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SUMMARY:Data-Driven Life Sciences Course 2024 (Online)
DESCRIPTION:Welcome to the Data-driven Life Sciences 2024 course\, where you will explore the intersection of data science\, artificial intelligence\, and life sciences to drive innovation and discovery. This fully online course culminates in an in-person hackathon\, fostering a vibrant community that gathers the DDLS and SciLifeLab members. \n\n\n\nThe 6 modules aim to introduce learners to computer-driven life sciences\, covering application areas in data-driven life sciences. Guest lecturers (DDLS Fellows\, SciLifeLab fellows\, and SciLifeLab facility training providers) will teach topics including technologies and analysis of data sets from proteomics\, transcriptomics\, biomolecular structure\, molecular dynamics simulations\, and various imaging techniques. These modules present\, analyze\, and discuss models of biological phenomena and related scientific breakthroughs based on such data analysis. \n\n\n\nRegistration\n\n\n\nAs prerequisites for the course\, we recommend that you have a look at the following resources: \n\n\n\n\nPlease have a look at the SciLifeLab Data-Driven Life Science (DDLS) initiative website to understand what data-driven life sciences are\, and how Sweden is investing in this area. Focus in particular on the concept of the data life cycle\, which is central in this class.\n\n\n\nWe will use Python as the main programming language in the computer lab\, so please make sure you know the basics of Python. \n\n\n\n\nFor the computer lab\, you will need a computer with internet access\, and make sure you have the following set up: \n\n\n\n\nInstall the latest browser\, e.g. Chrome\n\n\n\nRegister a Google account for the Google Colab access and use the Google Drive\n\n\n\nRegister a ChatGPT account (Note: No need to subscribe to the paid version of ChatGPT\, using the free version is sufficient for this course)\n\n\n\nRegister a Github account for versioning of the code\n\n\n\n\nLearning objectives:  \n\n\n\n\nDescribe the field of data-driven life sciences\n\n\n\nPresent an overview of various application areas\n\n\n\nProvide examples of applications and their associated analysis methods\n\n\n\nApply statistical and machine learning analysis to biological data sets\n\n\n\nFormulate models of biological phenomena\n\n\n\nPresent and review scientific literature in computer-driven life sciences\n\n\n\nReflect on the ethical consequences of data-driven life sciences\n\n\n\nPractice good data management\, including collection\, handling\, sharing\, and analysis\n\n\n\n\nFor questions\, contact the course leader Wei Ouyang at weio@kth.se
URL:https://www.scilifelab.se/event/data-driven-life-sciences-course-2024-online/
LOCATION:Online event via Zoom
CATEGORIES:Course
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DTSTART;TZID=Europe/Stockholm:20241001T090000
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DTSTAMP:20260510T160739
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SUMMARY:Spatial Biology - The 2024 SciLifeLab Science Summit
DESCRIPTION:Spatial Biology is an emerging field driven by recent advances in Spatial Omics technologies. The aim of the summit is to present the spatial omics capabilities at SciLifeLab\, and examples of uses of such methods to address various research areas in Life Science. A lot of pioneering work in Spatial Biology originates from researchers associated with SciLifeLab\, and we hope to inspire more researchers to explore this approach and to join this growing spatial community. \n\n\n\nThe Annual Conference SciLifeLab Science Summit is a one-day symposium with a new topic each year. The topic for 2024 is Spatial Biology. \n\n\n\nWe warmly welcome international visitors to attend this free event. The conference also offers fantastic opportunities for networking and discussions with top academic researchers and industry leaders in spatial omics technology. \n\n\n\nWelcome! \n\n\n\nMats Nilsson\, Chair of the Scientific Committee\, Charlotte Stadler\, Per Andrén and Stefania Giacomello \n\n\n\n\n\n\n\nProgram\n\n\n\nScience Summit Program 2024Download\n\n\n\n\n\n\n\nPosters\n\n\n\nPoster Presentation Guidelines \n\n\n\nPoster Format \n\n\n\nThe poster screens are 103 cm wide and 143 cm high. Please ensure your poster fits within these measurements. \n\n\n\nMount your poster \n\n\n\nThe venue will be open from 8:45 AM. Please proceed to the 6th floor and hang your poster at your designated number. A numbered poster list will be provided closer to the event date. \n\n\n\nPoster sessions \n\n\n\nPoster Session I: During the morning coffee break\, from 10:55 AM to 11:35 AM\, presenters of posters with odd numbers (1\, 3\, 5\, 7…) should be present by their posters. \n\n\n\nPoster Session II: During the afternoon break\, from 3:15 PM to 3:55 PM\, presenters of posters with even numbers (2\, 4\, 6\, 8…) should be present by their posters. \n\n\n\nBest Poster Award \n\n\n\nAll poster presenters should attend the Best Poster Award ceremony at the end of the conference\, where the winners will be announced. The Scientific Committee will evaluate the posters throughout the day. \n\n\n\nDismount of posters \n\n\n\nPlease remove your poster immediately after the closing session at 5:00 PM. Poster screens will be collected at 5:30 PM\, and any remaining posters will be