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DTSTART;TZID=Europe/Stockholm:20220328T090000
DTEND;TZID=Europe/Stockholm:20220401T170000
DTSTAMP:20260404T050731
CREATED:20211216T145021Z
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SUMMARY:Introduction to bioinformatics using NGS data - ONLINE
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within or affiliated to Swedish academia. This workshop is organized by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nDue to the Covid-19 situation\, this workshop will be held online. \n\n\n\nIf you have questions regarding the workshop\, please email: edu.intro-ngs@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication opens:  10 January 2022 \n\n\n\nApplication closes: 27 February 2022 \n\n\n\nConfirmation to accepted students:  Week 9\, 2022 \n\n\n\nResponsible teachers:  Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK workshop fee* \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nThis is an intense one-week beginner level workshop that introduces the analysis of next generation sequencing (NGS) data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures. \n\n\n\nAfter this workshop you should be able to: \n\n\n\n●      Use the Linux command line interface to manage simple file processing operations and organize directory structures. \n\n\n\n●      Connect to and work on a remote high performance compute cluster. \n\n\n\n●      Apply programs in Linux for analysis of NGS data. \n\n\n\n●      Describe the basic principles of NGS. \n\n\n\n●      Summarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them. \n\n\n\n●      Explain common NGS file formats. \n\n\n\n●      Interpret quality control of NGS reads. \n\n\n\n●      Explain the steps involved in variant calling using whole genome sequencing data. \n\n\n\n●      Independently perform a basic variant calling workflow on example data. \n\n\n\n●      Explain the steps involved in differential gene expression using RNA seq data. \n\n\n\n●      Independently perform differential gene expression analysis on example data. \n\n\n\nEntry requirements\n\n\n\nA background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to: \n\n\n\n●      Have relevant previous experience in sequencing or analysis. \n\n\n\n●      Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing. \n\n\n\n●      It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others. \n\n\n\n\n\n\n\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. \n\n\n\nDue to the high volume of applications from Swedish institutions\, we currently do not accept international applicants. \n\n\n\n\n\n\n\n\nAPPLICATION
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online-3/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220404T140000
DTEND;TZID=Europe/Stockholm:20220404T150000
DTSTAMP:20260404T050731
CREATED:20220316T072135Z
LAST-MODIFIED:20220331T055237Z
UID:10000559-1649080800-1649084400@www.scilifelab.se
SUMMARY:Information meeting – Call for Therapeutic Oligonucleotide Projects at OligoNova Hub / SciLifeLab DDD
DESCRIPTION:The mission of the Drug Discovery and Development Platform at SciLifeLab is to support researchers in developing new drugs\, transforming academic ideas into new treatments. Therapeutic oligonucleotides is a recent addition to the Drug Discovery and Development platform’s capacity\, available through the OligoNova Hub in Gothenburg.  \n\n\n\nNow\, the first call for therapeutic oligonucleotide projects is opening (March 28 – May 13\, 2022). \n\n\n\nAt this online information meeting\, there will be a presentation of the call and you as an applicant will have the opportunity to ask questions about the call and the application process.  \n\n\n\nThe call text will be published via the SciLifeLab and OligoNova websites on March 28. \n\n\n\nRegister here\n\n\n\n\n\n\n\nOligoNova Hub is a national facility providing academic researchers in Sweden with support and capabilities to convert ideas and discoveries into potential new oligonucleotide therapies. OligoNova Hub is part of the SciLifeLab Drug Discovery and Development platform\, and is located at the AZ BioVentureHub campus in Gothenburg. The OligoNova Hub offers full capacity for the design\, synthesis\, evaluation and optimization of therapeutic oligonucleotides to academic researchers. The hub has been made possible through support from the Knut and Alice Wallenberg foundation\, SciLifeLab\, University of Gothenburg\, Region Västra Götaland\, and a donation from Carl Bennet.
URL:https://www.scilifelab.se/event/information-meeting-call-for-therapeutic-oligonucleotide-projects-at-oligonova-hub-scilifelab-ddd/
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:20220404T140000
DTEND;TZID=Europe/Stockholm:20220404T150000
DTSTAMP:20260404T050731
CREATED:20220325T125600Z
LAST-MODIFIED:20220325T143719Z
UID:10000569-1649080800-1649084400@www.scilifelab.se
SUMMARY:Information Meeting: Call for therapeutic oligonucleotide projects
DESCRIPTION:This digital information meeting will be held April 4\, 2022 at 14.00–15.00. At this meeting\, there will be a presentation of the call and you as an applicant will have the opportunity to ask questions about the call and the application process. \n\n\n\nregister here to receive zoom link\n\n\n\nApply in the call here\n\n\n\nThe mission of the Drug Discovery and Development Platform at SciLifeLab is to support researchers in developing new drugs\, transforming academic ideas into new treatments. To this end\, the DDD platform provides state-of-the-art drug discovery technologies to scientists across the country. Therapeutic oligonucleotides are a recent addition to the DDD platform’s capacity\, complementing the previous focus on small molecule and protein drugs. Oligonucleotide drugs have different modes of action\, and a potentially faster development compared to other drug types. Therapeutic oligonucleotide development is supported by the OligoNova Hub\, based in Gothenburg and part of SciLifeLab’s DDD platform. \n\n\n\nIn this call\, we are looking for project ideas for new therapeutic oligonucleotides that can be developed at DDD and OligoNova Hub. Approved project ideas will be developed in close collaboration between the academic laboratory and drug development experts at DDD and OligoNova Hub. The costs of the projects will mainly be covered by OligoNova\, but academic partners will be expected to contribute by paying for reagent costs. \n\n\n\nThe call is open for scientists with a doctoral degree at a Swedish university or higher institution. English should be used when filling out this application. You are responsible for ensuring that the application is complete. Incomplete applications will not be processed. Attach only material that we explicitly request. SciLifeLab DDD/OligoNova will not accept additional information after the closing date for applications\, except for information we ourselves explicitly request. Applications are reviewed by a review committee with international representation. \n\n\n\nCall Announcement FlyerDownload\n\n\n\nThe call is open March 28\, 2022 to May 13\, 2022.
