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TZID:Europe/Stockholm
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BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210512T130000
DTEND;TZID=Europe/Stockholm:20210512T140000
DTSTAMP:20260404T003521
CREATED:20210503T144526Z
LAST-MODIFIED:20210503T144529Z
UID:10000383-1620824400-1620828000@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Rui Shao and Yerma Pareja Sanchez
DESCRIPTION:Introducing the new Campus Solna Seminar Series – a new initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 13:00-13:50 and following current regulations\, they will be broadcast via zoom. \n\n\n\n\n\n\nRui Shao\n\n\n\nEstimating RNA transcription speed with multi-omics \n\n\n\nSimon Elsässer Group – Alpha 4 \n\n\n\n\n\nYerma Pareja Sanchez\n\n\n\nDiscovering new factors involved in transcriptional memory \n\n\n\nVincent Pelechano Group – Gamma 5 \n\n\n\n\n\n\nRegister to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series\, i.e. only one registration is necessary. \n\n\nPlease select a valid form
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-rui-shao-and-yerma-pareja-sanchez/
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210510T131500
DTEND;TZID=Europe/Stockholm:20210510T140000
DTSTAMP:20260404T003521
CREATED:20210428T092922Z
LAST-MODIFIED:20210507T075745Z
UID:10000367-1620652500-1620655200@www.scilifelab.se
SUMMARY:A more sustainable chemistry with elemental sulfur
DESCRIPTION:Thanh Binh Nguyen\n\n\n\nUniversité Paris-Saclay\, France\n\n\n\nLINK TO THE SEMINAR\n\n\n\nAbstract\n\n\n\nFacing a more and more rapid depletion of natural resources\, one of the most challenging problems to be solved of modern organic chemistry is to develop reactions enabling access to target molecules from simple and readily available starting materials with higher efficiency in number of atoms while reducing the number of steps\, unnecessary redox changes and waste. With this idea in mind\, we have been concentrating on the use of elemental sulfur – an abundant waste of oil and gas industry with annual product up to 70 MT –  as a polyvalent synthetic tool. This lecture will focus on organic redox reactions developed in our laboratory involving this element as a new synthetic strategy that satisfies most of the requirements of a more sustainable chemistry. \n\n\n\nBiography\n\n\n\nThanh Binh Nguyen received his BS degree (2004) from the University of Natural Sciences in Hochiminh city\, Vietnam and subsequently his MS (2005) and PhD degrees (2008) from the the Université du Maine – Le Mans -France. After a two-year postdoctoral stay at the Institut de Chimie des Substances Naturelles – Gif-sur-Yvette – France\, he obtained a permanent research associate position (Chargé de Recherche) of the Centre National de la Recherche Scientifique (CNRS) in 2011\, working in the same institute. His main research interest is the development of new synthetic methods for carbon-nitrogen bond formation with a strong emphasis on using elemental sulfur\, molecular iodine and iron–sulfur catalysts. \n\n\n\nHost\n\n\n\nDuc Duy Vo\, Uppsala University
URL:https://www.scilifelab.se/event/a-more-sustainable-chemistry-with-elemental-sulfur/
CATEGORIES:Event
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
LOCATION:https://uu-se.zoom.us/j/65768822626
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210507T100000
DTEND;TZID=Europe/Stockholm:20210507T120000
DTSTAMP:20260404T003521
CREATED:20210428T092256Z
LAST-MODIFIED:20210428T092313Z
UID:10000366-1620381600-1620388800@www.scilifelab.se
SUMMARY:SciLifeLab Data Repository Launch
DESCRIPTION:SciLifeLab Data Centre invites you to join the launch of the SciLifeLab Data Repository! The event will feature presentations of the repository by representatives from Data Centre and Figshare\, presentation of the user perspective of the repository and opportunities to ask questions.   \n\n\n\nRegister to the launch event to learn more about the SciLifeLab Data Repository and how it can be of use to you! \n\n\n\n \n\n\n\nIntroductionJohan Rung – Head of Data Centre\, SciLifeLabStoring\, sharing\, and citing your data with SciLifeLab’s FigshareMegan Hardeman – Head of Engagement at FigshareUser perspectives:Vicent Pelechano – Researcher at the Department of Microbiology\, Tumor and Cell Biology\, Karolinska Institutet and SciLifeLab FellowJonne Rietdijk – PhD student at the Department of Pharmaceutical Biosciences\, Uppsala UniversityMikael Sellin – Senior lecturer/Associate Professor at the Departement of Medical Biochemistry and Microbiology\, Uppsala University and SciLifeLab FellowFAIR as a factor for bigger research impactWolmar Nyberg Åkerström – Data Steward at NBISQ&A sessionModerated by Data Centre\n\n\n\n\n\n\n\n\nAbout the SciLifeLab Data Repository\n\n\n\nThe SciLifeLab Data Repository\, powered by Figshare\, is a repository for publishing any kind of research-related data\, e.g. documents\, figures\, or presentations. Figshare is an open data repository used by researchers in numerous disciplines. Through an agreement with Figshare\, SciLifeLab offers researchers and units the opportunity to upload and publish their research data through a dedicated portal. The purpose of the SciLifeLab Data Repository is to serve publishing of data.  \n\n\n\n\nContact: datacentre@scilifelab.se
URL:https://www.scilifelab.se/event/scilifelab-data-repository-launch/
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210506T130000
DTEND;TZID=Europe/Stockholm:20210506T140000
DTSTAMP:20260404T003521
CREATED:20210503T144618Z
LAST-MODIFIED:20220202T083122Z
UID:10000384-1620306000-1620309600@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Meike Latz and Daniel Gyllborg
DESCRIPTION:Introducing the new Campus Solna Seminar Series – a new initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 13:00-13:50 and following current regulations\, they will be broadcast via zoom. \n\n\n\n\n\n\nVesna Grujcic\n\n\n\nCombined imaging and single cell transcriptomics of eukaryotic plankton \n\n\n\nAnders Andersson – Alpha 3 \n\n\n\n\n\nDaniel Gyllborg\n\n\n\nApplications and advancements of in situ sequencing for cell atlas projects \n\n\n\nMats Nilsson – Gamma 4 \n\n\n\n\n\n\nRegister to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series\, i.e. only one registration is necessary. \n\n\nPlease select a valid form
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-meike-latz-and-daniel-gyllborg/
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210504T090000
DTEND;TZID=Europe/Stockholm:20210504T100000
DTSTAMP:20260404T003521
CREATED:20210428T091829Z
LAST-MODIFIED:20210428T091856Z
UID:10000365-1620118800-1620122400@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:The April version of the Call4Help session will be a “special edition”. We will present ZeroCostDL4Mic. ZeroCostDL4Mic is a toolbox for the training and implementation of common Deep Learning approaches to microscopy imaging. It exploits the ease-of-use and access to GPU provided by Google Colab. https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki \n\n\n\nPresenter:Petter Ranefall\, BIIF \n\n\n\nTime and location:4 May 2021 (Tuesday)\, 09:00 – 10:00 AMzoom (link will be sent to registered users)
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260404T003521
CREATED:20210414T092540Z
LAST-MODIFIED:20210506T225135Z
UID:10000364-1620028800-1620406800@www.scilifelab.se
SUMMARY:Quick and clean: advanced Python for data science in biology - ONLINE
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of Advanced Python skills within all Swedish universities. \n\n\n\nImportant dates\n\n\n\nApplication is open!Application closes: April 15\, 2021Confirmation to accepted students: April 21\, 2021For questions about the course\, please contact Ashfaq Ali (ashfaq.ali@nbis.se)\, Sergiu Netotea (sergiu.netotea@nbis.se)\n\n\n\nCourse fee\n\n\n\nThe course is free of charge but a no show fee course fee of 2000 SEK will be invoiced to accepted participants who failed to attend the course after accepting to participate. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nThe main aim of this course is to introduce students to the so-called Zen of Python for quick and clean application of python in data science. The workshop is structured around  based on the industry way of classifying big data jobs: data analytics\, data science\, data engineering.  \n\n\n\nParticipants will have an opportunity to learn the following topics \n\n\n\nGeneral overview of computer choke points for various architectures together with a fast paced tutorial on advanced language concepts.Scientific computing\, statistics\, visualization and data mining\, via libraries such as numpy\, pandas\, statmodels and several other “science stack” libraries.Programming with focus on how to perform machine learning\, deep learning\, statistical learning and pattern recognition using python\, via scikit-learn\, tensorflow\, pymc3 and other more exotic libraries.Engineering the computing infrastructure and Python’s role in it. How to run Python on clouds and GPU machinesLearning how Python can be used to organize your workflow with efficiency and reproducibility in mind.Application to research themes where you will either pick one real ‘omics subject from a given task list or you will use Python in your project under our assistance. This is a great time to solidify your knowledge by applying it to your own research scope!