discarded. \n\n\n\nPoster List \n\n\n\nScience Summit Posterlist 2024Download\n\n\n\nAbstracts \n\n\n\nAbstracts Science Summit 2024 – PostersDownload\n\n\n\nRegistration\n\n\n\nFor late registrations (after September 13)\, we cannot guarantee lunch\, coffee\, nor can we accommodate any allergies or dietary requirements. These will be subject to availability. We appreciate your understanding. \n\n\n\nRegister here\n\n\n\nQuestions? If you have any inquiries regarding the event or your registration\, please contact events@scilifelab.se \n\n\n\nThe conference is free of charge; however\, if you do not attend and fail to cancel\, your department or organization will be charged a no-show fee of 500 SEK. \n\n\n\n\nImportant Notice Regarding Venue Regulations\n\n\n\nPlease be advised that for security reasons\, Uppsala Konsert & Kongress (UKK) has a strict policy regarding bags and outside clothing.  \n\n\n\nBags larger than A4 size and outside clothing (jackets\, coats etc.) are not permitted inside the auditorium.  \n\n\n\nHowever\, you are welcome to store these items in the venue’s cloakroom. Laptops can be brought into the auditorium in laptop sleeves. \n\n\n\nWe apologize for any inconvenience this may cause and appreciate your understanding and cooperation in adhering to the venue’s regulations. \n\n\n\n\nInvited Speakers – abstract and bio sketch\n\n\n\nClick on the arrow to read the speaker’s title\, abstract\, and bio. \n\n\n\nGonçalo Castelo-Branco\, Karolinska Institutet\, Sweden\nTalkOligodendroglia in Development and Multiple Sclerosis: Insights from Single-Cell and Spatial Omics \n\n\n\nAbstractOligodendroglia (OLG) mediate myelination of neurons\, a process that allows efficient electrical impulse transmission in the central nervous system. An autoimmune response in multiple sclerosis (MS) leads to OLG cell death\, loss of myelin and neuropathology. Using single cell transcriptomics\, we have previously identified disease-specific OLG populations in the EAE mouse model of MS and in human MS brain archival tissue\, characterized by the expression of immune genes.By assessing chromatin accessibility and the transcriptome simultaneously at the single cell level at different stages of the disease course\, we found that immune genes exhibit a primed chromatin state in mouse and human OLG in a non-disease context\, compatible with rapid transitions to immune-competent states in MS. Moreover\, we found dynamic and distinct transcriptomic and epigenomic responses of OLG subpopulations to the evolving environment in EAE mouse model of MS\, which might modulate their response to regenerative therapeutic interventions in MS.While single-cell genomics are powerful for investigating disease-specific cellular states\, these methods involve isolating the tissue under study from its niche\, leading to a loss of spatial information. Such information is essential for determining cell-to-cell communication in disease niches. We have applied in situ sequencing to investigate disease evolution in MS at a spatial level\, both in the EAE mouse model of MS and in human post-mortem MS samples. We annotated disease neighborhoods during lesion evolution and found centrifugal propagation of active lesions. We demonstrated that disease-associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course.We have also applied dBIT-Seq\, a ligation-based method for deterministic barcoding in tissue\, to probe different histone modifications and chromatin accessibility in the mouse brain tissue sections\, either in an unimodal or simultaneously with transcriptomics. This spatial epigenome–transcriptome co-profiling has allowed us to identify cellular lineage progression and epigenomic priming events that precede transcription during development with spatial resolution. We are currently applying these methods to disease paradigms in MS\, to uncover how transitions to pathological cellular states occur at epigenomic and transcriptomic levels. \n\n\n\nBio \n\n\n\nGonçalo Castelo-Branco researches oligodendrocytes’ epigenetic states\, focusing on how transcription factors\, non-coding RNA\, and chromatin enzymes drive cell changes. His work has potential for multiple sclerosis therapies. \n\n\n\n\nRon Heeren\, Maastricht University\, The Netherlands\nTalk \n\n\n\nSpatial biology and translation life sciences \n\n\n\nAbstract \n\n\n\nModern molecular analytical technologies in the “omics” arena plays a crucial role in many scientific disciplines ranging from material sciences to clinical diagnostics. Technological advances have increased methodological sensitivity allowing researchers to acquire detailed molecular information of smaller and smaller samples. The biggest challenge is to put that concerted information in the context of the biological problem the samples originate from. This lecture describes how innovative mass spectrometry based molecular imaging technologies\, have impacted translational clinical research and beyond. Or: how a mass spectrometer can be used as a sensitive and selective molecular microscope in modern spatial biology. Targeted  and untargeted imaging technologies now offer new insights in the complexity that can be employed for systems medicine. Innovations in mass spectrometry based chemical microscopes have now firmly established themselves in translational molecular research. One key aspect of translational success is the ability to obtain this