URL:https://www.scilifelab.se/event/information-meeting-call-for-therapeutic-oligonucleotide-projects/
LOCATION:Online event via Zoom
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T080000
DTEND;TZID=Europe/Stockholm:20220407T170000
DTSTAMP:20260404T050731
CREATED:20211202T132557Z
LAST-MODIFIED:20211202T132705Z
UID:10000497-1649145600-1649350800@www.scilifelab.se
SUMMARY:Introduction to Data Management Practices
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. \n\n\n\nNote: We follow the recommendations and guidelines from Swedish authorities and Folkhälsomyndigheten. The course is designed to be an interactive face-to-face event. However\, we follow the situation carefully and will deliver the course online if needed. \n\n\n\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\nAPPLICATION\n\n\n\n\n\n\n\n\nContact: edu.intro-dm@nbis.se \n\n\n\nImportant dates\n\n\n\nApplication is open now \n\n\n\nApplication closes: 2022-03-15 \n\n\n\nConfirmation to accepted students: 2022-03-21 \n\n\n\nCourse fee\n\n\n\n1500 SEK paid by invoice to NBIS. This includes lunches\, coffee and snacks. Please note that NBIS cannot invoice individuals. \n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nEntry requirements\n\n\n\nNo previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. \n\n\n\nInstallation instructions will be provided before the course starts. \n\n\n\nCourse content\n\n\n\nTopics covered will include: \n\n\n\n  • Open Science and FAIR in practice \n\n\n\n  • Organising data\, files and folders in research projects \n\n\n\n  • Versioning data\, documents and scripts with Git \n\n\n\n  • Describing data with metadata \n\n\n\n  • Cleaning tabular data and metadata with OpenRefine \n\n\n\n  • Submitting data to public data repositories \n\n\n\n  • Writing basic recipes for data analysis and visualisation with R \n\n\n\n(Links to an external site.) \n\n\n\n\n\n\n\nLearning objectives: \n\n\n\n  • To get acquainted with\, and reflect upon\, the principles of Open \n\n\n\nScience and FAIR \n\n\n\n  • To understand the importance of metadata\, and how it affects \n\n\n\n“FAIRness” \n\n\n\n  • To learn how to organise files to make project work more efficient \n\n\n\n  • To learn to clean up messy tabular data and metadata \n\n\n\n  • To learn how to find\, and submit to\, relevant public repositories for \n\n\n\ndata publication \n\n\n\n  • To learn to apply simple version control practices on files \n\n\n\n  • To learn to start using R to analyse data
URL:https://www.scilifelab.se/event/introduction-to-data-management-practices-2/
LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T090000
DTEND;TZID=Europe/Stockholm:20220405T120000
DTSTAMP:20260404T050731
CREATED:20220121T160038Z
LAST-MODIFIED:20220121T160039Z
UID:10000513-1649149200-1649160000@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, April 5\, 2022\, 9.00-12.00. Deadline for application: Friday\, April 1\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-3/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T120000
DTEND;TZID=Europe/Stockholm:20220405T130000
DTSTAMP:20260404T050731
CREATED:20220315T135352Z
LAST-MODIFIED:20220318T161436Z
UID:10000557-1649160000-1649163600@www.scilifelab.se
SUMMARY:Unbiased characterization of cells using the single-cell facility
DESCRIPTION:In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”\, Johan Henriksson\, Research fellow at the Dept. of Molecular Biology & Molecular Infection Medicine Sweden (MIMS)\, will present the Single-cell facility. If you want to learn how you can benefit from single-cell analysis\, join for 30 min presentation of cases & opportunities\, followed by 30 min discussion of practicalities & project design. \n\n\n\nPresenter:Johan Henriksson\, Dept. Molecular Biology / Molecular Infection Medicine Sweden (MIMS) \n\n\n\nRegistration:To register your physical attendance and reserve your free sandwich\, please go to the Registration Link \n\n\n\nRegistration\n\n\n\nPhysical Attendance:Glasburen seminar roomChemical Biological Centre (KBC) BuildingUmeå University \n\n\n\nOnline Attendance:You can join the seminar on Zoom:https://umu.zoom.us/j/63138997026
URL:https://www.scilifelab.se/event/unbiased-characterization-of-cells-using-the-single-cell-facility/
LOCATION:Glasburen Seminar Room\, Chemical Biological Centre (KBC) Building\, Umeå University\, Umeå\, 901 87\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220405T153000
DTEND;TZID=Europe/Stockholm:20220405T163000
DTSTAMP:20260404T050731
CREATED:20220321T101658Z
LAST-MODIFIED:20220321T101728Z
UID:10000563-1649172600-1649176200@www.scilifelab.se
SUMMARY:Sustainability in Science: My Green Lab
DESCRIPTION:Cristalle Ruiz\n\n\n\nMarket Development Representative\, My Green Lab  \n\n\n\nResearchers in all stages of their career are welcome to attend and could find the talk useful. Kindly feel free to extend the invitation to your home universities. \n\n\n\nMy Green Lab is an internationally recognised non-profit organisation run by scientists aimed at introducing sustainable laboratory practices across the globe. We can find out more about My Green Lab’s mission\, the highly successful ‘Ambassador programme’ and other resources available from Cristalle Ruiz\, Market Development Representative of My Green Lab. The talk is intended to provide valuable insight into sustainability in science and the steps that could be implemented in our labs. \n\n\n\nCristalle Ruiz is the Market Development Representative for My Green Lab\, the leading global nonprofit supporting laboratory sustainability. Her role is to bring awareness to the benefits of sustainable practices across laboratories and manufacturers of laboratory products through My Green Lab’s market-leading programs. In her previous position\, Cristalle advocated for implementing renewable energy in the United States. She holds a bachelor’s degree in Environmental Business and Economics from Rutgers University. She will discuss and provide resources to build a culture of sustainability in the science industry. \n\n\n\n  \n\n\n\n \n\n\n\n PhD & Postdoc council (phd-council@scilifelab.se)
URL:https://www.scilifelab.se/event/sustainability-in-science-my-green-lab/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220407T120000
DTEND;TZID=Europe/Stockholm:20220407T130000
DTSTAMP:20260404T050731
CREATED:20220331T160453Z
LAST-MODIFIED:20220331T160512Z
UID:10000577-1649332800-1649336400@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series - Joel Hallgren
