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DTSTART;TZID=Europe/Stockholm:20240926T120000
DTEND;TZID=Europe/Stockholm:20240926T130000
DTSTAMP:20260404T195131
CREATED:20240708T135748Z
LAST-MODIFIED:20240926T080910Z
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SUMMARY:Campus Solna Seminar Series: Qiuzhen Li & Luca Panconi
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nQiuzhen Li\n\n\n\nPatrick Bryant – alpha 2 \n\n\n\nDesign Peptide Binder Using Machine Learning \n\n\n\n\n\nLuca Panconi\n\n\n\nJuliette Grifflé – gamma 6 \n\n\n\nTowards computationally-optimised immunotherapy \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-qiuzhen-li-ines-cunha/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
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ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20240930T080000
DTEND;TZID=Europe/Stockholm:20241002T170000
DTSTAMP:20260404T195131
CREATED:20240521T064747Z
LAST-MODIFIED:20240521T064748Z
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SUMMARY:Metabolomics in Molecular Medicine - from idea to data interpretation
DESCRIPTION:A jointly organized workshop by the Swedish Metabolomics Centre (SMC) and FIMM’s Metabolomics Unit – University of Helsinki providing an introduction to different aspects of metabolomics\, from experimental design to data analysis. The programme consists of a public symposium on the first day and practical elements for workshop participants on days 2-3. Workshop participants are also expected to attend the symposium on the first day. \n\n\n\nRead more\n\n\n\nMetabolomics measures small molecules commonly known as metabolites that all together comprise a metabolome of a biological system. Since metabolome is a reflection of physiological status\, metabolomics helps us to understand molecular mechanisms such as drug responses and to find new indicators for diseases. \n\n\n\nThis workshop provides an introduction to mass spectrometry-based metabolomics with a special focus on its applications in molecular medicine. The workshop starts with a mini-symposium where the experts in the field discuss the recent advancements and applications in metabolomics research in life sciences. The following two days of practical training will cover the metabolomics workflow from the principles of experimental design\, sample preparation\, theory of chromatographic separation and mass spectrometry to data acquisition\, pre-processing\, analysis and interpretation. \n\n\n\nContact \n\n\n\nAnnika Johansson \n\n\n\nEmail \n\n\n\n+46 90 786 55 51
URL:https://www.scilifelab.se/event/metabolomics-in-molecular-medicine-from-idea-to-data-interpretation/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Event
ORGANIZER;CN="Swedish Metabolomics Centre (SMC)":MAILTO:annika.johansson01@umu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241001T080000
DTEND;TZID=Europe/Stockholm:20241003T170000
DTSTAMP:20260404T195131
CREATED:20240529T151443Z
LAST-MODIFIED:20240529T151527Z
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SUMMARY:Basic Course in Scanning and Transmission Electron Microscopy (SEM/TEM) for Life Sciences
DESCRIPTION:This course covers lectures and practical demonstrations in SEM and TEM techniques. The contents include principles of electron microscopy\, specimen preparation\, cryo-electron microscopy and correlative light-electron microscopy. The main focus will be on imaging biological samples\, but the course may also be suitable for material scientists interested in high-resolution electron microscopy. \n\n\n\nRead more\n\n\n\nApplication deadline:10 September 2024 \n\n\n\nLocation:Lectures at the KBC Building and laboratory demonstrations at UCEM. \n\n\n\nParticipants:18 persons \n\n\n\nInstructors:UCEM staff \n\n\n\nDuration:3 days \n\n\n\nBreaks/Refreshments:Coffee\, cookies and fruit. \n\n\n\nCosts:No course fee\, but full attendance is required! \n\n\n\nExamination/Credits:Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.
URL:https://www.scilifelab.se/event/basic-course-in-scanning-and-transmission-electron-microscopy-sem-tem-for-life-sciences/
LOCATION:KBC Building Umeå\, Linneaus Väg 6\, Umeå
CATEGORIES:Course
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ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241001T090000
DTEND;TZID=Europe/Stockholm:20241001T170000
DTSTAMP:20260404T195131
CREATED:20230927T131415Z
LAST-MODIFIED:20240930T075234Z
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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
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/09/Science-summit_urothelial-cancer-tumor.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241002T150000
DTEND;TZID=Europe/Stockholm:20241002T153000
DTSTAMP:20260404T195131
CREATED:20240919T115545Z
LAST-MODIFIED:20240919T115655Z
UID:10001355-1727881200-1727883000@www.scilifelab.se
SUMMARY:CSI Seminar: Imposter Syndrome
DESCRIPTION:Dear Everyone\, \n\n\n\nWe are excited to host a new Coaching in Science Initiative (CSI) Seminar titled: ‘Imposter Syndrome’ \n\n\n\nImposter Syndrome is a common yet often overlooked challenge in academia\, affecting scholars at every stage—from graduate students to senior faculty. Despite your accomplishments\, do you often feel like you don’t belong or fear being “exposed” as a fraud? In this seminar\, we will examine what imposter syndrome is\, when and why it manifests\, and reflect on the deeper psychological and social factors that contribute to it. We will also provide practical strategies and tools to help you cope with these feelings of self-doubt\, overcome perfectionism\, and reclaim your confidence. \n\n\n\nDate: 02/10/2024 \n\n\n\nTime: 15:00 – 15:30 \n\n\n\nZoom link: https://kth-se.zoom.us/j/65426414592 \n\n\n\nOn-site location: Gamma 2 lunch room \n\n\n\nWe will begin with a ~ 20 min talk\, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties\, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI. \n\n\n\nTo help facilitate discussion and reflection\, consider