\n\n\n\nLearning Outcomes\n\n\n\nAt the end of the course the course participants will have achieved following objectives \n\n\n\nGeneral knowledge about computational workflow using pythonHave knowledge about computer architecture and use of python for efficient computingKnowledge about python libraries for machine learning\, deep learning and statistical learning and their applicationsAbility to apply advanced python libraries in own research field\n\n\n\nWorkshop organization\n\n\n\nWe aim for a balance between lecturing and exercise in Jupyter notebooks (jupyter.org) which is used for taking notes\, self study\, hands on tasks and interaction. Considering that the course is online\, lectures will be delivered via zoom links and exercises will be carried out in zoom breakout rooms with the help of teaching assistants. Course session leaders will be available to answer theoretical and practical questions. Questions are welcome at any time. \n\n\n\nYou will be asked to prepare your laptop a week before the course starts. We will also use a slack channel for communication\, posting links or code tips. \n\n\n\nImportant to Know\n\n\n\nThe workshop covers some of the basic concepts of python programming and each session will have advanced material on the topic that may test the limits of the participant’s knowledge of python and computers. Difficulties during learning are expected and are part of the course design. \n\n\n\nFor the sessions on analyses of your own data\, students are encouraged to send their topic of interest before the start of the course.   \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises \n\n\n\nA computer with any OS.           Python\, R or any other computer language basic knowledge.Basic skills handling your own computer.For those interested in tasks involving cloud computing\, access to Amazon AWS is required. (user configuration)\n\n\n\nDesirable to have \n\n\n\nYou have bioinformatics or systems biology background\, statistical and machine learning skills.Have Linux on your laptop\, or access to a Linux server.You did programming before (not just courses) and can handle the command line.Have a good idea for a task you want to achieve on the fourth day.\n\n\n\nDue to limited space the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on several criteria including entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nGithub page (older version)
URL:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
CATEGORIES:Course
LOCATION:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260404T003521
CREATED:20210414T092106Z
LAST-MODIFIED:20210414T093012Z
UID:10000363-1620028800-1620406800@www.scilifelab.se
SUMMARY:Genome Assembly and Annotation 2021 – Online
DESCRIPTION:Elixir course open for PhD students\, postdocs\, researchers and other employees in need of Genome assembly and annotation skills. \n\n\n\nImportant dates\n\n\n\nApplication opens: 30th of March Application closes:19th of AprilConfirmation to accepted students: 26th of April \n\n\n\nResponsible teachers:  Christophe Klopp (FR)\, Lucile Soler (SE)\, Mahesh Binzer-Panchal (SE)\, Nima Rafati (SE)\, Tomas Larsson (SE)\, Henrik Lantz (SE)\, Brane Leskosek (SI)\, Marko Vidak (SI) and Erik Hjerde (NO) \n\n\n\nIf you do not receive information according to the above dates please contact:  Erik Hjerde \n\n\n\nCourse fee\n\n\n\nThe course is free of charge. \n\n\n\nCourse content\n\n\n\nThis course will introduce the best practice bioinformatics methods to assemble and annotate genomes via a series of lectures\, group work and computer practicals. Topics covered will include: \n\n\n\nQuality Assessment of sequencing dataLong read technologies and assemblies and assembly polishingAssembly ValidationHi-C sequencingMethod in Structural AnnotationAbinitio annotationAnnotation with makerAbinitio trainingFunctional annotationSubmission to DBBacterial annotation\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\nMandatory to complete a short command line course prior to the event. This will be made available to enrolled participants\n\n\n\nThe course is limited to 25 people\, and maximum 2 participants per national ELIXIR node (except Norway). The course is an advanced course. Based on the information collected upon registration\, the course organizers will enroll participants.