molecular information on thousands of molecules on a timescale relevant to translation. Single cells can be analyzed in great molecular detail and in the context of their native tissue. Combined this offers a true multi-omics approach that reveals contextual molecular complexity for systems medicine. \n\n\n\nBio \n\n\n\nProf. Dr. Ron M.A. Heeren obtained a PhD degree in technical physics in 1992 at the University of Amsterdam on plasma-surface interactions. He was the research group leader at FOM-AMOLF for macromolecular ion physics and biomolecular imaging mass spectrometry in the period 1995-2015. In 2001 he was appointed professor at the chemistry faculty of Utrecht University lecturing on the physical aspects of biomolecular mass spectrometry. In 2014 he was appointed as distinguished professor and Limburg Chair at the University of Maastricht. He is scientific director of M4I\, the Maastricht MultiModal Molecular Imaging institute and heads the division of imaging MS. He is the vice-president of the international mass spectrometry foundation and has been active in many professional societies to advance mass spectrometric research\, education and professionalization. His academic research interests are mass spectrometry based personalized medicine\, translational molecular imaging research\, high-throughput bioinformatics and the development and validation of new mass spectrometry based “omics” imaging techniques for the life sciences. \n\n\n\n \n\n\n\n\nArutha Kulasinghe\, The University of Queensland\, Australia\nTalk \n\n\n\nUncoupling Pathways Involved in Immunotherapy Resistance: Insights from Deep Tissue Profiling \n\n\n\nAbstract \n\n\n\nSpatially resolved multi-omic phenotyping is revolutionizing how we study tissue and immune responses to cancer treatments. In this talk\, we will describe our integrated approaches to characterizing the tumour microenvironment in head and neck\, lung\, and skin cancers using ultra high-plex spatial proteomics and transcriptomics\, benchmarking to ground truth\, and developing functionally characterised immuno-metabolic signatures associated with resistance and sensitivity to immunotherapy. \n\n\n\nBio \n\n\n\nDr. Arutha Kulasinghe is a Senior Research Fellow and leads the Clinical-oMx Lab at the University of Queensland. Dr Kulasinghe has pioneered spatial transcriptomics using digital spatial profiling approaches in the Asia-Pacific region\, contributing to world-first studies for lung cancer\, head and neck cancer\, skin cancer and COVID-19. His research aims to understand the underlying pathobiology by using an integrative multi-omics approach. \n\n\n\n\nCecilia Lindskog\, Uppsala University\, Sweden\nTalkA spatio-temporal single-cell type map of the human proteome based on transcriptomics\, high-resolution antibody-based imaging and artificial intelligenceAbstractFor a fundamental understanding of human health\, molecular medicine and targeted treatment\, it is necessary to map processes unique to each tissue and cell type. We here aimed to set up a stringent\, workflow for mapping human tissues at the single-cell type level\, and utilized this workflow to create high-resolution spatio-temporal maps of tissue or cell type-specific proteins in human tissues. One of these tissues is testis\, which is a complex organ with spermatogenesis involving thousands of genes and proteins activated or repressed through multiple cell states\, from spermatogonial stem cells to mature sperm. Understanding the intricate functions and mechanisms at each step of this process requires a multi-dimensional approach that integrates both quantitative and qualitative methods.Based on single-cell RNA sequencing data\, we identified 12 distinct cell types and subsets of germ cells in testis\, some of which cannot be distinguished by regular immunohistochemistry. Using a multiplex immunofluorescence pipeline\, we then built antibody panels specifically outlining each of these cell types. The fixed antibody panels were stained together with the candidate protein of interest\, one at a time\, to pinpoint the exact protein localization at a cellular and subcellular level. Using artificial intelligence\, the high-resolution images were quantified using an automated image analysis workflow. The integrated data allowed us to study temporal mRNA and protein expression gradients along with maturation processes and identify which mRNAs that are consistently translated into proteins from those that vary from a spatio-temporal aspect. We were also able to assign presumed functions to numerous uncharacterized proteins not previously described in the context of human reproduction.In summary\, we present a strategy for high-resolution spatio-temporal mapping of human tissues and cells\, presented as a single-cell type reference map of adult human testis. The data which is freely available on www.proteinatlas.org decodes the complexity of human germ cells and links quantitative data with tissue morphology\, and the validated workflow has the potential to be used for other tissues\, contributing to valuable insights into molecular function and processes linked to disease.BioDr. Lindskog is a research group leader and associate professor at the Department of Immunology\, Genetics and Pathology\, Cancer Precision Medicine unit\, Uppsala University\, Sweden. Her research group uses a multi-dimensional approach and combination of various