the following starter questions: \n\n\n\nAwareness: where do we experience imposter syndrome in our lives? \n\n\n\nAnalysis: how do I currently interact with imposter thinking? \n\n\n\nAlternative: how could we relate to imposter syndrome\, in ourselves and others? \n\n\n\nAction: how will knowledge of imposter thinking change my decisions going forward? \n\n\n\nPlease forward this to friends and colleagues! \n\n\n\nYours sincerely\, \n\n\n\nThe CSI Team \n\n\n\n  \n\n\n\nWays to keep in touch with CSI \n\n\n\n  \n\n\n\n\nVisit our webpage for coaching material\, access to older seminars\, links to external resources and our events: https://www.thecoachinginscienceinitiative.org/\n\n\n\nWe will also post our events in the SciLifeLab event calendar: https://www.scilifelab.se/event\n\n\n\nOur seminars has/will be recorded and can be watch and re-used as workshops to raise awareness on this YouTube channel\, the first CSI seminar is already there: https://www.youtube.com/@TheCoachinginScienceInitiative\n\n\n\nIf you have a scilifelab e-mail\, find our channel in the scilifelab.slack.com workspace #coaching-in-science-initiative\n\n\n\nReach our committee thought our e-mail: csi@scilifelab.se\n\n\n\n\n 
URL:https://www.scilifelab.se/event/csi-seminar-imposter-syndrome/
LOCATION:Hybrid event in Gamma 2 lunchroom and zoom\, Tomtebodavägen 23 B\, Solna\, 17165\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/09/CSI_logo_square.png
ORGANIZER;CN="Coaching in Science Initiative (CSI)":MAILTO:sami.saarenpaa@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241002T160000
DTEND;TZID=Europe/Stockholm:20241002T170000
DTSTAMP:20260404T195131
CREATED:20240829T094923Z
LAST-MODIFIED:20240829T095938Z
UID:10001341-1727884800-1727888400@www.scilifelab.se
SUMMARY:Deciphering the mysteries of sleep: toward the molecular substrate for “sleepiness”
DESCRIPTION:KVA-JSPS lecture about orexins. Prof. Masashi Yanagisawa\, MD\, PhD\, International Institute for Integrative Sleep Medicine\, University of Tsukuba\, Japan\, \n\n\n\nProfessor Masashi Yanagisawa\, the discoverer of both endothelin and orexin\, which are extremely important peptides for blood pressure and sleep regulation\, will give a lecture in Uppsala\, H:son Holmdahlsalen\, Entrance 100\, Akademiska sjukhuset. His lecture will focus on the regulation of sleep and wakefulness. The Lecture will follow after a short presentation of JSPS. \n\n\n\nThe lecture is possible thanks to a travel grant from Japan Society for the Promotion of Science (JSPS). \n\n\n\nHost: Professor Dan Larhammar\, Department of Medical Cell Biology\, SciLifeLab affiliated group leader\, Uppsala University. Please contact Prof. Larhammar if you wish to meet with Prof. Yanagisawa during his visit to Uppsala.  \n\n\n\nAbstract\n\n\n\nAlthough sleep is a ubiquitous behavior in animal species with a nervous system\, many aspects in the neurobiology of sleep remain mysterious. Our discovery of orexin\, a hypothalamic neuropeptide involved in the maintenance of wakefulness\, has triggered intensive research examining the exact role of the orexinergic and other neuronal pathways in the regulation of sleep/wakefulness. Orexin receptor antagonists\, which specifically block the endogenous waking system\, have been approved as a new strategy to treat insomnia. Also\, since the sleep disorder narcolepsy-cataplexy is caused by orexin deficiency\, orexin receptor agonists are expected to provide mechanistic therapy for the disease; they will likely be also useful for treating excessive sleepiness due to other etiologies. \n\n\n\nEven though the executive neurocircuitry and neurochemistry for sleep/wake switching\, including the orexinergic system\, has been increasingly revealed in recent years\, the mechanism for homeostatic regulation of sleep\, as well as the neural substrate for “sleepiness” (sleep pressure)\, remains unknown. To crack open this black box\, we have initiated a large-scale forward genetic screen of sleep/wake phenotype in mice based on true somnographic (EEG/EMG) measurements. We have so far screened >10\,000 heterozygous ENU-mutagenized founders and established several pedigrees exhibiting heritable and specific sleep/wake abnormalities. By combining linkage analysis and the next-generation whole exome sequencing\, we have molecularly identified and verified the causal mutation in several of these pedigrees. Since these dominant mutations cause strong phenotypic traits\, we expect that the mutated genes will provide new insights into the elusive pathway regulating sleep/wakefulness. Indeed\, through a systematic cross-comparison of the SIK3 Sleepy mutants and sleep-deprived mice\, we have found that the cumulative phosphorylation state of a specific set of mostly synaptic proteins may represent the molecular substrate of sleep pressure. We have also found that the neuronal molecular pathway LKB1-SIK3-HDAC4/5 may represent the level of sleep pressure\, regulating the amount\, depth\, and timing of sleep by acting in different brain regions\, respectively (Kim et al. Nature 612: 512-518\, 2022; Zhou et al. Nature 612: 519-527\, 2022). \n\n\n\nBio sketch\n\n\n\nProf. Yanagisawa received his PhD at the University of Tsukuba where he discovered the powerful vasoconstrictor peptide endothelin. His group later identified a receptor for endothelin which is now an important target for treatment of hypertension. After moving to Texas Southwestern Medical Center in Dallas he identified the endothelin-converting enzyme and later described the role of the endothelin pathway in embryonic development. \n\n\n\nHis project to deorphanize G protein-coupled receptors resulted in the discovery of the hypothalamic neuropeptide orexin in 1998. The year after\, he showed that the sleep disorder narcolepsy is caused by orexin deficiency. This knowledge has resulted in orexin receptor antagonists approved for treatment of insomnia. An ongoing project in Tsukuba has led to identification of several new genes and molecular pathways that are importantly involved in the regulation of sleep amounts and the level of sleep need. \n\n\n\nProf. Yanagisawa has receved numerous honours and awards\, most recently the Breakthrough Prize in Life Sciences. He was elected to the U.S. National Academy of Sciences in 2003. Since 2012 he is the director for the International Institute for Integrative Sleep Medicine at the University of Tsukuba. \n\n\n\n\n\n\n\nAnnouncement Yanagisawa 2401002Download