URL:https://www.scilifelab.se/event/genome-assembly-and-annotation-2021-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210426T120000
DTEND;TZID=Europe/Stockholm:20210426T130000
DTSTAMP:20260404T003521
CREATED:20210414T085430Z
LAST-MODIFIED:20210414T085517Z
UID:10000362-1619438400-1619442000@www.scilifelab.se
SUMMARY:Nationella studier av värdet av breda genpaneler och helgenomsekvensering för patienter med hematologiska maligniteter
DESCRIPTION:Flera internationella studier tyder på att storskalig sekvensering kan förbättra diagnostik och behandling av patienter med hematologiska maligniteter. Arbetsutskottet för hematologi inom Genomic Medicine Sweden har initierat två nationella studier för att utvärderat potentialen av breda genpaneler och helgenomsekvenserig i svensk sjukvård. I det här webbinariet kommer vi informera om upplägget för studierna och diskutera detaljer kring patientrekrytering och genomförande. \n\n\n\nMålgrupp: Vi vänder oss till hematologer\, forskningssjuksköterskor\, diagnostiker\, laboratoriepersonal och bioinformatiker som arbetar med hematologiska maligniteter i Sverige\, samt alla andra professioner med intresse av frågan. \n\n\n\nDag och tid: 13 och 26 april\, kl 12-13 (samma webbinarium ges vid två tillfällen)Plats: Digitalt via Zoom https://uu-se.zoom.us/j/61739315319 \n\n\n\nVid webbinariet kommer följande nyckelfrågor att tas upp: \n\n\n\nHur ser etikansökan för studierna ut?Hur är studieupplägget för genpaneler?Hur är studieupplägget för helgenomsekvensering?\n\n\n\nMedverkande: \n\n\n\nRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppenLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi\n\n\n\nAnmälan: Ingen formell anmälan behövs. Anslut bara till länken på utsatt tid. \n\n\n\n\n\n\n\nProgram \n\n\n\n12.00-12.10Välkomna\, Introduktion till GMS och GMS hematologiRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS Hematologi \n\n\n\n12.10-12.20Upplägg för etikansökan och samtyckesblankettThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppen \n\n\n\n12.20-12-30Studieupplägg för genpanelerLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi \n\n\n\n12.30-12.40Studieupplägg för helgenomsekvenseringRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMS \n\n\n\n12.40-13.00Frågor\, diskussion \n\n\n\n\n\n\n\nOm du har frågor om webbinariet är du välkommen att kontakta Eva Berglund\, eva.berglund@scilifelab.uu.se
URL:https://www.scilifelab.se/event/nationella-studier-av-vardet-av-breda-genpaneler-och-helgenomsekvensering-for-patienter-med-hematologiska-maligniteter/2021-04-26/
CATEGORIES:Event
LOCATION:https://uu-se.zoom.us/j/61739315319
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210423T131000
DTEND;TZID=Europe/Stockholm:20210423T140000
DTSTAMP:20260404T003521
CREATED:20210414T084939Z
LAST-MODIFIED:20210414T084942Z
UID:10000359-1619183400-1619186400@www.scilifelab.se
SUMMARY:The open source ecosystem for genome-scale metabolic models
DESCRIPTION:Mihail Anton\, National Bioinformatics Infrastructure Sweden \n\n\n\nWhen: April 23\, 13:10  \n\n\n\nZoom link to the seminar: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nAs science is advancing towards full reproducibility\, the ecosystem of tools and resources for genome-scale metabolic modelling is increasingly open-source. The talk will showcase how Metabolic Atlas is contributing to this ecosystem by integrating several open-source GEMs\, and providing visualisations for these\, with the aim of aiding discovery of disease-related alterations of metabolism.