qualitative and quantitative methods to generate high-resolution spatial maps of the human body at the single-cell type level. By combining scRNA-seq\, spatial technologies for mRNA and protein detection and machine learning\, she aims to link single cell type-specific expression profiles with molecular function and mechanisms of disease\, a first step towards precision medicine. Since 2006\, Dr. Lindskog is also affiliated with the Human Protein Atlas (HPA) project\, the largest biological database for spatial proteomics\, publicly available at www.proteinatlas.org. She received her PhD in Pathology at Uppsala University in 2013\, and since 2014 she has been director of the tissue-based efforts of the HPA project\, leading the team that generates the mRNA and protein expression data in human tissues. \n\n\n\n \n\n\n\n\nJoakim Lundeberg\, KTH\, Sweden\nTalk \n\n\n\nTissue ecosystems in time and space \n\n\n\nAbstract \n\n\n\nTools in spatial biology offer a wide range of technologies that quantify different types of biomolecules in tissue sections. These technologies provide information about distinct aspects of tissue anatomy\, such as its morphology\, genome\, transcriptome\, proteome\, and metabolome. Here\, several multiomics computational and experimental methodologies approaches that capture the tissue ecosystem from a single tissue section will be described. \n\n\n\nBio \n\n\n\nJoakim Lundeberg\, Ph.D.\, Professor in Molecular Biotechnology\, has\, during the most recent years\, focused on spatial transcriptomics\, which enables a detailed description of gene expression patterns in tissue sections. The methodology is now available worldwide through 10x Genomics Inc\, as Visium. The technology was also featured in Nature Methods as the Method of the Year 2020. Dr. Lundeberg has publications demonstrating technology development into several new spatial modalities and examples of its impact in biology. The current research focuses on expanding the spatial modalities and developing new tools and applications in human cell atlas\, neurology\, and cancer. \n\n\n\n\nSinem Saka\, EMBL\, Germany\nTalkA DNA toolbox for spatial biology from imaging to sequencingAbstractDNA is not only a fundamental constituent of cells\, but has also great capacity for information storage. We leverage the predictability of DNA hybridization kinetics and orthogonality of DNA sequences to utilize DNA oligos as tagging and barcoding tools for improving the major limitations of in situ visualization of molecules. We have previously developed multiplexed imaging approaches such as SABER-FISH and Immuno-SABER that utilize DNA barcoding and a flexible in situ signal amplification system for efficient visualisation of many protein\, DNA or RNA targets in cells and tissues. More recently\, we have implemented DNA barcoding for a new spatial transcriptomics approach\, Light-Seq\, which directly integrates fluorescence imaging and whole-transcriptome next-generation sequencing of the same cells in fixed biological samples. Light-Seq combines spatially-targeted\, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled\, spatially-indexed sequencing libraries. This light-directed barcoding enables imaging-based in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location\, morphology\, or protein stains\, without cellular dissociation. Applying Light-Seq to mouse retinal sections\, we discovered new biomarkers for a very rare neuronal subtype\, dopaminergic amacrine cells\, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells\, leaving the sample intact for further analysis post-sequencing. We are using these methods to directly link multi-dimensional and high-resolution microscopic phenotypes to transcriptomic profiles for diverse sample types. \n\n\n\nBio \n\n\n\nPhD in Molecular Biology\, 2013\, University of Göttingen/International Max Planck Research School\, Germany.Postdoctoral research at Wyss Institute for Biologically Inspired Engineering\, Harvard University\, USA.EMBO Postdoctoral Fellow 2016–2017.Human Frontier Science Program Fellow 2017–2020.Group leader at EMBL since December 2020. \n\n\n\n\nJeffrey Spraggins\, Vanderbilt University\, Nashville\, USA\nTalkBringing human disease into focus through integrated multimodal molecular imagingAbstractCellular interactions within tissue micro-environments form the basis of health and disease for all organisms. Exposure to nutrients\, toxins\, and neighboring cells triggers coordinated molecular responses that impact cellular function and metabolism in a beneficial\, adaptive\, or detrimental manner. Acquiring molecular information at cellular resolution is thus crucial for developing a comprehensive understanding of the biology of an organism. Matrix-assisted laser desorption/ionization (MALD) imaging mass spectrometry (IMS) addresses this need by combining the spatial fidelity of classical microscopy with the molecular specificity of a mass spectrometer. This presentation will highlight our work developing new\, high-performance technologies for improving the spatial resolution\, sensitivity\, and specificity of MALDI IMS for metabolite\, lipid\, and protein mapping. This will include the utilization of novel MALDI methods and development efforts using high spatial resolution Q-TOF platforms to address the molecular complexity associated with direct tissue analysis. Further\, I will describe recent advances