URL:https://www.scilifelab.se/event/deciphering-the-mysteries-of-sleep-toward-the-molecular-substrate-for-sleepiness/
LOCATION:H:son Holmdahlsalen\, Entrance 100\, Akademiska sjukhuset\, Dag Hammarskjölds väg 8\, Uppsala
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241003T120000
DTEND;TZID=Europe/Stockholm:20241003T130000
DTSTAMP:20260404T195131
CREATED:20240708T140029Z
LAST-MODIFIED:20240926T081101Z
UID:10001297-1727956800-1727960400@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Linnea Påvenius
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n \n\n\n\n\n\nLinnea Påvenius\n\n\n\nHjalmar Brismar – gamma 3 \n\n\n\nLive-Imaging of mitochondrial dynamics in relation to metabolic flux. \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-alberto-arenas-molina-linnea-pavenius/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/12/IMG_4110-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241007T120000
DTEND;TZID=Europe/Stockholm:20241008T150000
DTSTAMP:20260404T195131
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
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/EBI_Icon.png
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241007T151500
DTEND;TZID=Europe/Stockholm:20241007T161500
DTSTAMP:20260404T195131
CREATED:20240920T145358Z
LAST-MODIFIED:20240920T145400Z
UID:10001364-1728314100-1728317700@www.scilifelab.se
SUMMARY:[The Svedberg seminar] - Patch-seq profiling of pancreatic islet cell types and cell-free RNA diagnostics
DESCRIPTION:Joan Camuñas-SolerAssistant ProfessorUniversity of Gothenburg\, Sweden \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\nJoan Camuñas\n\n\n\n\n\n\n\nBio\n\n\n\nDr. Camuñas-Soler is an Assistant Professor and Wallenberg Molecular Medicine Fellow at the University of Gothenburg since 2022. His current research focuses on data-driven genomics and precision medicine. Previously\, as a postdoctoral scholar at Stanford University\, he pioneered novel single-cell genomic techniques to study islet-cell function in health and diabetes. Additionally\, he developed liquid biopsy tools for the early prediction of pregnancy complications\, which led to the creation of a molecular diagnostics startup. His research is highly interdisciplinary\, combining approaches from molecular engineering\, biophysics\, and computational biology. His work has been recognized with several awards\, patents\, and prestigious establishment grants. \n\n\n\n \n\n\n\nPatch-seq profiling of pancreatic islet cell types and cell-free RNA diagnostics \n\n\n\nMethods to simultaneously profile transcriptome and cell function at the single-cell level are scarce. In this talk\, I will show that single-cell RNA sequencing (scRNAseq)\, in combination with electrophysiological measurements of exocytosis (patch-seq)\, can be used to study the connection between human endocrine physiology and transcriptomes at the single cell level. I will discuss the application of patch-seq to investigate normal physiology of pancreatic islet cells and their dysfunction in diabetes. \n\n\n\nUsing data from 1\,369 patch-seq cells from the pancreata of 34 human donors; I will show how this technology can be used to identify novel regulators of β-cell biology and transcriptomic alterations indicative of β-cell maladaptation and α-cell dysfunction in type 2 diabetes (T2D). Additionally\, I will introduce a complementary approach to measure the secretory capacity of these cells based in the use of fluorescent tracers of endocytic membrane retrieval\, which can then be combined with FACS sorting ad scRNAseq to characterize β-cell states associated with higher secretory capacity. \n\n\n\nIn the second part of this talk\, I will also discuss how sequencing of circulating RNA in the blood (cell-free RNA) can be used as a ‘liquid biopsy’ tool to monitor human physiology and disease. I will focus on the use of cell-free RNA to establish a molecular clock of pregnancy\, and as a tool to track autoimmune disorders with poorly understood pathophysiology. Some of this molecular diagnostics work is currently being translated into clinical validation. \n\n\n\nRead more: Camuñas-Soler Group   \n\n\n\n \n\n\n\n \n\n\n\n\n\n\n\nHost: Jessica Nordlund jessica.nordlund@medsci.uu.se
URL:https://www.scilifelab.se/event/the-svedberg-seminar-joan-camunas-soler/
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
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241008T090000
DTEND;TZID=Europe/Stockholm:20241008T163000
DTSTAMP:20260404T195131
CREATED:20240523T131511Z
LAST-MODIFIED:20240913T130839Z
UID:10001265-1728378000-1728405000@www.scilifelab.se
SUMMARY:Stockholm Single Cell Genomics 2024 Symposium
DESCRIPTION:The National Genomics Infrastructure is pleased to announce the Stockholm Single Cell Genomics 2024 Symposium\, taking place on October 8th this fall. Join us for a day of engaging talks by experts in the field\, a chance to explore the latest technologies\, and networking opportunities. \n\n\n\nregister here\n\n\n\nConfirmed speakers:  \n\n\n\n\nGonçalo Castelo-Branco\, KI\, \n\n\n\nJessica Nordlund\, UU\, \n\n\n\nRickard Sandberg\, KI\, \n\n\n\nJoan Camuñas-Soler\, GU\, \n\n\n\nMartin Enge\, KI\, \n\n\n\nKasper Karlsson\, KI\, \n\n\n\nMohanraj Ramachandran\, UU\, \n\n\n\nTuuli Lappalainen\, KTH and \n\n\n\nAlexander Steemers\, Princess Maxima Center.\n\n\n\n\nSponsors: Scale Biosciences\, Pixelgen Technologies\, BioSkryb\, Techtum\, Parse Biosciences\, 10X Genomics\, Illumina\, Oxford Nanopore Technologies and BD Biosciences. \n\n\n\nCheck here to see any updates! 