DESCRIPTION:Welcome to 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 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 12:00-12:50 and in Air&Fire\, SciLifeLab Stockholm. \n\n\n\n\n\n\nJoel Hallgren\n\n\n\nKristina Jonas-group\, gamma 5 \n\n\n\nTo stay or to leave? – (p)ppGpp signaling determines bacterial lifestyle decisions during distinct starvation conditions
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-3/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220408T090000
DTEND;TZID=Europe/Stockholm:20220408T093000
DTSTAMP:20260404T050731
CREATED:20220330T131410Z
LAST-MODIFIED:20220330T132843Z
UID:10000574-1649408400-1649410200@www.scilifelab.se
SUMMARY:[Clinical Talks]Seeing is believing\, unraveling the discovery of a centimeter-long macro-bacteria
DESCRIPTION:On April 8\, Dr. Jean-Marie Volland\, Scientist at Berkeley Lab and Laboratory for Research in Complex Systems (LRC Systems)\, and Shailesh Date\, CEO of LRC Systems (Adj. Assoc. Professor at UCSF)\,will talk about their recent discovery and characterization of the macro-bacteria Ca. Thiomargarita magnifica. The threadlike single-cell bacterium\, commonly found in the Caribbean Mangroves\, is visible to the naked eye\, and able to grow up to 2 centimeters in length. In a recent effort\, an international team studied the “magnificent” organism using fluorescence\, x-ray\, and electron microscopy\, and fully sequenced the genome.  \n\n\n\nThrough a unique strategy of polyploidy\, along with compartmentalization of genomic material and protein synthesis in membrane-bound organelle\, the organism has been able to grow orders of magnitude over the theoretical limits for bacterial cells. The traditional view\, which has almost become dogmatic\, is that prokaryotes (bacteria and single-cell microbes) have free-floating DNA\, whereas eukaryotes (yeast and multicellular organisms) package their DNA in a nucleus. This new model organism blurs that line and offers amazing potential insights into biological evolutionary strategies\, many of which are as yet unexplored. One can only wonder at the type and number of new clinical innovations that will emerge as we continue exploring the frontiers of biology and biological complexity. \n\n\n\nRegister to receive zoom link\n\n\n\n  \n\n\n\n\n\n\n\nJean-Marie Volland is a Scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and at Laboratory of Research in Complex Systems (LRC Systems) in Menlo Park California. He obtained his PhD at the Université des Antilles\, in the French West Indies\, studying biology and tropical ecology in the Indian Ocean and Caribbean. Jean-Marie then continued to pursue his Postdoctoral research at University of Vienna\, Austria during 2012-2017. Initially in the Monika Bright´s Lab at the Department of Limnology and Biological Oceanography studying symbiosis in chemosynthetic ecosystems\, and then also in the Silvia Bulgheresi´s Lab at the Archea Biology and Ecogenomics Division studying tropical ecology pathways of microorganisms. In 2018 Jean-Marie joined the Berkeley Lab as an affiliate Scientist to continue working on uncovering highly divergent forms of life together with LRC Systems. The story of the discovery of Thiomargarita magnifica dates back a decade ago\, when marine biologist Olivier Gros\, from the Université of Antilles\, first discovered microbial filaments on leaves buried in the mangrove of Guadeloupe. Gros lab member and microbiologist colleague Silvina González-Rizzo identified it to be in fact be one bacterium. Jean-Marie\, together with his Université of Antilles colleagues and LRC Systems set forth to methodologically study and categorize the new organism. \n\n\n\n\n\n\n\nShailesh Date is the CEO and Founder of Laboratory for Research in Complex Systems (LRC Systems). He is also Adjunct Professor of Biology at San Francisco State University and an Associate Adjunct Professor of Epidemiology and Biostatistics at the University of California San Francisco (UCSF). Shailesh obtained his PhD at The University of Texas\, Austin in Molecular Biology in 2004\, and completed a postdoctoral fellowship at the University of Pennsylvania School of Medicine in 2008\, focusing on computational biology of infectious diseases. Between 2008-2015\, Shailesh worked as a scientist at Genentech\, and during a brief sabbatical in 2013\, completed the prestigious Ignite Program at the Stanford Graduate School of Business. He left Genentech in 2015 to join Global Viral (GV)\, a nonprofit organization with roots in public health research. He founded the LRC Systems in 2019\, transforming Global Viral into a new organization focused on complex systems research in a wide variety of areas. \n\n\n\nAbout Global Viral and LRC SystemsGlobal Viral was founded by Nathan Wolfe in 2007 as the Global Viral Forecasting Initiative (GVFI)\, focusing on public health and field epidemiology while supporting programs like HIV prevention run by USAID\, WHO and other similar organizations in Africa and South East Asia.In 2012\, the organization split into Metabiota\, a for-profit company that took over epidemiology and forecasting-related work\, and Global Viral\, a nonprofit that retained and concentrated on basic research.In 2019\, under the leadership of a new Chief Executive and a new board\, the organization reoriented its research towards complex systems and adopted the “Laboratory for Research in Complex Systems (LRC Systems)”\, which was initially founded as a new division within GV\, as its new name.https://www.lrc.systems \n\n\n\n\n\n\n\n\n“Clinical Talks” has been renewed for yet another exciting\, innovative\, and enlightening season. This season will focus on sustainable innovations within Life Sciences\, that have the potential to contribute to a better climate friendly future for our future generations. Also new this year is that the seminar is co-organized in a collaboration between SciLifeLab and KI Innovations . \n\n\n\nSeason 5\, will be held September 2021 until March 2022 with scheduled Talks\, during Friday mornings 09-09:30 am via ZOOM (with some time-zone friendly adjustments for our international speakers). Each session consists of a talk given by our invited speaker followed by Q&A. The seminar is an open educational seminar series for our ever-expanding Life Science community.
URL:https://www.scilifelab.se/event/seeing-is-believing-unraveling-the-discovery-of-ca-thiomargarita-magnifica-a-centimeter-long-macro-bacteria/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220411T151500
DTEND;TZID=Europe/Stockholm:20220411T161500
DTSTAMP:20260404T050731
CREATED:20220315T160745Z
LAST-MODIFIED:20220404T080634Z
UID:10000558-1649690100-1649693700@www.scilifelab.se
SUMMARY:Decreased levels of oxygen radicals cause autoimmune disease.