in integrated\, multimodal methods that correlate molecular signals to specific biological tissue features and cell types. These technologies will be demonstrated through various biomedical research applications that include the construction of molecular atlases and understanding the molecular drivers of normal aging and disease.BioJeff Spraggins is an Associate Professor in the Department of Cell and Developmental Biology\, Director of the Biomolecular Multimodal Imaging Center (BIOMIC)\, and Director of the Mass Spectrometry Research Center at Vanderbilt University. He received his B.A. in Chemistry from the College of Wooster and his Ph.D. in Analytical Chemistry from the University of Delaware. Dr. Spraggins’ research program focuses on the development of next-generation imaging mass spectrometry (IMS) technologies to elucidate the molecular basis of health and disease. Modern instrumentation and computing capabilities have enabled researchers to move beyond reductionist biology and\, instead\, probe how the components of biological entities (e.g.\, molecules\, cells\, and tissues) interact to reveal the underlying biology of disease. This systems biology approach has been accelerated by advancements in high-throughput ‘omics’ technologies; however\, genetic and molecular information is only part of the story. The challenge lies in understanding how these parts interact and how perturbations to the system relate to disease. Molecular imaging effectively offers a ‘blueprint’ as to how biological components work together by providing spatial context to molecular information. Broadly\, Dr. Spraggins’ research falls into two categories: (1) Developing novel mass spectrometry technologies to maximize imaging performance\, enabling molecular histology at cellular resolution\, and (2) combining imaging mass spectrometry with a variety of other biomedical imaging technologies to create new integrated modalities capable of providing a systems biology view of tissue at cellular resolution. The Spraggins group applies these technologies to the construction of molecular atlases as part of the NIH Human Biomolecular Atlas Program (HuBMAP)\, the NIDDK Kidney Precision Medicine Project (KPMP)\, and the NCI Human Tumor Atlas Network (HTAN); and also\, to understanding the molecular drivers of Alzheimer’s\, kidney\, and infectious diseases. \n\n\n\n\nCarolina Wählby\, Uppsala University\, Sweden\nTalkMeasuring tissue morphology in spatial biologyAbstractSpatial omics has transformed our understanding of tissue architecture by preserving spatial context of gene expression patterns. Simultaneously\, advances in imaging AI have enabled extraction of morphological features describing the tissue. The intersection of spatial omics and imaging AI presents opportunities for a more holistic understanding: morphological features can be translated or integrated into spatial omics analyses. By translation we mean finding morphological features that spatially correlate with gene expression patterns with the purpose of predicting gene expression. Such features can be used to generate super-resolution gene expression maps or infer genetic information from clinical H&E-stained samples. By integration we mean finding morphological features that spatially complement gene expression patterns with the purpose of enriching information. Such features can be used to define spatial domains\, especially where gene expression has preceded morphological changes and where morphology remains after gene expression.BioCarolina Wählby is professor in Quantitative Microscopy at the Dept. of Information Technology\, Uppsala University\, and Scientific Director of the National SciLifeLab Bioimage Informatics facility. Her research lies in the intersection between life science and computational image analysis\, developing image analysis\, deep learning\, and visualization approaches for understanding the organization and dynamics of cells and tissue\, funded primarily by the ERC and the Swedish Foundation for Strategic research. She has a MSc in molecular biotechnology and a PhD in digital image analysis\, and carried out postdoc research within genetics and pathology. She was part of the Imaging Platform of the Broad Institute 2009-2015\, developing CellProfiler\, and became full professor at Uppsala University in 2014\, and is a member of the Royal Swedish Academy of Engineering Sciences. \n\n\n\n\n \n\n\n\nSpeaker abstracts 2024Download\n\n\n\nImportant dates\n\n\n\nOctober 1: Science Summit Opens at Uppsala Konsert & Kongress \n\n\n\nExhibitors\n\n\n\nMeet representatives from companies providing products and services in relevant fields. The following companies will be present during the day \n\n\n\n\n10x Genomics\n\n\n\nAkoya Biosciences\n\n\n\nBioNordika AB\n\n\n\nBruker (Canopy Biosciences and NanoStrings)\n\n\n\nLunaphore\n\n\n\nNavinci Diagnostics AB\n\n\n\nSaveen & Werner AB\n\n\n\nThermo Fisher Scientific\n\n\n\nVizgen Incorporated\n\n\n\n\nScientific Committee\n\n\n\nMats Nilsson\, Chair and Platform Director Spatial Biology\, SciLifeLab/Stockholm UniversityCharlotte Stadler\, Platform Co-Director Spatial Biology\, SciLifeLab/KTHPer Andrén\, SciLifeLab/Uppsala UniversityStefania Giacomello\, SciLifeLab/KTH \n\n\n\nProject leader Operations Office: Erika Bergqvist Erkstam \n\n\n\n\n\nSS24-Flyer_2Download
URL:https://www.scilifelab.se/event/scilifelab-science-summit/