URL:https://www.scilifelab.se/event/stockholm-single-cell-genomics-2024-symposium/
LOCATION:IVA Conference center\, Grev Turegatan 16\, Stockholm
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241009T090000
DTEND;TZID=Europe/Stockholm:20241011T163000
DTSTAMP:20260404T195131
CREATED:20240909T104734Z
LAST-MODIFIED:20240910T082733Z
UID:10001350-1728464400-1728664200@www.scilifelab.se
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:20241010T120000
DTEND;TZID=Europe/Stockholm:20241010T130000
DTSTAMP:20260404T195131
CREATED:20240708T140138Z
LAST-MODIFIED:20241001T092646Z
UID:10001298-1728561600-1728565200@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Daniela Huhn & Mariya Mardamshina
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nDaniela Huhn\n\n\n\nOscar Fernandez-Capetillo – alpha 4 \n\n\n\nOne-Two punch approach for improved treatment of ERa+ Breast Cancer \n\n\n\n\n\nMariya Mardamshina\n\n\n\nEmma Lundberg – alpha 2 \n\n\n\nExpanding the limits: Measuring more proteins beyond current multiplexed imaging capabilities \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-daniela-huhn-varun-kumar-rajendran/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_124630107_HDR-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241011T100000
DTEND;TZID=Europe/Stockholm:20241011T160000
DTSTAMP:20260404T195131
CREATED:20240918T071315Z
LAST-MODIFIED:20240920T060502Z
UID:10001357-1728640800-1728662400@www.scilifelab.se
SUMMARY:Microsampling- New Avenues for Metabolomics in Precision Health
DESCRIPTION:The Metrabolomics Platform arranges a one day seminar on “Microsampling- New Avenues for Metabolomics in Precision Health” together with the Nordic Metabolomics Society.  \n\n\n\n\n\n\n\nProgram\n\n\n\n10.00Welcome\,Rikard Landberg (SciLifeLab& Chalmers) & Alex Dickens (Nordic Metabolomics Society10.10Microsampling in Metabolomics- Enabler of Precision Health?Timothy Garrett (University of Florida)10.40High-throughput NMR-based metabolmics on microsamplesPeter Würtz (Nightingale)11.10New microsampling techniquesNiclas Roxhed (KTH)11.30Evaluation of microsampling techniques for lipidomics and exposomicsTuulia Hyötyläinen (Örebro University)11.50Metabolomics and microsampling across labsAlex Dickens (University of Turku)12.10SciLife-platform microsampling project and the SCAPIS2-HOME studyRikard Landberg (Scilifelab & Chalmers)12.30Lunch13.30Microsampling devices for nontarget chemical exposomicsSolveigh Thiele (SciLifeLab & Stockholm University)13.50Microsampling in high-through proteomicsClaudia Fredolini (Scilifelab)14.10Pitches of available microsampling techniquesProducers/vendors of microsampling devices15.00Discussion focused on the way forward15.45Concluding remarks and the way forwardRikard Landberg (SciLifeLab& Chalmers\n\n\n\nRegistration\n\n\n\nHow to get there\n\n\n\nBusLine 3\, 6\, 77\, 507 from S:t Eriksplan. Get off at Karolinska Institutet\, Biomedicum.Line 53 and 72 från Odenplan. Get off at Karolinska Institutet west which is next to Berzeliuslaboratory.  \n\n\n\nSubwayNearest station is S:t Eriksplan (exit Torsgatan)\, from where it takes 15-20 min walking to the Berzelius laboratory Odenplan – take bus 53 och 72. \n\n\n\nCarIf you arrive by car\,  parkeringshuset Skruven is the closest partking to the Berzeliuslaboratory https://www.aimopark.se/stader/solna/campus-solna/ \n\n\n\nPlease note that the Main Entrance to Campus Solna is currently closed due to the construction of a new subway station. There are several options to enter the campus from Solnavägen for those who walk or cycle. For those coming by car\, you must come via Tomtebodavägen\, where the nearest parking garage in connection with the conference is also located. \n\n\n\n\n\n\n\n\n\n\n\n\n\nContact: Rikard Landberg rikard.landberg@chalmers.se
URL:https://www.scilifelab.se/event/microsampling-new-avenues-for-metabolomics-in-precision-health/
LOCATION:Andreas Vesalius Lecture Hall\, Karolinska Institutet\, Berzelius väg 3\, Solna\, 171 65\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/09/21A6061_frikopt-scaled.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241014T080000
DTEND;TZID=Europe/Stockholm:20241025T170000
DTSTAMP:20260404T195131
CREATED:20240617T081347Z
LAST-MODIFIED:20240617T081528Z
UID:10001279-1728892800-1729875600@www.scilifelab.se
SUMMARY:New Super-Resolution\, Light-Sheet\, and FCS-Methods at Scilifelab
DESCRIPTION:The Advanced Light Microscopy Facility\, ALM\, at Scilifelab gives a two-week PhD-level course on four new imaging and fluorescence spectroscopy techniques: \n\n\n\nDepletion-based Super-Resolution Imaging \n\n\n\n\nSTED-imaging\, 2D and 3D\, 30-50 nm resolution\n\n\n\nIn Living Cells – MoNaLISA\, 1-2 Hz\, 100 x 100 mm field of view\n\n\n\n\nMINFLUX \n\n\n\n\nImaging with 3 nm resolution\n\n\n\nTracking single molecules at 10 kHz\n\n\n\n\nLight-Sheet Imaging \n\n\n\n\nLong time-lapse imaging of live model organisms with low phototoxicity\n\n\n\nUltrafast volumetric imaging of cells with lattice light-sheet microscopy\n\n\n\n\nFCS-Methods \n\n\n\n\nMeasurements of concentrations\, diffusion coefficients\, molecular dynamics and interactions\, in solution or living cells\n\n\n\nCross-correlation\, FRET-\, STED-\, and line-scan-FCS are covered\n\n\n\n\nLecturers: \n\n\n\nSteven Edwards \n\n\n\nErdinc Sezgin \n\n\n\nAna Agostinho \n\n\n\nFrancesca Pennacchietti \n\n\n\nHans Blom \n\n\n\nStefan Wennmalm \n\n\n\nDates: Monday October 14th – Friday October 25th 2024 \n\n\n\nCredits: 3 hp for PhD students \n\n\n\nLocation: Gamma 3\, Scilifelab\, Solna \n\n\n\nRegistration: stewen@kth.se latest September 30th
URL:https://www.scilifelab.se/event/new-super-resolution-light-sheet-and-fcs-methods-at-scilifelab/
LOCATION:Gamma 3\, Tomtebodavägen 23 A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241014T090000
DTEND;TZID=Europe/Stockholm:20241018T170000
DTSTAMP:20260404T195131
CREATED:20240326T120939Z
LAST-MODIFIED:20240403T083011Z