DESCRIPTION:Prof. Rikard Holmdahl \n\n\n\nKarolinska Institute\, Sweden \n\n\n\nRegister HERE\n\n\n\nRikard Holmdahl made his PhD (1985) and MD (1987) at Uppsala University. Professor in medical inflammation research Lund University 93-07. Professor at Karolinska Institute from 2008 \n\n\n\n\n\n\n\nVenue: Hybrid meeting – Trippelrummet\, Navet and zoom \n\n\n\n\n\n\n\n\n\n \n\n\n\nTitle of the seminar: Finding and understanding genes associated with common diseases; decreased levels of oxygen radicals cause autoimmune disease\n\n\n\nA long-standing challenge is to understand which genes that cause common complex diseases\, such as rheumatoid arthritis\, atherosclerosis or cancer\, and thereby understand the disease causes. However\, even though we know the human sequence and can genotype millions of individuals it is very difficult to conclusively identify the single nucleotide variants that cause the diseases. We have taken another approach through animal models. Both genetics and diseases show similarities with humans\, and we have shown that it is possible to not only identify the loci associated with disease but also exactly position the polymorphic nucleotides for common autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE).  \n\n\n\nI will focus on the first gene that we cloned\, Ncf1\, which regulate immune tolerance through different levels of oxygen radicals\, or more precisely hydrogen peroxide. It is the major gene causing SLE and is important in Sjögren’s syndrome and RA and most likely most autoimmune disease. \n\n\n\nTo understand the role of Ncf1 is also complicated as peroxide seem to regulate many different pathways leading to autoimmune diseases. I will discuss how we think it regulates RA and SLE but also how it could explain our normal behaviour\, thus explaining why Ncf1 variants are common in both rat and human population. \n\n\n\nRead more about ikard Holmdahl´s research http://ki.se/en/mbb/research-division-of-medical-inflammation-research
URL:https://www.scilifelab.se/event/decreased-levels-of-oxygen-radicals-cause-autoimmune-disease/
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/2022/02/Picture1-The-Svedberg.png
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220412T003000
DTEND;TZID=Europe/Stockholm:20220412T010000
DTSTAMP:20260404T050731
CREATED:20220412T121106Z
LAST-MODIFIED:20220715T121407Z
UID:10000582-1649723400-1649725200@www.scilifelab.se
SUMMARY:γδSTO workshop –  Mini-symposium of Stockholm’s γδ T cell community
DESCRIPTION:A workshop on the May 5\, on gamma delta T cells for our scientific community in Stockholm. Different labs from SciLifeLab\, KI (Solna and Fleminsberg) and Stockholm University are invited. \n\n\n\nProgram: \n\n\n\n13:15 / Introduction \n\n\n\nTaras Kreslavskiy(KI): Transcriptome-wide screen for γδTCR specificities identifies a novel superantigen-like ligand candidate for Vγ7 γδTCRs \n\n\n\nLola Boutin (KI): Evaluation of the potential of using non-conventional (NC) T cell- based immunotherapy in Medulloblastoma \n\n\n\nPatrick Sandoz (KTH): Dynamics of Vγ9Vδ2 T cell cytotoxic functions at the single-cell level \n\n\n\n14:30 / Coffee break \n\n\n\nFaisal Alagrafi (KI):γδ T cells reconstitution in long term survivors after hematopoietic stem cell transplantation \n\n\n\nClàudiaArasa(SU): Functional characteristics of γδ T cells in prematurity and early life\, and their response to staphylococcal enterotoxins \n\n\n\nJulius Lautenbach (KI): Systems level analysis indicates an interplay between cytophilic antibodies\, monocytes\, and γδ T cells in malaria tolerance \n\n\n\n16:15 / Drinks and Discussion (γ2 lunchroom)
URL:https://www.scilifelab.se/event/%ce%b3%ce%b4sto-workshop-mini-symposium-of-stockholms-%ce%b3%ce%b4-t-cell-community/
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/2022/03/infrastructure.png
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220413T151500
DTEND;TZID=Europe/Stockholm:20220413T164500
DTSTAMP:20260404T050731
CREATED:20220315T132014Z
LAST-MODIFIED:20220331T120240Z
UID:10000555-1649862900-1649868300@www.scilifelab.se
SUMMARY:SciLifeLab COVID-19 seminar: Jinal Bhiman and Vicent Pelechano
DESCRIPTION:Topic: Detection of virus \n\n\n\nThe second SciLifeLab COVID-19 seminar this spring starts with Jinal Bhiman\, PhD and Scientific lead for the Global Immunology and Immune Sequencing South Africa (GIISER-SA)\, talking about SARS-CoV-2 viral evolution in South Africa and hybrid immunity profiles. Vicent Pelechano\, PhD\, SciLifeLab and Wallenberg Academy Fellow and Principal Researcher at Karolinska Institutet\, then continues the seminar with his talk on Development of LAMP-based point of care strategies for simplified SARS-CoV-2 detection \n\n\n\n\n\n\n\nSchedule \n\n\n\n15:15- 16:00 – SARS-CoV-2 viral evolution in South Africa and hybrid immunity profiles                        Jinal Bhiman\, PhD and Scientific lead for the Global Immunology and Immune Sequencing South Africa (GIISER-SA)16:00-16:45 – Development of LAMP-based point of care strategies for simplified SARS-CoV-2 detection                       Vicent Pelechano\, PhD\, SciLifeLab and Wallenberg Academy Fellow and Principal Researcher at Karolinska Institutet\n\n\n\n\n\n\n\nRegistration is mandatory to get the Zoom link for the event  \n\n\n\n\nREGISTRATION\n\n\n\nBIOS & ABSTRACTS
URL:https://www.scilifelab.se/event/scilifelab-covid-19-seminar-jinal-bhiman-and-vicent-pelechano-online/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2021/05/covid_3d_model-min-1536x864-1.jpg
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220414T120000
DTEND;TZID=Europe/Stockholm:20220414T130000
DTSTAMP:20260404T050731
CREATED:20220411T093214Z
LAST-MODIFIED:20220411T093231Z
UID:10000579-1649937600-1649941200@www.scilifelab.se
SUMMARY:Campus Solna Seminar - Martin Kosar and Ryan Hull
DESCRIPTION:Welcome to 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 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 12:00-12:50 and in Air&Fire\, SciLifeLab Stockholm. \n\n\n\n\n\n\nMartin Kosar\n\n\n\nJiri Bartek-group\, alpha 5 \n\n\n\nTRole of nucleoporin Tpr in the maintenance of genomic integrity \n\n\n\n \n\n\n\n \n\n\n\n\n\nRyan Hull\n\n\n\nVicent Pelechano-group\, Gamma 5 \n\n\n\n5PSeq-TS: Capturing the degradome in humans and single-cells
URL:https://www.scilifelab.se/event/campus-solna-seminar-martin-kosar-and-ryan-hull/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220421T110000
DTEND;TZID=Europe/Stockholm:20220421T120000
DTSTAMP:20260404T050731
CREATED:20220323T161559Z
LAST-MODIFIED:20220323T161633Z
UID:10000567-1650538800-1650542400@www.scilifelab.se
SUMMARY:WGS & WTS – gamechangers in AML and ALL diagnostics
DESCRIPTION:Speaker: Manja Meggendorfer\, Head of Molecular Genetics at MLL Munich Leukemia Laboratory \n\n\n\nThe webinar is jointly organized by the Unit of Clinical Genetics at the Department of Molecular Medicine\, KI\, the Clinical Genomics platform and Genomic Medicine Sweden. \n\n\n\n \n\n\n\nRegister to receive zoom link