LOCATION:Uppsala Konsert & Kongress\, Vaksala torg 1\, Uppsala\, 75331\, Sweden
CATEGORIES:Event
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241007T120000
DTEND;TZID=Europe/Stockholm:20241008T150000
DTSTAMP:20260510T160739
CREATED:20240620T093344Z
LAST-MODIFIED:20241003T140306Z
UID:10001284-1728302400-1728399600@www.scilifelab.se
SUMMARY:DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases
DESCRIPTION:The DDLS research area Epidemiology and Biology of Infection invites you to its second in-person symposium. (The event is fully in-person only). The symposium will focus on promoting and enhancing data-driven environmental assessment for infectious diseases (including antibiotic-resistant bacteria) across various settings using diverse approaches. \n\n\n\nThe symposium will feature both local and international high-profile speakers in the field and will cover topics ranging from sewage surveillance\, monitoring of airborne infectious agents\, as well as environmental and animal disease monitoring for pathogens\, antimicrobial resistance and harmful substances. The symposium will also include more technical aspects of implementations as well as data-driven advancements and challenges. \n\n\n\nThere will also be a possibility to submit abstracts for short talks! \n\n\n\nPlease join us for this one-and-a-half-day symposium on 7-8 October 2024\, in Navet\, SciLifeLab’s meeting place in Uppsala\, to meet the research area Fellows\, the Expert Group and excellent researchers of the area. Engage in discussions\, enjoy refreshments\, and network with experts across a range of infectious disease monitoring topics! \n\n\n\nWelcome! \n\n\n\nScientific committeeAnna Székely (SLU)Johan Bengtsson-Palme (Chalmers) \n\n\n\nRegistration\n\n\n\nDeadline for abstract submission: 23 September (Extended deadline)Deadline to register to attend: 25 September \n\n\n\nIf seats are available and you register after September 25\, we can not accommodate allergies or special requirements and you will write your name tag upon arrival to the venue.. \n\n\n\nRegistration\n\n\n\n\n\n\n\nProgram\n\n\n\nDDLS symposium EBI_PROGRAM_3Download\n\n\n\n\n\n\n\n\n\nMembers of The Data-driven Epidemiology and biology of infection expert group:\n\n\n\nTom Britton\, Stockholm UniversityJoakim Dillner\, Karolinska Institutet and Karolinska Univ. HospitalTove Fall\, Uppsala UniversityBirgitta Henriques-Normark\, Karolinska InstitutetErik Kristiansson\, Chalmers University of TechnologyPatrik Medstrand\, Lund UniversityStaffan Svärd\, Uppsala UniversityOliver Billker\, chair (DDLS SG member)
URL:https://www.scilifelab.se/event/ddls-symposium-on-data-driven-environmental-monitoring-of-infectious-diseases/
LOCATION:BMC Trippelrummet\, Husargatan 3\, entrance C11\, Uppsala\, Sweden
CATEGORIES:Event
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DTSTART;TZID=Europe/Stockholm:20241009T090000
DTEND;TZID=Europe/Stockholm:20241011T163000
DTSTAMP:20260510T160739
CREATED:20240909T104734Z
LAST-MODIFIED:20240910T082733Z
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SUMMARY:Data-Driven Life Sciences Hackathon
DESCRIPTION:Join us at the DDLS Hackathon in person at SciLifeLab in Solna\, where participants will choose and collaborate on a range of provided projects. With the support of teaching assistants in a hands-on environment\, groups will innovate and develop solutions in the dynamic field of data-driven life science. \n\n\n\nDuring the three day hackathon\, participants will select a dataset and apply the skills and knowledge gained during the course (see link above for each module) to create AI models\, analyze the data\, and produce meaningful insights. At the end of the hackathon\, teams will present their achievements. \n\n\n\nEveryone affiliated with the DDLS programme or interested in data-driven life science is welcome to join–from PIs\, PhD students\, postdocs\, and facility experts/trainers. Participants will form pairs or small groups of 2-3 people on-site to work on projects\, exchange ideas and experiences\, and engage in pair programming. This collaborative environment will foster innovation and provide a unique opportunity to apply the concepts learned throughout the course to real-world problems in data-driven life sciences.  \n\n\n\nWhat will you gain attending the hackathon?If you are to be selected to participate you will get the opportunity not only to work hands-on on a data-driven life science project\, but also to network with experts within the field of data-driven life science\, researchers and research infrastructure experts \n\n\n\nRegistration deadline:Monday\, September 30th\, 2024 \n\n\n\n \n\n\n\nRegistration\n\n\n\nThis hackathon is part of the 2024 DDLS course and will gather data-driven life science researchers (MSc students\, PhD students\, post-docs\, staff-scientists\, experts and group leaders). \n\n\n\n \n\n\n\nFor questions\, contact Wei Ouyang at weio@kth.se or traininghub@scilifelab.se
URL:https://www.scilifelab.se/event/data-driven-life-sciences-hackathon/
LOCATION:Gamma 7 Lunchroom\, Tomtebodavägen 23A\, Solna\, 17121
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T100000
DTEND;TZID=Europe/Stockholm:20241015T110000
DTSTAMP:20260510T160739
CREATED:20240919T131404Z
LAST-MODIFIED:20251204T144057Z
UID:10001362-1728986400-1728990000@www.scilifelab.se
SUMMARY:Research involving human data - what do I need to think of as a researcher?