UID:10001215-1728896400-1729270800@www.scilifelab.se
SUMMARY:Omics Integration and Systems Biology
DESCRIPTION:National course open for PhD students\, postdocs\, researchers\, and other employees in all Swedish universities\, in need of a general description of different approaches for working with multiple types of biological data. We also welcome applications from outside of Sweden and from the non-academic sector\, for more info contact us! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2024-08-05 \n\n\n\nApplication closes: 2024-09-16 \n\n\n\nConfirmation to accepted students: 2024-09-23 \n\n\n\nCourse Leader and teachers: \n\n\n\nNikolay Oskolkov (Lund University\, course leader) \n\n\n\nRasool Saghaleyni (Chalmers University of Technology\, course leader) \n\n\n\nSergiu Netotea (Chalmers University of Technology\, course lecturer) \n\n\n\nJennifer Fransson (Uppsala University\, course lecturer) \n\n\n\nYuan Li (Lund University\, TA) \n\n\n\nNima Rafati (Uppsala University\, TA) \n\n\n\nIn case you miss information on any of the above dates\, please contact: \n\n\n\nNikolay Oskolkov\, nikolay.oskolkov@scilifelab.se \n\n\n\nRasool Saghaleyni\, rasools@chalmers.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK for academic participants and 15 000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes all coffee breaks\, all lunches and 1 course dinner. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an integrated view of data-driven analysis of biological data through machine learning\, graph and network analysis as well as constraint-based modeling integration methods. A general description of different approaches for working with multiple layers of biological information\, i.e. Omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing their advantages and pitfalls. The techniques will be discussed in terms of their rationale and applicability. \n\n\n\nTopics covered will include: \n\n\n\n\nData pre-processing\, cleaning and feature selection prior to integration;\n\n\n\nApplication of key machine learning methods for multi-omics analysis including deep learning;\n\n\n\nMulti-omics factor analysis\, dimension reduction and clustering;\n\n\n\nSingle Cell and Spatial transcriptomics integration;\n\n\n\nBiological network inference\, community and topology analysis and visualization;\n\n\n\nCondition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic\, proteomic\, metabolomic and fluxomic data;\n\n\n\nIdentification of key biological functions and pathways;\n\n\n\nIdentification of potential biomarkers and targetable genes through modeling and biological network analysis;\n\n\n\nApplication of network approaches in meta-analyses;\n\n\n\nSimilarity network fusion and matrix factorization techniques;\n\n\n\nIntegrated data visualization techniques\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\nIdentify key methods for analysis and integration of omics data based on a given dataset;\n\n\n\nPerform  feature selection and dimension reduction techniques; \n\n\n\nUnderstand strengths and pitfalls of key machine learning techniques in multi-omic analysis;\n\n\n\nApply unsupervised and supervised machine learning data integration techniques;\n\n\n\nBuild biological networks based on different omics data including integrated multi-omics networks;\n\n\n\nPerform centrality and community analyses in graphs;\n\n\n\nApply network approaches in meta-analyses;\n\n\n\nApply similarity network fusion of patient data;\n\n\n\nCompare different cell-types or conditions through the application of different biological network analysis techniques;\n\n\n\nSimulate biological functions using constraint-based models and flux balance analysis;\n\n\n\nIdentify potential confounding factors and sources of bias.\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 understanding of frequentist statistics;\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with NGS and omics analysis\n\n\n\nCompleting “Introduction to bioinformatics using NGS data” and “Introduction to biostatistics and machine learning” NBIS courses\n\n\n\n\n\n\n\n\nDue to limited space the course can accommodate a maximum of 35 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/omics-integration-and-systems-biology/
LOCATION:Lund University\, Lund\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T100000
DTEND;TZID=Europe/Stockholm:20241015T110000
DTSTAMP:20260404T195131
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:20241015T100000
DTEND;TZID=Europe/Stockholm:20241015T111500
DTSTAMP:20260404T195131
CREATED:20240902T120825Z
LAST-MODIFIED:20240902T120852Z
UID:10001345-1728986400-1728990900@www.scilifelab.se
SUMMARY:Deriving actionable insight from omics data – an industry perspective
DESCRIPTION:Speaker: Daniel Muthas\, Head of Data Science & Bioinformatics at AstraZeneca \n\n\n\nAbstract \n\n\n\nThis talk will focus on how advancement in omic analysis is enabling the realisation of precision medicine in chronic complex diseases. Large\, well phenotyped cohorts highlights the heterogeneity of disease and through single cell technologies we are able to study disease processes at unprecedented granularity\, but how do we take these insights into actionable and deployable applications? Here I will focus on how we employ a breadth of bioinformatic techniques of different modalities to bridge between populations\, patients\, and cellular level to identify novel targets\, biomarkers and patient populations. \n\n\n\nBackground \n\n\n\nDaniel’s team is working with applied bioinformatics across the whole drug discovery and development pipeline\, from target identification to indication expansion and exploratory biomarker analysis in clinical trials.   \n\n\n\nHost: Rasool Saghaleyni\, NBIS Chalmers University\, Gothenburg (rasool.saghaleyni@scilifelab.se) \n\n\n\nDate: October 15\, 10:00 – 11:15 CET online on zoom \n\n\n\nBroadcast link (live event): link\, pass: spd996 The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.