URL:https://www.scilifelab.se/event/wgs-wts-gamechangers-in-aml-and-all-diagnostics/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/03/Seminar_Manja-Meggendorfer.png
ORGANIZER;CN="Clinical Genomics Platform":MAILTO:marcela.davila@gu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220421T120000
DTEND;TZID=Europe/Stockholm:20220421T130000
DTSTAMP:20260404T050731
CREATED:20220420T120242Z
LAST-MODIFIED:20220420T120310Z
UID:10000585-1650542400-1650546000@www.scilifelab.se
SUMMARY:Campus Solna Seminars
DESCRIPTION:Welcome to 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 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 12:00-12:50 and in Air&Fire\, SciLifeLab Stockholm. \n\n\n\n\n\n\nOlena Berkovka\n\n\n\nJanne Lehtiö\,  alpha 1 \n\n\n\nTo stay or to leave? – (p)ppGpp signaling determines bacterial lifestyle decisions during distinct starvation conditions \n\n\n\n \n\n\n\n \n\n\n\n\n\nRuben Soares\n\n\n\nMats Nilsson\, gamma 4 \n\n\n\nLock on target: padlock probes and rolling circle amplification towards next-gen pathogen diagnostics and genotyping at the point-of-care
URL:https://www.scilifelab.se/event/66941/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220421T140000
DTEND;TZID=Europe/Stockholm:20220421T170000
DTSTAMP:20260404T050731
CREATED:20220328T144508Z
LAST-MODIFIED:20220330T181116Z
UID:10000572-1650549600-1650560400@www.scilifelab.se
SUMMARY:Career in Life Science - MTLS Networking Event
DESCRIPTION:The MTLS Alumni Network is a student-led initiative to connect current students and alumni of the Joint Master’s Programme in Molecular Techniques in Life Science (MTLS). The programme was created through a collaboration between Karolinska Institutet\, Stockholm University\, and KTH Royal Institute of Technology. Launched in 2015\, it has since reached a network of over 150 alumni and 60 current students.   \n\n\n\nAt the ‘Careers in Life Science – MTLS Networking Event’\, you will meet recruiters from biotech and pharma as well as representatives from diverse life science companies. It is a great opportunity for current students and graduates of MTLS to network and to look for employment post-grad\, summer internships\, and even master thesis projects. There will also be speakers from “alternative” life science career paths\, such as science communicators\, facility managers\, and policy makers. Getting to engage with this unique “human library” is sure to inspire you if what you are looking for is an unconventional career path in the life sciences!  \n\n\n\nAgenda \n\n\n\n14:00-17:00 Networking\, mingle with recruiters and representatives\, and “human library” speakers  \n\n\n\n15:00-16:00 Zoom Session with Illumina and Randstad in Water   \n\n\n\nRead more about the program
URL:https://www.scilifelab.se/event/career-in-life-science-mtls-networking-event/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Community
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220421T150000
DTEND;TZID=Europe/Stockholm:20220421T160000
DTSTAMP:20260404T050731
CREATED:20220330T110000Z
LAST-MODIFIED:20220421T112532Z
UID:10000573-1650553200-1650556800@www.scilifelab.se
SUMMARY:FAIRPoints-Things you need to know about Data Access Statements
DESCRIPTION:Location: Online via Zoom \n\n\n\n\n\nSee Event in your Time Zone \n\n\n\nSpeaker: Juliane Schneider & Chris Erdmann \n\n\n\nSpeakers Juliane Bio\, Chris Bio \n\n\n\nFAIRPoints is an event series highlighting pragmatic measures developed by the community towards the implementation of the FAIR (Findable\, Accessible\, Interoperable\, Reusable) data principles\, in collaboration with GoFAIR US\, SDSC\, AGU\, and SciLifeLab Data Centre.  \n\n\n\nData access statements (DAS)\, also known as data availability statements\, are key elements that can be used in multiple diverse disciplines and have a huge impact in providing essential information as it outlines where and how any underlying data may be accessed and reused\, listing specific restrictions (if any) and authorization requirements. It is therefore integral to the FAIRification process.  \n\n\n\nJoin us in this talk to discover how an effective data access statement should look like!  \n\n\n\n\n\n\n\nRegister here\n\n\n\nSign up for future events here \n\n\n\nTwitter: @FAIR_Points
URL:https://www.scilifelab.se/event/fairpoints-das/
LOCATION:Online event via Zoom
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220422T090000
DTEND;TZID=Europe/Stockholm:20220422T093000
DTSTAMP:20260404T050731
CREATED:20220330T133354Z
LAST-MODIFIED:20220405T153635Z
UID:10000575-1650618000-1650619800@www.scilifelab.se
SUMMARY:[Clinical Talks] Introduction to AI-driven image analysis in pathology: from preclinical research to clinical diagnostics
DESCRIPTION:Dr. Sami Blom leads Aiforia’s application development team with an ambition to build impactful image analysis solutions to advance histopathology. He has a background in the fields of translational cancer research and pathology and he has extensive expertise in staining and imaging methods for histology specimens. Dr. Blom joined Aiforia in 2016 to develop and advance Aiforia’s applications\, products and services. \n\n\n\nIntroduction to AI-driven image analysis in pathology: from preclinical research to clinical diagnostics \n\n\n\nAiforia equips pathologists and scientists with powerful deep learning artificial intelligence for translating images into discoveries\, decisions\, and diagnoses. The cloud based Aiforia software aims to escalate the efficiency and precision of preclinical and clinical medical image analysis from oncology to neuroscience and more. Deep learning artificial intelligence enables increased speed\, accuracy and consistency in medical image analysis.  \n\n\n\nAiforia was founded in 2013 and our mission is to provide the highest quality solutions for AI-assisted image analysis to enable personalized and democratized care for patients. Year 2021 was historic for the company: Aiforia was listed on Nasdaq Helsinki First North Market Finland in December 2021. In connection with the listing\, the Company raised approximately 29 million euros in gross assets. This\, together with the B-financing round implemented earlier in the same year\, provides a strong foundation for Aiforia’s growth. \n\n\n\nRegister to receive zoom link\n\n\n\n \n\n\n\n\n“Clinical Talks” has been renewed for yet another exciting\, innovative\, and enlightening season. This season will focus on sustainable innovations within Life Sciences\, that have the potential to contribute to a better climate friendly future for our future generations. Also new this year is that the seminar is co-organized in a collaboration between SciLifeLab and KI Innovations . \n\n\n\nSeason 5\, will be held September 2021 until March 2022 with scheduled Talks\, during Friday mornings 09-09:30 am via ZOOM (with some time-zone friendly adjustments for our international speakers). Each session consists of a talk given by our invited speaker followed by Q&A. The seminar is an open educational seminar series for our ever-expanding Life Science community.
