Reference Genome SequencingEcology & EvolutionBiogeochemistry & EcosystemsData-driven Planetary Biology\,\n\n\n\nAs well as invited keynote speakers and panel discussions. \n\n\n\nread more and sign up here\n\n\n\nDay 1\, Monday 16th May\, 2022 \n\n\n\n13:00Welcome and opening remarksEdith HeardDirector General of EMBLOlli KallioniemiDirector of SciLifeLab13:10Introduction and overview of Planetary BiologyDetlev ArendtPlanetary Biology Co-Chair\, Senior Scientist\, Group Leader\, EMBLOlga Vinnere Pettersson & Stefan BertilssonCo-Leads Planetary Biology Capability\, SciLifeLab13:30Session 1: Biodiversity Genomics & Reference Genome Sequencing (15 mins + 5 mins Q&A per speaker in each session)ModeratorPeter Harrison\, Genome Analysis Team Leader\, EMBL-EBISpeakersFergal Martin\, Vertebrate Annotation Coordinator\, EMBL-EBIKerstin Lindblad Toh (remote)\, Professor in Comparative Genomics\, Uppsala University\, Scientific Director of Vertebrate Genome Biology\, Broad InstituteDetlev Arendt\, Planetary Biology Co-Chair\, Senior Scientist\, Group Leader\, EMBLOve Nilsson\, Group Leader Control of Flowering Time and Tree Phenology\, Umeå Plant Science Center14:50 Coffee break15:10Session 2: Ecology and EvolutionModeratorOlga Vinnere Pettersson\, Co-Lead Planetary Biology Capability\, SciLifeLabSpeakersLove Dalén\, Professor of Evolutionary Genetics\, Swedish Museum of Natural History\, Research Leader at Center for Palaeogenetics\, StockholmMichael Dorrity\, Group Leader Structural and Computational Biology\, EMBLJames Sharpe (remote) \, Head of EMBL Barcelona\, Group Leader in Tissue Biology and Disease ModellingAnna Rosling\, Group Leader Ecology and Evolution in Soil Fungi\, Uppsala University16:30Keynote by Mark BlaxterWellcome Sanger Institute17:15Summary and Q&A\n\n\n\nDay 2\, Tuesday 17th May\, 2022 \n\n\n\n09:00Arrival and Coffee09:30Keynote by Martin PolzUniversity of Vienna10:20Session 3: Biogeochemistry & Ecosystems(15 mins + 5 mins Q&A per speaker in each session)ModeratorStefan Bertilsson\, Co-Lead Planetary Biology Capability\, SciLifeLabSpeakersMichael Zimmermann\, Group Leader in Structural and Computational Biology\, EMBLFlora Vincent\, Incoming Group Leader in Developmental Biology; Post Doctoral Fellow at Weizmann Institute of Science\, RehovotSara Hallin\, Professor at the Department of Forest Mycology and Plant Pathology\, Swedish University of Agricultural SciencesMark Dopson\, Professor at the Department of Biology and Environmental Science\, Linnaeus University11:40 Break12:40Session 4: Data-driven Planetary BiologyModeratorOliver Stegle\, Associate Group Leader in Genome Biology\, EMBLSpeakersTomas Roslin (remote)\, Professor at the Department of Ecology\, Swedish University of Agricultural SciencesPeer Bork\, Director of EMBL Heidelberg\, Group Leader in Structural and Computational Biology\, EMBLAnders Andersson\, Group Leader in Environmental Genomics\, Royal Institute of TechnologyAnna Kreshuk\, Group Leader in Cell Biology and Biophysics14:00Summary and Q&A14:15Coffee break14:45Panel Discussion 1: Technological Infrastructure Needs for PB ResearchModeratorStefan Bertilsson\, Co-Lead Planetary Biology Capability\, SciLifeLabPanelistsYannick Schwab\, Team Leader Volume Correlative Light and Electron Microscopy and Head of Electron Microscopy Core Facility\, EMBLTimo Zimmermann\, Team Leader Advanced Light Microscopy Technology Development and Service Provision\, EMBLLinda Sandblad\, Scientific Platform Director Cellular and Molecular Imaging\, Umeå University\, SciLifeLabOlga Vinnere Pettersson\, Project coordinator at Department of Immunology\, Genetics and Pathology\, Uppsala University; Co-Lead Planetary Biology Capability\, SciLifeLabAnnika Johansson\, Head of Swedish Metabolomics Centre\, Umeå University\, SciLifeLab16:00Short break16:10Panel Discussion 2: Data Collection in PB ResearchModeratorOlga Vinnere Pettersson\, Co-Lead Planetary Biology Capability\, SciLifeLabPanelistsRainer Pepperkok\, Director of Scientific Core Facilities and Scientific Services\, Team Leader Membrane traffic and Organelle Biogenesis\, EMBLStefan Bertilsson\, Professor in Functional Ecology of Freshwaters\, Swedish University of Agricultural Sciences; Director of the Swedish Infrastructure for Ecosystem Science (SITES); Co-Lead Planetary Biology Capability\, SciLifeLabFredrik Ronqvist\, Professor in the Department of Bioinformatics and Genetics\, Swedish Museum of Natural History; Swedish Biodiversity Data Infrastructure (SBDI)16:40Panel Discussion 3: Data Management and Processing in PB ResearchModeratorFergal Martin\, Eukaryotic Annotation Team Leader\, EMBL-EBIPanelistsGuy Cochrane (remote)\, Team Leader Data Coordination and Archiving\, EMBL-EBIBlokeshwaran Manoharan\, Expert in Metagenomics; National Bioinformatics Infrastructure Sweden (NBIS)Johan Rung\, Head of Data Center\, SciLifeLab17:00Conclusion and Closing Remarks\n\n\n\n \n\n\n\n \n\n\n\n \n\n\n\n \n\n\n\n \n\n\n\nScientific committee SciLifeLab\n\n\n\nStefan Bertilsson\, SLUOlga Vinnere Pettersson\, Uppsala University
URL:https://www.scilifelab.se/event/planetary-biology-workshop/
LOCATION:EMBL Heidelberg\, Meyerhofstraße 1\, Heidelberg\, Germany
CATEGORIES:Event
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