URL:https://www.scilifelab.se/event/deriving-actionable-insight-from-omics-data-an-industry-perspective/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241015T110000
DTEND;TZID=Europe/Stockholm:20241015T120000
DTSTAMP:20260404T195131
CREATED:20240919T090941Z
LAST-MODIFIED:20240926T111646Z
UID:10001359-1728990000-1728993600@www.scilifelab.se
SUMMARY:Trade secrets for Academic Startups\, Pharma and Biotech Companies in the Life Sciences
DESCRIPTION:Welcome to this Drug Discovery Webinar\, organized by OligoNova and SciLifeLab Drug Discovery and Development\, to learn more about how academic and biotech interventions can be protected with the goal to benefit patients. \n\n\n\nThis webinar is an introduction to trade secrets as a form of intellectual property\, with a focus on its potential importance to a life sciences start up.   \n\n\n\nTrade secrets are often an overlooked form of intellectual property\, thought by many to be of little relevance in the life sciences.  However\, as part of a well-developed IP strategy\, trade secrets have an increasingly important role to play\, with the potential to not only supplement a patent-based strategy but\, in some cases\, to provide a more suitable alternative. \n\n\n\nIn this seminar\, we will discuss how trade secrets can be identified\, protected\, and used to increase value and support investment. \n\n\n\nregistration\n\n\n\nAgenda \n\n\n\n\nIntroduction – Fredrik Wångsell\, OligoNova\n\n\n\nTrade secrets in the Life Sciences – Fiona Hey\, Tony Proctor and Michel\, Pears Potter Clarkson\n\n\n\nQ&A and discussion\n\n\n\n\nWelcome \n\n\n\nSciLifeLab DDD and OligoNova \n\n\n\nOther Seminars\n\n\n\nOligaNova organizes three seminars during the fall 2024 \n\n\n\nTrade secrets in the Life Sciences\, October 15 \n\n\n\nMaximizing exclusivity in the Life Sciences\, November 6 \n\n\n\nIP Strategies in the Life Sciences\, December 18
URL:https://www.scilifelab.se/event/trade-secrets-in-the-life-sciences/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="OligoNova - Part of the Drug Discovery and Development Platform":MAILTO:par.matsson@oligonova.org
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241017T090000
DTEND;TZID=Europe/Stockholm:20241017T170000
DTSTAMP:20260404T195131
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:20241017T120000
DTEND;TZID=Europe/Stockholm:20241017T130000
DTSTAMP:20260404T195131
CREATED:20240708T140852Z
LAST-MODIFIED:20241007T074153Z
UID:10001299-1729166400-1729170000@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Quentin Verron & Annika Bendes
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nQuentin Verron\n\n\n\nMagda Bienko – alpha 4 \n\n\n\nExploring the Role of Trans-Interacting Intronic RNAs in Neuronal Genome Organization \n\n\n\n\n\nAnnika Bendes\n\n\n\nJochen Schwenk – alpha 2 \n\n\n\nInsights from highly frequent microsampling of the circulating proteome — A study of virus induced diabetes in mice \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-quentin-verron-josefin-kenrick/
LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_120135408_HDR-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241017T130000
DTEND;TZID=Europe/Stockholm:20241017T141500
DTSTAMP:20260404T195131
CREATED:20240909T141724Z
LAST-MODIFIED:20240913T114033Z
UID:10001352-1729170000-1729174500@www.scilifelab.se
SUMMARY:Generation of context-specific genome-scale metabolic models using single-cell RNA-Seq data
DESCRIPTION:Johan Gustafsson\, Postdoc researcher\, Broad Institute\, USA \n\n\n\nAbstract \n\n\n\nThe metabolic networks in cells vary across tissues and cell types\, and to accurately model the metabolism of cells\, the full generic metabolic network defined in the genome needs to be reduced to a context-specific network representing the network expressed specifically in the cells of interest. Single-cell RNA-Seq promises to provide the information needed for such a reduction\, but noise in the form of data sparsity is a challenge. Here\, we present methods to handle data sparsity and estimate the uncertainty of modeling results. \n\n\n\nBiography \n\n\n\nJohan is an expert in modeling cancer metabolism and analyzing single-cell RNA/DNA sequencing data\, aiming to uncover vulnerabilities in cancer. With a background in both computer science and biochemistry\, Johan has completed a PhD in metabolic modeling at Chalmers University of Technology and now works as a postdoc in the Getz lab at the Broad Institute\, focusing on CLL/Richter’s syndrome and hypoxia in solid tumors. \n\n\n\nHost: Rasool Saghaleyni\, NBIS Chalmers University\, Gothenburg (rasool.saghaleyni@scilifelab.se) \n\n\n\nDate: October 17\, 13:00 – 14:15 CET online on zoom \n\n\n\nBroadcast link (live event): link\, pass:spd996The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.
URL:https://www.scilifelab.se/event/oimcs-integration-and-systems-biology/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241018T100000
DTEND;TZID=Europe/Stockholm:20241018T110000
DTSTAMP:20260404T195131
CREATED:20240815T085623Z
LAST-MODIFIED:20241014T143808Z
UID:10001324-1729245600-1729249200@www.scilifelab.se
SUMMARY:Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
DESCRIPTION:Accurate assessment of progression and disease course in multiple sclerosis (MS) is vital for timely and appropriate clinical intervention. The transition from relapsing-remitting MS (RRMS) to secondary progressive MS (SPMS) is gradual and diagnosed retrospectively with a typical delay of three years. To address this diagnostic delay\, we developed a predictive model that is able to distinguish between RRMS and SPMS with high accuracy\, trained on data from electronic health records collected at routine hospital visits obtained from the Swedish MS Registry containing 22\,748 patients with 197\,227 hospital visits. To be useful within a clinical setting\, we applied conformal prediction to deliver valid measures of uncertainty in predictions at the level of the individual patient. We showed that the model was theoretically and empirically valid\, having the highest efficiency at a 92% confidence level\, and demonstrated on an external test set that it enables effective prediction of the clinical course of a patient with individual confidence measures. We applied the model to a set of patients who transitioned from RRMS to SPMS during the cohort timeframe and showed that we can accurately predict when patients transition from RRMS to SPMS. We also identified new patients who\, with high probability\, are in the transition phase from RRMS to SPMS but have not yet received a clinical diagnosis. We conclude that our methodology can assist in monitoring MS disease progression and proactively identify patients undergoing transition to SPMS. An anonymized\, publically accessible version of the model is available at https://msp-tracker.serve.scilifelab.se/. \n\n\n\n \n\n\n\nA preprint is available here: https://www.medrxiv.org/content/10.1101/2024.03.01.24303566v1  \n\n\n\nKim Kultima\, Uppsala University \n\n\n\nNBIS 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 approx. 45 min long presentation and 15 min discussion. 