URL:https://www.scilifelab.se/event/clinical-talks-introduction-to-ai-driven-image-analysis-in-pathology/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220425T090000
DTEND;TZID=Europe/Stockholm:20220429T153000
DTSTAMP:20260404T050731
CREATED:20220131T095506Z
LAST-MODIFIED:20220201T080802Z
UID:10000518-1650877200-1651246200@www.scilifelab.se
SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
DESCRIPTION:NBIS / ELIXIR-SE course is open for PhD students\, postdocs\, group leaders and core facility staff interested in making their computational analysis more reproducible. International applications are welcome\, but we will give approximately half of the participant slots to applicants from Swedish universities at minimum\, due to the national role NBIS plays in Sweden. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: John Sundh\, Erik Fasterius \n\n\n\nContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nAPPLICATION\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Feb 1\, 2022 \n\n\n\nApplication deadline: Mar 25\, 2022 \n\n\n\nConfirmation to accepted participants: Apr 1\, 2022 \n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2\,000 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis\, e.g. bioinformatics or computational biology\, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete\, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study\, all the code and/or computational notebooks needed to produce results from the raw data\, and the computational environment or a complete description thereof. \n\n\n\nReproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly\, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! \n\n\n\nCourse content\n\n\n\nTopics covered: \n\n\n\nGood practices for data analysisVersion control and collaborative code developmentPackage and environment managementWorkflow managementDocumentation and reportingContainerized computational environments\n\n\n\n\n\n\n\nLearning outcomesBy the end of the course the student will be able to: \n\n\n\nOrganize and structure computational projectsTrack changes and collaborate on code using GitInstall packages and manage software environments using CondaStructure computational steps into workflows with Snakemake and NextflowCreate automated reports and document their analyses with RMarkdown and JupyterPackage and distribute computational environments using Docker and Singularity\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)A computer with a webcamYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseSome knowledge in R and/or python is beneficial but not strictly required\n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 20 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.  \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/nbis-elixir-se-tools-for-reproducible-research-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220426T093000
DTEND;TZID=Europe/Stockholm:20220426T120000
DTSTAMP:20260404T050731
CREATED:20220411T114853Z
LAST-MODIFIED:20220411T115121Z
UID:10000581-1650965400-1650974400@www.scilifelab.se
SUMMARY:New developments in upstream bioprocessing technologies seminar
DESCRIPTION:Presentation och demonstration av nya single use bioreactors (SUB) för mammalieceller.  \n\n\n\nregister to attend\n\n\n\nProgram:  \n\n\n\n9:30-10:15 Matthijs Neimeijer\, Cultivating red blood cells in singe-use bioreactors \n\n\n\n10:15-10:45 Fika och demonstration \n\n\n\n10:45-11:30 Michel Kensler\, Comparisons in scale up and down scale \n\n\n\n11:30-12:00 Questions
URL:https://www.scilifelab.se/event/new-developments-in-upstream-bioprocessing-technologies-seminar/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220426T120000
DTEND;TZID=Europe/Stockholm:20220426T130000
DTSTAMP:20260404T050731
CREATED:20220411T113030Z
LAST-MODIFIED:20220411T113031Z
UID:10000580-1650974400-1650978000@www.scilifelab.se
SUMMARY:Measuring metabolites\, the building blocks of biology
DESCRIPTION:In the frame of the SciLifeLab Site Umeå / KBC Infrastructure Seminar Series\, the seminars will be organised every second Tuesday during spring 2022 in turn with IceLab Lunch Pitches. The seminars will be held in a hybrid format IRL in Glasburen\, KBC\, and online via Zoom. Take the chance to get information on facilities\, possibilities and services that infrastructure\, both SciLifeLab-associated and local\, can offer! Learn more about the seminar series and Schedule for Spring 2022 here. \n\n\n\nOn April 26th\, 12:00-13:00\, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:  \n\n\n\n“Measuring metabolites\, the building blocks of biology” \n\n\n\nby Annika Johansson\, Head of the Swedish Metabolomics Centre (SMC) facility. \n\n\n\nThe presentation will give an introduction to metabolomics and small molecule analysis by mass spectrometry. We will present our different services and also give examples of different research projects in which SMC has been involved. \n\n\n\nLearn more about the Swedish Metabolomics Centre on its homepage. \n\n\n\nSign up (latest by April 25th\, 10 a.m.) for on-site participation or follow online via Zoom: https://umu.zoom.us/j/63138997026 \n\n\n\nregistration
URL:https://www.scilifelab.se/event/measuring-metabolites-the-building-blocks-of-biology/
LOCATION:Glasburen Seminar Room\, Chemical Biological Centre (KBC) Building\, Umeå University\, Umeå\, 901 87\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Ume%C3%A5":MAILTO:umea@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220427T080000
DTEND;TZID=Europe/Stockholm:20220429T170000
DTSTAMP:20260404T050731
CREATED:20220125T121449Z
LAST-MODIFIED:20220128T090507Z
UID:10000517-1651046400-1651251600@www.scilifelab.se
SUMMARY:Workshop on Data Visualization in R - Lund
DESCRIPTION:National course open for PhD students (prioritized)\, postdocs\, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus Ringner \n\n\n\nContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\naPPLY HERE\n\n\n\n\n\n\n\n\n\nCOURSE WEBSITE\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jan 31\, 2022 \n\n\n\nApplication deadline: Mar 18\, 2022 \n\n\n\nConfirmation to accepted participants: Mar 25\, 2022 \n\n\n\nCourse fee\n\n\n\nThis training event has no fee. However\, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nCourse description\n\n\n\nThis course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data. \n\n\n\nCourse content\n\n\n\nIn this course you will learn how to visualize your data in R. \n\n\n\nIn particular\, you will learn: \n\n\n\n·          how to format the data necessary for ggplot \n\n\n\n·          how to make bar-charts\, box-plots and others using ggplot \n\n\n\n·          how to make PCA plots in ggplot \n\n\n\n·          how to use R packages for heatmaps \n\n\n\n·          how to plot data on maps using R (optional) \n\n\n\n·          how to plot and handle phylogenetic trees in R (optional) \n\n\n\n·          how to make interactive plots in R using Rshiny \n\n\n\n·          how to host a Rshiny app in one of the available servers \n\n\n\nLearning outcomes\n\n\n\nBy the end of the course the participant will be able to: \n\n\n\n·          handle data in R for visualizations \n\n\n\n·          apply the grammar efficiently in ggplot to get the desired plot \n\n\n\n·          combine different data and/or different plots that are of publication-grade \n\n\n\n·          write your own simple Rshiny app \n\n\n\n·          deploy Rshiny apps in public servers.  \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\nfamiliarity with using R and Rstudioa computer with R and Rstudioyou will be asked to install different R packages necessary for the course prior to the course. \n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 25 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry. \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.