DESCRIPTION:This seminar will focus on collecting and using personal data in research. We will guide you through the different phases of a typical research project and discuss some commonly asked questions. We will\, for example\, talk about GDPR\, and secure management and sharing of sensitive data\, among others. \n\n\n\nWhen: Tuesday October 15\, 10-11 CET (Zoom) \n\n\n\nSpeaker: Markus Englund and Erik Hedman\, Data Steward\, NBIS \n\n\n\nSciLifeLab Data Management seminar series is an event series by the SciLifeLab Data Centre and NBIS joint Data Management team aimed at both the life science research community and infrastructure\, and others with an interest in research data management in life sciences. The events will showcase how to put the FAIR principles\, and good data management into practice. The goal of the events in this seminar series is to provide interesting seminars around topics related to research data management in general but also to foster discussions around best practices and how they can be improved. The events takes place virtually (over Zoom) and are open to everyone\, (researchers\, staff\, RDM professionals etc.) working at or affiliated with a Swedish research institute or university. Each event is scheduled for 60 minutes\, including 15 minutes for discussions and Q & A. The videos (excluding Q&A) will be published openly after the seminars at the SciLifeLab YouTube channel.More information about SciLifeLab Data Centre and NBIS joint Data Management team: https://data-guidelines.scilifelab.se/ \n\n\n\nWelcome! \n\n\n\nOrganisers: SciLifeLab Data Centre and NBIS National Bioinformatics Infrastructure SwedenFor more information or inquiries please contact: data-management@scilifelab.se
URL:https://www.scilifelab.se/event/research-involving-human-data-what-do-i-need-to-think-of-as-a-researcher/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/02/DC_seminar-series_background1-1.png
ORGANIZER;CN="Open Science Seminar Series":MAILTO:data-management@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241017T090000
DTEND;TZID=Europe/Stockholm:20241017T170000
DTSTAMP:20260510T160739
CREATED:20240314T102017Z
LAST-MODIFIED:20241011T115004Z
UID:10001207-1729155600-1729184400@www.scilifelab.se
SUMMARY:SciLifeLab Uppsala Site Day
DESCRIPTION:The SciLifeLab site in Uppsala welcomes you to a full day of vibrant and inspiring science. During this event\, SciLifeLab Uppsala will highlight the research and infrastructure located in Uppsala. \n\n\n\nExperience the wide variety of research infrastructures at SciLifeLab Uppsala. Listen to talks from SciLifeLab/DDLS fellows. Join the panel discussion with the nationwide capability programs in Planetary Biology\, Precision Medicine\, and Pandemic Laboratory Preparedness. Enjoy poster sessions and exhibitions from SciLifeLab facilities. \n\n\n\nThe SciLifeLab Uppsala Site Day aims to foster discussions and interaction among participants. The event will be held exclusively on-site in Sal X\, which has a seating capacity of 221 people\, and will be streamed to Sal IX\, which can accommodate 141 people. Since the seats are limited\, remember to cancel if you cannot attend. \n\n\n\nAll attendees are invited to enjoy fika\, lunch\, and mingling sessions. Please note that no Zoom link will be available. \n\n\n\nRegistration\n\n\n\nRegistration closes on October 14 at 09:00. \n\n\n\nRegistration\n\n\n\nIf you have questions\, please contact events@scilifelab.se \n\n\n\n\n\n\n\nProgram\n\n\n\nSciLifeLab Day Uppsala_Program_v4.0Download\n\n\n\n\n\n\n\nExhibition List\n\nU-Print\, 3D printing facility Paul O’Callaghan\n\n\n\nDanioReadout Beata Filipek-Gorniok\n\n\n\nNMR-UppsalaRuisheng Xiong\n\n\n\nMicrofluidicsMaria Tenje\n\n\n\nAffinity Proteomics UppsalaMikael Åberg\n\n\n\nGenomics PlatformSusanne Hellstedt Kerje\n\n\n\nBioImage Informatics Anna KlemmBioinformatics (NBIS/ELEXIR-SE)\,Bengt Persson\n\n\n\nChemical Biology Consortium Sweden Uppsala Jordi Carreras Puigvert\n\n\n\nClinical Genomics UppsalaMalin Melin\n\n\n\nDrug Discovery and Development Platform Rebecka Klintenberg\n\n\n\nSpatial Mass SpectrometryAnna Nilsson\n\n\n\nUppsala International HubCharlotte Walker\n\n\n\nTesta CenterAlexandra Patriksson\n\n\n\nSciLifeLab CapabilitiesPrecision Medicine Capability\, Eva Berglund. Pandemic Laboratory Preparedness Capability\, Alice Sollazzo. Planetary Biology Capability\, Anabella Aguilera\n\n\n\nEATRIS Ulrika BäckmanInnovation coaching Kerstin Ekelöf\, UU Innovation\, Liza Nilsson\, UU Innovation\n\n\n\nUppsala Clinical Research Center (UCR)\, Maria Sörby\n\n\n\nSciLifeLab Data Centre and Data Science Node in Evolution and Biodiversity\, Angela Fuentes Pardo\n\n\n\nSciLifeLab\, Training Hub\, Data-driven Life Science Program (DDLS) supported by KAW and SciLifeLab\, Hampus Pehrsson Ternström\n\n\n\n\n\nPosters and Flash Talks\nWe have reserved space for selected SciLifeLab/DDLS fellow PhD students\, eSSENCE PhD students to bring a scientific poster. Four submitted abstracts have been selected for a 5-minute Flash Talk. The selected Flash Talks are highlighted. \n\n\n\nInstructions \n\n\n\nMount your poster during the Coffee & Registration at 08:30-09:00\, poster presentation during the lunch