URL:https://www.scilifelab.se/event/the-open-source-ecosystem-for-genome-scale-metabolic-models/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210423T110000
DTEND;TZID=Europe/Stockholm:20210423T120000
DTSTAMP:20260404T003521
CREATED:20210414T085113Z
LAST-MODIFIED:20210414T085116Z
UID:10000360-1619175600-1619179200@www.scilifelab.se
SUMMARY:Systems biology approaches for translational cancer research
DESCRIPTION:Francesco Gatto\, CSO Elypta\, Sweden \n\n\n\nWhen: April 23\, 11:00  \n\n\n\nZoom: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nIn this seminar\, I will illustrate how we investigated regulation of cancer metabolism using systems biology approaches and leading to the discovery of potential disease biomarkers. The talk will further focus on the challenge to translate fundamental discoveries in clinical practice and the foundation of Elypta – a start-up university spin-off that is executing this transition.
URL:https://www.scilifelab.se/event/systems-biology-approaches-for-translational-cancer-research/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210422T150000
DTEND;TZID=Europe/Stockholm:20210422T160000
DTSTAMP:20260404T003521
CREATED:20210414T084404Z
LAST-MODIFIED:20210414T084407Z
UID:10000358-1619103600-1619107200@www.scilifelab.se
SUMMARY:The evolution of human Genome Scale Metabolic models
DESCRIPTION:Jonathan Robinson\, Scientific Data Developer Bioinnovation Institute\, Denmark \n\n\n\nWhen: April 22\, 15:00 \n\n\n\nZoom: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nMetabolism provides the energy and building blocks necessary to support life\, but the complexity of the metabolic network presents a challenge when trying to determine how changes to one component affects the system as a whole. Genome-scale metabolic models (GEMs) were developed to address this challenge by providing computational reconstructions of metabolic networks. GEMs have been developed for hundreds of species including humans\, supporting new approaches to study human health and disease.In my talk\, I will present our work in developing the most recent human GEM\, Human1\, and the different ways in which the model can be used to interpret omics data in a metabolic context. I will also share the challenges that we faced while developing Human1\, and the challenges that we still face over a year after its initial release in 2020. Finally\, I will discuss how we envision the future of GEMs\, and our efforts to make them more accessible and useful for bioinformaticians.
URL:https://www.scilifelab.se/event/the-evolution-of-human-genome-scale-metabolic-models/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210421T131500
DTEND;TZID=Europe/Stockholm:20210421T140000
DTSTAMP:20260404T003521
CREATED:20210414T084108Z
LAST-MODIFIED:20210414T084111Z
UID:10000357-1619010900-1619013600@www.scilifelab.se
SUMMARY:Data-driven approaches towards studying context-specific cell signalling
DESCRIPTION:Evangelia Petsalaki\, Group Leader EMBL/EBI\, United Kingdom \n\n\n\nWhen: April 21\, 13:15 \n\n\n\nZoom: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nOur group aims to understand and describe the organisation principles of cell signalling that allow the diverse and context-specific cell responses and phenotypes.It is well established that signalling responses happen through complex networks. However\, most signalling research still uses linear pathways as the ground truth. Moreover\, signalling responses are highly dependent on context\, such as tissue type\, genetic background etc and therefore these static pathways are not always suitable. There is also a high bias in the literature towards kinases and pathways for which reagents and prior knowledge is readily available. This leaves a huge dark space in our understanding of cell signalling and significantly hinders studies of its general principles.In this talk I will present two projects where we try to mitigate some of the above issues. For the first one I will present CEN-tools\, an integrative webserver and python package\, that allows users to navigate the contexts of different gene essentialities. I will demonstrate examples of its use in discovering new gene-gene relationships and important putative signalling targets for different cancers. For the second one I will present a method that combines paired transcriptomics and imaging data to extract context-specific signalling networks\, with the context in this case cell shape in breast cancer. The method is generalisable to any paired transcriptomics/phenotype data.