URL:https://www.scilifelab.se/event/workshop-on-data-visualization-in-r-lund/
LOCATION:Retina D227\, Biologihuset\, Sölvegatan 35\, Lund\, 223 62
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220427T140000
DTEND;TZID=Europe/Stockholm:20220427T153000
DTSTAMP:20260404T050731
CREATED:20220420T102001Z
LAST-MODIFIED:20220420T102506Z
UID:10000584-1651068000-1651073400@www.scilifelab.se
SUMMARY:Developmental origins of cell heterogeneity in the human lung
DESCRIPTION:HDCA Seminar Series 2022 | Lung \nChristo Samakovlis and Alexandros Sountoulidis \nThe lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity\, we created a first comprehensive topographic atlas of early human lung development. We report 83 cell states\, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatial transcriptomics into a web-based\, open platform for interactive exploration. To illustrate the utility of our approach we show distinct states of secretory and neuroendocrine cells\, largely overlapping with the programs activated either during lung fibrosis or small cell lung cancer progression. We define the origin of uncharacterized airway fibroblasts associated with airway smooth muscle in bronchovascular bundles\, and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases. \n  \n– \nHuman developmental cell atlas (HDCA) is the Swedish effort within the human cell atlas (HCA)\, one of the largest international scientific projects. The project aim is to create a comprehensive molecular atlas of human prenatal development at the molecular resolution using state-of-the-art multi-omic technologies such as single-cell RNA-seq\, Spatial Transcriptomics\, in situ sequencing in order to provide deeper insight into how variations and deviations contribute to health and disease. \nThe HDCA Seminar Series 2022 invites you to join us on a journey of early human organogenesis of several organs at the single-cell and spatial resolution. Seminars will be held at SciLifeLab Gamma building on Wednesdays at 14:00 or 15:00 and also via Zoom. After each seminar\, we will have up to 30 min round up discussions with the speaker on how you can contribute to the atlas!  \nWarm Welcome! \n  \n\n\nregistration
URL:https://www.scilifelab.se/event/developmental-origins-of-cell-heterogeneity-in-the-human-lung/
LOCATION:Gamma 2 Lunchroom\, SciLifeLab\, Tomtebodavägen 23\, Solna\, Sweden
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/04/logo_hdca2.png
ORGANIZER;CN="The Human Developmental Cell Atlas":MAILTO:hdca-sweden@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220428T080000
DTEND;TZID=Europe/Stockholm:20220429T170000
DTSTAMP:20260404T050731
CREATED:20220308T124733Z
LAST-MODIFIED:20220308T142609Z
UID:10000547-1651132800-1651251600@www.scilifelab.se
SUMMARY:Nordic Precision Medicine Forum
DESCRIPTION:Just prior to the pandemic Sweden launched its first ever national Life Science Strategy in eight priority areas covering the strengthening of academic research\, facilitating collaboration between academia and industry\, attracting more industry initiated clinical trials\, and the continuous skills development needed for precision medicine and highly advanced production of pharmaceuticals and medtech devices. Across the Nordic countries precision medicine and technology developments continue at pace\, truly putting them in a favourable position when it comes to taking on the opportunities and challenges of implementing precision medicine\, with its promise to really transform future healthcare as well as the entire life science sector. \n\n\n\nSince 2016 we have convened the regions leading scientists\, healthcare practitioners\, and industry pioneers at our annual meeting. For 2022 you can expect a whole lot more interaction as we finally get back to in-person events. \n\n\n\nRead more\n\n\n\nWe very much hope to see you in Stockholm in April 2022 and hope that you and your loved ones remain safe and healthy throughout these troubling times.
URL:https://www.scilifelab.se/event/nordic-precision-medicine-forum/
LOCATION:Hotel Birger Jarl\, Birger Jarlsgatan 61\, Stockholm\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220428T120000
DTEND;TZID=Europe/Stockholm:20220428T130000
DTSTAMP:20260404T050731
CREATED:20220421T115540Z
LAST-MODIFIED:20220421T115541Z
UID:10000589-1651147200-1651150800@www.scilifelab.se
SUMMARY:Campus Solna Seminars
DESCRIPTION:Welcome to 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 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 12:00-12:50 and in Air&Fire\, SciLifeLab Stockholm. \n\n\n\n\n\n\nCasper Winsnes\n\n\n\nEmma Lundberg\,  alpha 2 \n\n\n\nMulti-scale mapping of cell structures using protein images and interactions \n\n\n\n \n\n\n\n \n\n\n\n\n\nSergio Perez Conesa\n\n\n\nLucie Delemotte\, gamma 3 \n\n\n\nK-Ion channel inactivation and lipid dependence through free energy surfaces
URL:https://www.scilifelab.se/event/campus-solna-seminars/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220428T170000
DTEND;TZID=Europe/Stockholm:20220428T190000
DTSTAMP:20260404T050731
CREATED:20220420T143019Z
LAST-MODIFIED:20220420T143132Z
UID:10000587-1651165200-1651172400@www.scilifelab.se
SUMMARY:Matchmaking Event – Data Science and Medical/Clinical Research
DESCRIPTION:Welcome to a matchmaking event between researchers within Data Science and Medical/Clinical research at KTH and Region Stockholm. The event is related to the project call: Health\, Medicine and Technology 2023. \n\n\n\nRead more\n\n\n\nRegion Stockholm and KTH opened the yearly call for collaboration in Health\, Medicine and Technology 14 April\, 2022. A key requirement to apply for this call is that one of the partners should be from KTH and one from Region Stockholm. With this event\, we hope to encourage collaborations between experts in data science and clinical research\, at KTH and Region Stockholm. The event is open for all researchers from KTH and from Region Stockholm who are eligible to submit a grant proposal for the Health\, Medicine and Technology Project Call. Postdoctoral researchers who can be co-PI are also encouraged to attend the event. Should you have any questions\, please contact: lifescienceplatform@kth.se ordigitalizationplatform@kth.se \n\n\n\nThe event is organised by the KTH Life Science Platform and KTH Digitalization Platform
URL:https://www.scilifelab.se/event/matchmaking-event-data-science-and-medical-clinical-research/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Event
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220429T140000
DTEND;TZID=Europe/Stockholm:20220429T150000
DTSTAMP:20260404T050731
CREATED:20220315T091430Z
LAST-MODIFIED:20220315T134837Z
UID:10000553-1651240800-1651244400@www.scilifelab.se
SUMMARY:AI-driven genomic precision diagnostics in hematologic malignancies
DESCRIPTION:In this webinar\, jointly organized by the Clinical Genomics platform and Genomic Medicine Sweden\, Dr. Aziz Nazha will present AI-based solutions to improve the diagnosis\, prognosis\, and selection of therapy in hematologic malignancies. The talk will also cover the clinical implication of AI/ML in diagnostic hematology\, current challenges and potential future opportunities. \n\n\n\n\n\n\n\nRegister to receive zoom link\n\n\n\n\n\n\n\nHost: Thoas Fioretos\, Director Clinical Genomics platform \n\n\n\nShort bio:  Aziz Nazha\, MD\, is currently a Global Tech Business Development for Healthcare Solutions at Amazon Web Services. Prior to joining Amazon\, Dr. Nazha was the director of the Cleveland Clinic Center for Clinical Artificial Intelligence and an Associate Medical Director at Enterprise Analytics. He is also an internationally recognized expert in treating patients with leukemia. His research focuses on the use of artificial intelligence\, machine learning\, and deep learning to translate genomic and complex healthcare data into useful clinical tools that can improve patient outcomes.