mingle. \n\n\n\nThe poster screens are portrait oriented\, 103×143 cm. \n\n\n\nPoster #Poster title and presenter1Investigating Islet Vasculature Alterations in Type I DiabetesCasian-Simon Aioanei – FLASH TALK2Optimal effect estimation in genome-wide association studies with censored biomarker measurements in large-scale biobanksYaqi Deng – FLASH TALK3Loss of chromogranin A and catestatin affect islet composition and neurotransmitters in the pancreasDali Epremidze – FLASH TALK4Chemoselective Primer Extension for Sequencing in Fixed and Living CellsChengxiang Yuan5Unraveling the Alzheimer’s Puzzle: The Role of ApoE4\, Mitochondria\, and Lipid Metabolism in neuronal settingSona Hakhverdyan6Adaptive Robust Learning using Latent Bernoulli VariablesAleksandr Karakulev7Deep Learning with Big Data for Genetic EpidemiologyMax Kovalenko8Strained Cyclooctynes with Photocages for Subcellular 3D Photolithographic BarcodingAlfred Larsson9The evolution of gene CNVs in C. rubellaFreja Lindstedt10Variational Approaches for Simulation-Based InferenceMayank Nautiyal11Deep Learning-driven Survival Prediction In Non-small Cell Lung Cancer Using Multiplex Immunofluorescent ImagingLove Nordling12Detection of protein-protein interactions by bio-orthogonal fluorogenic proximity probesAndreas Torell – FLASH TALK13Copy number variations and adaptation along environmental gradients in Picea abies and P. obovataQiujie Zhou\n\n\n\n\n \n\n\n\nOrganizers\n\n\n\n\nEva Tiensuu Janson\, chair SciLifeLab Uppsala committee\, Integration Director\n\n\n\nAristidis Moustakas\, SciLifeLab Uppsala committee\n\n\n\nMikael Widersten\, SciLifeLab Uppsala committee\n\n\n\nJenny Alfredsson\, SciLifeLab Uppsala committee\n\n\n\nAnna Dimberg\, SciLifeLab Uppsala committee\n\n\n\nTitti Ekegren\, project coordinator\, SciLifeLab Uppsala committee
URL:https://www.scilifelab.se/event/scilifelab-day-uppsala/
LOCATION:University Main Building\, Biskopsgatan 3\, Uppsala\, 75310
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/02/C13089-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241024T100000
DTEND;TZID=Europe/Stockholm:20241024T123000
DTSTAMP:20260510T160739
CREATED:20241002T123645Z
LAST-MODIFIED:20241004T071259Z
UID:10001367-1729764000-1729773000@www.scilifelab.se
SUMMARY:Discover services for data-driven life science
DESCRIPTION:Welcome to join SciLifeLab Data Centre and SciLifeLab Data Management for “Discover services for data-driven life science“-  an overview of data-driven services\, tools\, and support aimed at the fellows community. The event will also include a feedback session to help SciLifeLab Data Centre best support your specific research needs. Share your views about your current and future research needs\, e.g. state-of-the-art services that would further your research or the general research of your field\, currently not available on the SciLifeLab Data Platform. \n\n\n\nWhen: Oct 24\, 10-12.30 CET (Zoom)Target group: Scilifelab Fellows\, DDLS Fellows\, and interested participants \n\n\n\n \n\n\n\nAgenda \n\n\n\n10.00-10.10   Welcome   Johan Rung\, Head of SciLifeLab Data Centre \n\n\n\n10.10-10.35   Open Science 101 Chris Erdmann\, Head of Open Science \n\n\n\n10.35-11.00   SciLifeLab Data Management services and support Angela Fuertes-Pardo\, Data Steward\, SciLifeLab Data Centre \n\n\n\n11.00-11.05  Coffee break \n\n\n\n11.05-11.30   How to get access to Compute\, Storage\, and Hosting to support your research\, speaker TBA \n\n\n\n11.30-12.30   Feedback session: Share your needs for data-driven life science services and tools. Moderators: Johan Rung\, Head of SciLifeLab Data Centre\, and Niclas Jareborg\, NBIS \n\n\n\n \n\n\n\nFor additional information please contact SciLifeLab Data Centre at datacentre@scilifelab.se
URL:https://www.scilifelab.se/event/discover-services-for-data-driven-life-science-2/
CATEGORIES:Event
LOCATION:https://uu-se.zoom.us/j/63809262140
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241024T100000
DTEND;TZID=Europe/Stockholm:20241024T130000
DTSTAMP:20260510T160739
CREATED:20240917T130711Z
LAST-MODIFIED:20250107T132341Z
UID:10001353-1729764000-1729774800@www.scilifelab.se
SUMMARY:Lund: Building and sharing machine learning demo applications within life sciences
DESCRIPTION:This event is open to everyone at Lund University. It consists of a workshop followed by a free lunch for participants. During the lunch the participants will have an opportunity to informally chat with AI data engineers from the SciLifeLab Data Centre to discuss the needs for services and research infrastructure in life science research using machine learning methods. \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: October 24\, 2024 at 10:00-13:00 at room Rådslaget\, BMC Hus E (Sölvegatan 19\, 223 62 Lund) \n\n\n\nAgenda:10:00-12:00: Workshop12:00-13:00: Lunch \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 35 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nAfter the workshop all participants are invited for lunch. \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\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/ml-demo-applications-lund/
LOCATION:BMC Hus E\, room Rådslaget\, Sölvegatan 19\, Lund\, 223 62\, Sweden
CATEGORIES:Event
END:VEVENT
END:VCALENDAR