URL:https://www.scilifelab.se/event/conformal-predictors-for-multiple-sclerosis/
LOCATION:Online event via Zoom
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241021T090000
DTEND;TZID=Europe/Stockholm:20241023T170000
DTSTAMP:20260404T195131
CREATED:20240327T140400Z
LAST-MODIFIED:20240327T140521Z
UID:10001220-1729501200-1729702800@www.scilifelab.se
SUMMARY:Long-Read Sequencing Uppsala Meeting 2024
DESCRIPTION:In recent years\, long-read DNA sequencing has replaced short-read technologies as the gold standard solution for a wide range of genomics applications. In addition to producing high-quality de novo genome assembly\, long-read technologies can be used to study complex structural variation\, full-length RNA isoforms\, detection of epigenetic signals\, and much more. The adaptation of long-read sequencing is sweeping through several areas of the life sciences\, including agricultural\, environmental\, and medical research. \n\n\n\nJoin us in Uppsala for a three-day international event to catch up with the latest developments in long-read sequencing technologies and their applications\, get inspired by peers presenting their research\, and enjoy discussions with leading experts and company representatives. \n\n\n\n\n\n\n\nRead more\n\n\n\n\n\n\n\nRegistration
URL:https://www.scilifelab.se/event/long-read-sequencing-uppsala-meeting-2024/
LOCATION:Universitetsaulan\, Biskopsgatan 3\, Uppsala\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2024/02/C13089-scaled.jpg
ORGANIZER;CN="National Genomics Infrastructure (NGI)":MAILTO:support@ngisweden.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241022T090000
DTEND;TZID=Europe/Stockholm:20241024T150000
DTSTAMP:20260404T195131
CREATED:20241004T140950Z
LAST-MODIFIED:20241014T105959Z
UID:10001368-1729587600-1729782000@www.scilifelab.se
SUMMARY:Exhibition in Navet at BMC
DESCRIPTION:On October 22-24\, between 09.00-15.00\, you have a new opportunity to visit our exhibition in Navet at BMC. This is a chance to receive information and updates from 30 of the leading life science companies in Sweden. The entrance to Navet will be open between 09:00-15:00 for external visitors.
URL:https://www.scilifelab.se/event/exhibition-in-navet-at-bmc-4/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2024/10/exhibition-in-Navet.png
ORGANIZER;CN="SciLifeLab Navet":MAILTO:lokalbokning@scilifelab.uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241022T151500
DTEND;TZID=Europe/Stockholm:20241022T160000
DTSTAMP:20260404T195131
CREATED:20241009T105214Z
LAST-MODIFIED:20241020T201426Z
UID:10001369-1729610100-1729612800@www.scilifelab.se
SUMMARY:Drips and SliPS and Retirees\, Oh My!
DESCRIPTION:Speaker: Jonathan Wilson Yewdell\n\n\n\nChief\, Cellular Biology Section Laboratory of Viral DiseasesNational Institute of Allergy and Infectious Diseases (NIAID)National Institute of Health (NIH)Bethesda\, MD\, USA \n\n\n\nBiography: \n\n\n\nJon Yewdell graduated from Princeton University in 1975 with an AB in biochemistry and received MD and immunology PhD degrees from the University of Pennsylvania in 1981.  After a post-doctoral fellowship at Imperial College in London with David Lane\, he spent 4 years as an Assistant Professor at the Wistar Institute in Philadelphia.  In 1987 he joined NIAID.  His lab uses influenza A\, SARS-CoV2\, vaccinia and other viruses to explore basic elements of cell biology\, virology\, and immunology\, and has contributed to understanding how peptides are generated for CD8+ T cell immunosurveillance. \n\n\n\n\nTitle: Drips and SliPS and Retirees\, Oh My! \n\n\n\n\nAbstract for the talk: \n\n\n\nMHC class I molecules present short peptides derived from biosynthesized proteins\, enabling CD8+ T cell immunosurveillance of tumors\, viruses and intracellular microbes.  Many cellular peptides\, and likely nearly all viral peptides\, derive from rapidly degraded proteins\, which consist of defective ribosomal products (DRiPs) and short-lived proteins (SLiPs).  I will describe the nature of a number of influenza virus DRiPs and how ribosome profiling facilitates the identification of peptides derived from non-canonically translated cellular DRiPs.  I will also discuss how cells with ribosomes lacking individual protein subunits demonstrate either enhanced or decreased peptide generation in a subunit-specific manner and how this can be exploited by cancer cells to escape immunosurveillance.  I will present a model to explain how peptide generation avoids the law of mass action to generate a highly diverse peptide repertoire (immunopeptidome) that enables pathogen and tumor recognition.  This talk will illustrate how\, in over 4 decades of research\, cell biology\, virology\, and immunology can be combined to dissect a medically important immune effector mechanism. \n\n\n\nHost: Adnane Achour\, adnane.achour@scilifelab.se
URL:https://www.scilifelab.se/event/spotlight-seminar-jon-yewdell/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/10/Campus-solna-seminar-picture.jpg
ORGANIZER;CN="Spotlight Seminar Series":MAILTO:events@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241024T100000
DTEND;TZID=Europe/Stockholm:20241024T123000
DTSTAMP:20260404T195131
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:20260404T195131
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
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241024T120000
DTEND;TZID=Europe/Stockholm:20241024T130000
DTSTAMP:20260404T195131
CREATED:20240708T141035Z
LAST-MODIFIED:20241014T123342Z
UID:10001300-1729771200-1729774800@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Alberto Arenas Molina & Kiana Hosseinpour Moghaddam
DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 20 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nPhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits\, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester. \n\n\n\nThis week:\n\n\n\n\n\n\nAlberto Arenas Molina\n\n\n\nSimon Elsässer – alpha 4 \n\n\n\nTranslating the untranslated: Microproteins encoded by “non-coding” regions and their role in tumorigenesis \n\n\n\n\n\nKiana Hosseinpour Moghaddam\n\n\n\nOla Larsson – gamma 5 \n\n\n\nDi-codon organization orchestrates the malignant proteome \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-sammy-se-whee-park-kiana-hosseinpour-moghaddam/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Community
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_123412496_HDR2-scaled.jpg