URL:https://www.scilifelab.se/event/ai-driven-genomic-precision-diagnostics-in-hematologic-malignancies/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/03/Banner-Clinical-Genomics-GMS.jpg
ORGANIZER;CN="Clinical Genomics Platform":MAILTO:marcela.davila@gu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220502T080000
DTEND;TZID=Europe/Stockholm:20220506T170000
DTSTAMP:20260404T050731
CREATED:20220224T100439Z
LAST-MODIFIED:20220224T131919Z
UID:10000535-1651478400-1651856400@www.scilifelab.se
SUMMARY:Spatial analysis of gene expression in tissues
DESCRIPTION:Single-cell genomics technologies have become widely used to study heterogeneous and dynamic biological systems. In order to meet the growing demand for a deeper understanding of tissue profiling\, a number of different spatial transcriptomics approaches have been developed and applied successfully. \n\n\n\nThe goal of this practical course is to provide participants with an overview of the different spatially resolved transcriptome mapping techniques\, learn about the differences and advantages of each technique\, and how to choose and employ the techniques when designing their study. \n\n\n\nThe course includes practical work with hands-on wet-lab work and imaging sessions as well as primary data analysis for three technologies in two practical formats: Visium/Spatial Transcriptomics (ST) as an unbiased method\, and In Situ Sequencing (ISS)/Scrinshot as targeted methods. \n\n\n\nThe lectures will cover the following topics: Visium/ST\, ISS/Scrinshot\, osmFISH\, seqFISH+\, Slide-seqV2\, MERFISH\, CellPhoneDB as well as Human Cell Atlas. \n\n\n\nThe course is aimed at the graduate student and postdoctoral level\, but applications from scientists at all levels are welcome.Registration deadline: 18 March \n\n\n\nRead more and register\n\n\n\n\n\n\n\nCourse Flyer
URL:https://www.scilifelab.se/event/spatial-analysis-of-gene-expression-in-tissues/
LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden
CATEGORIES:Course
ORGANIZER;CN="Joakim Lundeberg":MAILTO:joakim.lundeberg@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220502T151500
DTEND;TZID=Europe/Stockholm:20220502T161500
DTSTAMP:20260404T050731
CREATED:20220422T104856Z
LAST-MODIFIED:20220422T111337Z
UID:10000590-1651504500-1651508100@www.scilifelab.se
SUMMARY:The use of systems biology in treatment of liver diseases
DESCRIPTION:Adil Mardinoglu\, Assoc. Prof.KTH SwendenKing s College London\, UK\n\n\n\n \n\n\n\nRegister here to get the zoom link\n\n\n\nAssoc. Prof. Adil Mardinoglu is an expert in the field of Systems Medicine\, Systems Biology\, Computational Biology and Bioinformatics. He lead a team of 25 researchers working in the area of computational biology\, experimental biology and drug development to develop new treatment strategies for Metabolic diseases\, Neurodegenerative diseases and certain type of cancers  \n\n\n\n Abstract: Biological networks can provide a scaffold for studying biological pathways operating in the liver in connection with disease development in a systematic manner. In my presentation\, I will present our recent work where biological networks have been employed to identify the reprogramming in liver physiology in response to NASH/NAFLD. I will further discuss how this mechanistic modelling approach can contribute to the discovery of biomarkers and identification of drug targets which may lead to design of targeted and effective personalized medicine. \n\n\n\nWebpage: https://sysmedicine.com/
URL:https://www.scilifelab.se/event/adil-mardinoglu/
LOCATION:Online event via Zoom
CATEGORIES:Event
ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20220503T090000
DTEND;TZID=Europe/Stockholm:20220503T120000
DTSTAMP:20260404T050731
CREATED:20220121T160156Z
LAST-MODIFIED:20220121T160157Z
UID:10000514-1651568400-1651579200@www.scilifelab.se
SUMMARY:BioImage Analysis support - Call4Help
DESCRIPTION:Every 1st week of the month (mainly on Tuesdays\, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI\, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate. \n\n\n\nThe ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji\, CellProfiler\, QuPath\, Ilastik\, KNIME)\, but also commercial systems\, if needed (Imaris). \n\n\n\nThe Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM. \n\n\n\nHow to participate? \n\n\n\nStep1: \n\n\n\nPrepare a short presentation (5-7 min)  – use the following template for your presentation: \n\n\n\nhttp://bit.ly/BIIF_C4H_slideTemplate \n\n\n\nSlide template by NEUBIAS/ScopeM \n\n\n\nStep2: \n\n\n\na) Upload your presentation \n\n\n\nUpload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nb) Upload example images for testing. \n\n\n\nUpload example images for testing either to the drive of your choice or our Call4Help google drive above. \n\n\n\nhttp://bit.ly/BIIF_C4H_Drive \n\n\n\nc) Register by filling out the registration form: \n\n\n\nhttp://bit.ly/BIIF_C4H_Registration \n\n\n\nStep 3: \n\n\n\nJoin the zoom-session. \n\n\n\nIf your problem is selected for presentation\, you will get a time-slot of 30 – 60 minutes within the session. \n\n\n\nWhat are the Deadlines \n\n\n\nSubmission of a problem and upload of example data: Friday the week before the session. \n\n\n\nNotification about participation: The day before the session. \n\n\n\nNext Call4Help session \n\n\n\nTuesday\, May 3\, 2022\, 9.00-12.00. Deadline for application: Friday\, April 29\, 2022.
URL:https://www.scilifelab.se/event/bioimage-analysis-support-call4help-4/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
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END:VCALENDAR