URL:https://www.scilifelab.se/event/data-driven-approaches-towards-studying-context-specific-cell-signalling/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210420T100000
DTEND;TZID=Europe/Stockholm:20210420T120000
DTSTAMP:20260404T003521
CREATED:20210414T081421Z
LAST-MODIFIED:20210414T083002Z
UID:10000356-1618912800-1618920000@www.scilifelab.se
SUMMARY:NGI webinar on Spatial Transcriptomics 10X Visium
DESCRIPTION:The National Genomics Infrastructure (NGI) at SciLifeLab invites you to participate in a webinar on the Spatial Transcriptomics 10X Visium technology.  \n\n\n\nSpatially resolved transcriptomics\, recently pronounced Method of the Year by Nature Methods\, has undoubtedly changed the way we understand complex tissues.  With the recent launch of the 10X Genomics Visium assay\, we can now offer spatially resolved transcriptome-wide analysis in tissue sections\, right here at NGI!  \n\n\n\nThis webinar will serve as a guide through how the technology has evolved\, how the protocol is run\, and how spatial transcriptomics data can be analysed.  \n\n\n\nOur line-up of talks include speakers from NGI and the Spatial Research lab\, as well as two keynote speakers; Dr. Alessondra Speidel\, who will present how Spatial Transcriptomics has helped her understand how wound healing responds to different hydrogel materials\, and Dr. James Chell\, a Senior Scientist at 10X Genomics who will update us on the Visium spatial platform and its FFPE application.  \n\n\n\nInterested? Find out more how NGI can support projects that can benefit from 10X Genomics Visium.
URL:https://www.scilifelab.se/event/ngi-webinar-on-spatial-transcriptomics-10x-visium/
CATEGORIES:Event
ORGANIZER;CN="National Genomics Infrastructure (NGI)":MAILTO:support@ngisweden.se
LOCATION:https://www.scilifelab.se/event/ngi-webinar-on-spatial-transcriptomics-10x-visium/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210413T120000
DTEND;TZID=Europe/Stockholm:20210413T130000
DTSTAMP:20260404T003521
CREATED:20210414T085430Z
LAST-MODIFIED:20210414T085517Z
UID:10000361-1618315200-1618318800@www.scilifelab.se
SUMMARY:Nationella studier av värdet av breda genpaneler och helgenomsekvensering för patienter med hematologiska maligniteter
DESCRIPTION:Flera internationella studier tyder på att storskalig sekvensering kan förbättra diagnostik och behandling av patienter med hematologiska maligniteter. Arbetsutskottet för hematologi inom Genomic Medicine Sweden har initierat två nationella studier för att utvärderat potentialen av breda genpaneler och helgenomsekvenserig i svensk sjukvård. I det här webbinariet kommer vi informera om upplägget för studierna och diskutera detaljer kring patientrekrytering och genomförande. \n\n\n\nMålgrupp: Vi vänder oss till hematologer\, forskningssjuksköterskor\, diagnostiker\, laboratoriepersonal och bioinformatiker som arbetar med hematologiska maligniteter i Sverige\, samt alla andra professioner med intresse av frågan. \n\n\n\nDag och tid: 13 och 26 april\, kl 12-13 (samma webbinarium ges vid två tillfällen)Plats: Digitalt via Zoom https://uu-se.zoom.us/j/61739315319 \n\n\n\nVid webbinariet kommer följande nyckelfrågor att tas upp: \n\n\n\nHur ser etikansökan för studierna ut?Hur är studieupplägget för genpaneler?Hur är studieupplägget för helgenomsekvensering?\n\n\n\nMedverkande: \n\n\n\nRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppenLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi\n\n\n\nAnmälan: Ingen formell anmälan behövs. Anslut bara till länken på utsatt tid. \n\n\n\n\n\n\n\nProgram \n\n\n\n12.00-12.10Välkomna\, Introduktion till GMS och GMS hematologiRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS Hematologi \n\n\n\n12.10-12.20Upplägg för etikansökan och samtyckesblankettThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppen \n\n\n\n12.20-12-30Studieupplägg för genpanelerLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi \n\n\n\n12.30-12.40Studieupplägg för helgenomsekvenseringRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMS \n\n\n\n12.40-13.00Frågor\, diskussion \n\n\n\n\n\n\n\nOm du har frågor om webbinariet är du välkommen att kontakta Eva Berglund\, eva.berglund@scilifelab.uu.se
URL:https://www.scilifelab.se/event/nationella-studier-av-vardet-av-breda-genpaneler-och-helgenomsekvensering-for-patienter-med-hematologiska-maligniteter/2021-04-13/
CATEGORIES:Event
LOCATION:https://uu-se.zoom.us/j/61739315319
END:VEVENT
END:VCALENDAR