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241028T083000
DTEND;TZID=Europe/Stockholm:20241029T130000
DTSTAMP:20260404T195131
CREATED:20240919T141910Z
LAST-MODIFIED:20240927T150822Z
UID:10001363-1730104200-1730206800@www.scilifelab.se
SUMMARY:Precision Omics Initiative Sweden (PROMISE) Symposium
DESCRIPTION:Sweden is uniquely positioned to advance medical research and implement precision medicine on a national scale\, benefiting its entire population. Integration of cutting-edge biomedical research technologies with Sweden’s uniform healthcare system has the potential to position our country as a global frontrunner\, leading the development of precision medicine in this new technological era. However\, data fragmentation and data isolation currently hinder the Swedish ability to fully capitalize on its potential and maximize the use of already available infrastructure and prior investments.  \n\n\n\nPrecision Omics Initiative Sweden (PROMISE)  is a new transformative initiative that will be centered around SciLifeLab and Genomic Medicine Sweden (GMS) to completely integrate medical research with the healthcare system in Sweden. \n\n\n\nPROMISE will have three major focus areas: 1) Generate extensive multi-omics data from both patients and the general population in Sweden\, 2) Develop a strong and effective infrastructure to integrate healthcare generated multi-omics data for research applications\, improve data sharing and data accessibility across Sweden\, 3) Develop legal and regulatory frameworks for better alignment with modern capabilities\, for maximum utilization of Sweden’s great potential. \n\n\n\nRegister for the PROMISE symposium\, October 28-29 2024\, to contribute to further developing the scientific foundation and design of this transformative initiative.  \n\n\n\nregistration\n\n\n\nProgram\n\n\n\nPROMISE Symposium Uppsala October 28-29_FINALDownload\n\n\n\nOrganizing committee  \n\n\n\n \n\n\n\n\nAnna Clareborn\n\n\n\nSanna Gudmundsson\n\n\n\nBo Jacobsson\n\n\n\nÅsa Johansson\n\n\n\nAnders Kämpe\n\n\n\nTuuli Lappalainen\n\n\n\nKerstin Lindblad-Toh\n\n\n\nAnna Lindstrand\n\n\n\nBengt Persson\n\n\n\nRichard Rosenquist Brandell\n\n\n\nTobias Sjöblom\n\n\n\nColum Walsh
URL:https://www.scilifelab.se/event/precision-omics-initiative-sweden-promise-symposium/
LOCATION:Lecture Hall X\, Uppsala University Main Building\, Biskopsgatan 3\, Uppsala\, Sweden
CATEGORIES:Event
ORGANIZER;CN="PROMISE":MAILTO:anna.clareborn@uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20241028T090000
DTEND;TZID=Europe/Stockholm:20241101T170000
DTSTAMP:20260404T195131
CREATED:20240808T121308Z
LAST-MODIFIED:20240809T075123Z
UID:10001316-1730106000-1730480400@www.scilifelab.se
SUMMARY:R Programming Foundations for Data Analysis
DESCRIPTION:The course is addressed to individuals with little or no experience in programming but who are enthusiastic about learning how to use R for data analysis and streamline their work. It is a national course open for PhD students\, postdocs\, researchers and other employees in all Swedish. We also welcome applications from outside of Sweden (EU-zone) and from the non-academic sector\, for more info contact us. NOTE: In October 2024\, the course will be a 5-day-course on-site both in Uppsala and Lund. \n\n\n\n\n\n\n\nVenue – onsite\n\n\n\n\nUppsala University: Experimental room\, Campus Blåsenhus\, von Kraemers allé 1A\, 2nd floor\n\n\n\nLund University: Retina D227\, Biologihuset\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\n\nApplication open: August 08\, 2024\n\n\n\nApplication deadline: September 30\, 2024\n\n\n\nConfirmation to accepted students: October 4\, 2024\n\n\n\n\nResponsible teachers: Nima Rafati\, Guilherme Dias\, Miguel Angel Redondo\, Marcin Kierczak\, Lokeshwaran Manoharan\, Louella Vasquez \n\n\n\nContact for questions: edu.r@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK for non-profit organizations or 15000 SEK for private companies will be invoiced to accepted participants. This includes lunches\, coffee\, snacks\, and one course dinner. \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 course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting. After introductory lectures on good programming practices\, basic software design theory and a brief overview of R\, we will delve into programming. We start by learning how to use R as a basic calculator\, what are variable types\, how to use data structures\, how to implement repeating actions with and without loops\, and how to take actions based on certain conditions. We gradually proceed to loading data\, importing data from common file formats\, some basic matrix algebra and learning how to perform basic statistical tests and visualize results. You will learn how to document your work and how to generate automatic reports using real-life datasets. During the course you will also be working on a small dataset to apply knowledge you learnt in the course and will present that in a report format towards the end of the workshop. \n\n\n\nTopics covered will include: \n\n\n\n\nVariables and Operators\n\n\n\nMatrices\, lists\, and dataframes\n\n\n\nData manipulation\n\n\n\nVisualization\n\n\n\nR packages\n\n\n\nBioconductor\n\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nDescribe different data structures commonly used in R.\n\n\n\nWork with different data types.\n\n\n\nImport and export data from and to R environment. \n\n\n\nManipulate data.\n\n\n\nWork with dataframes and lists.\n\n\n\nVisualize the data.\n\n\n\nUse R Markdown to create reports containing text\, code\, tables and/or figures.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nGood general computer literacy is expected\, but no previous experience in programming or R is required. You are expected to know basic concepts in mathematics and statistics\, but the emphasis of the course is to learn how to use R. \n\n\n\nParticipants are expected to use their own computers with pre-installed R and R Studio (detailed instructions will be given upon acceptance). \n\n\n\nDue to our best practice to have a high teacher to student ratio\, there are a maximum number of allowed participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/r-programming-foundations-for-data-analysis/
LOCATION:Uppsala University\, Lund University
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
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END:VCALENDAR