BEGIN:VCALENDAR VERSION:2.0 PRODID:-//SciLifeLab - ECPv6.15.18//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-WR-CALNAME:SciLifeLab X-ORIGINAL-URL:https://www.scilifelab.se X-WR-CALDESC:Events for SciLifeLab REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/Stockholm BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20200329T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20201025T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20210328T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20211031T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20221030T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210915T151500 DTEND;TZID=Europe/Stockholm:20210915T164500 DTSTAMP:20260403T230832 CREATED:20210907T145743Z LAST-MODIFIED:20210909T064420Z UID:10000440-1631718900-1631724300@www.scilifelab.se SUMMARY:SciLifeLab COVID-19 seminars: Cornelis Melief and Sara Mangsbo DESCRIPTION:The second seminar in this series starts with Cornelis Melief\, Emeritus professor of immunology at Leiden University and Chief Scientific Officer (CSO) of ISA Pharmaceuticals\, who will talk about T cell-based vaccination against SARS-CoV-2. \n\n\n\nSara Mangsbo\, Senior lecturer in Antibody drugs and Associate professor in Experimental clinical immunology\, Uppsala University\, then continues the seminar by talking about T cell responses to SARS-CoV-2\, what have we learned so far? \n\n\n\nHost:  Alice Sollazzo\, Project coordinator\, SciLifeLab Operations Office \n\n\n\n\n\n\n\nRegistration is mandatory to get the Zoom link for the event \n\n\n\n\n\n\n\n\nREGISTRATION\n\n\n\n\n\n\n\n\nProgram\n\n\n\n15:15T cell-based vaccination against SARS-CoV-2 Cornelis Melief\, Emeritus professor of immunology at Leiden University16:00T cell responses as SARS-CoV-2\, what have we learned so far? Sara Mangsbo\, Senior lecturer in Antibody drugs\, Uppsala University\n\n\n\nBios and abstracts\n\n\n\nDownload:Download URL:https://www.scilifelab.se/event/scilifelab-covid-19-seminars-cornelis-melief-and-sara-mangsbo/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210914T130000 DTEND;TZID=Europe/Stockholm:20210914T150000 DTSTAMP:20260403T230832 CREATED:20210826T065213Z LAST-MODIFIED:20210914T065424Z UID:10000415-1631624400-1631631600@www.scilifelab.se SUMMARY:The future of life science is data-driven - DDLS update and strategy DESCRIPTION:Welcome\n\n\n\nto an online meeting where the Data-driven Life Science (DDLS) strategy will be introduced and discussed. The SciLifeLab and Wallenberg National Program on Data-Driven Life Science (DDLS) program’s ongoing activities and progress of the program will also be presented.   \n\n\n\nAim\n\n\n\nThe purpose of the meeting is to introduce and discuss the DDLS strategy; to present ongoing activities and program achievements; and to engage community and stakeholders. The aim of the panel discussion and input from participants is to facilitate further development of the strategy.   \n\n\n\nTarget group\n\n\n\nWe welcome partner organizations\, collaborators nationally\, the Swedish life science community\, industry\, healthcare as well as other stakeholders in the society at large.   \n\n\n\nProgram\n\n\n\nWelcome wordsOlli Kallioniemi\, Director of SciLifeLab and DDLS program and Siv Andersson\, KAWThe initiative and its importanceHans Adolfsson\, vice-chancellor Umeå University\, chairman of HuvudmannarådetEuropean perspective\, experience from EMBLJan Korbel\, Senior Scientist Genome Biology & Head of Data Science\, EMBL HeidelbergDDLS update and presentation of DDLS strategyOlli Kallioniemi DDLS research areasEvolution and Biodiversity: Fredrik RonquistPrecision Medicine and Diagnostics: Janne LehtiöCell and Molecular Biology: Emma LundbergEpidemiology and Infection Biology: Oliver BillkerData processJohan Rung\, Head of SciLifeLab Data centrePanel discussion​​Moderator: Anna Frejd\, Communications manager\, SciLifeLabClosing wordsOlli Kallioniemi and Siv Andersson\n\n\n\n\n\n\n\nRead the strategy\n\n\n\nShare your thoughts on the strategy URL:https://www.scilifelab.se/event/the-future-of-life-science-is-data-driven-ddls-update-and-strategy/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2020/10/Map-DDLS-illustration_dove.png ORGANIZER;CN="Data-Driven Life Science @ SciLifeLab":MAILTO:ddls@scilifelab.se LOCATION:https://www.scilifelab.se/event/the-future-of-life-science-is-data-driven-ddls-update-and-strategy/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210913T161500 DTEND;TZID=Europe/Stockholm:20210913T173000 DTSTAMP:20260403T230832 CREATED:20210830T090518Z LAST-MODIFIED:20210907T143831Z UID:10000419-1631549700-1631554200@www.scilifelab.se SUMMARY:The Svedberg seminar series: Dr. Aviv Regev DESCRIPTION:Genentech\, USA \n\n\n\nHost: Erik Sonnhammer \, Stockholm University \n\n\n\nZOOM LINK \n\n\n\n\n\n\n\n\n\nAviv Regev is a leader in deciphering molecular circuits that govern cells\, tissues and organs in health and their malfunction in disease. Her lab has pioneered foundational experimental and computational methods in single-cell genomics\, working toward greater understanding of the function of cells and tissues in health and disease\, including autoimmune disease\, inflammation and cancer \n\n\n\nCell atlases as roadmaps in health and disease\n\n\n\nCells are the basic unit of life\, and form a key intermediate between genotype and phenotype\, that is essential to explain how the gene variants that contribute to disease risk act. The recent advent of methods for high-throughput single-cell and spatial profiling has opened the way to create a human cells atlas: comprehensive reference maps of all human cells as a basis for both understanding human health and diagnosing\, monitoring\, and treating disease. From such maps we recovered rich aspects of biology\, including cell types and states\, differentiation and other temporal processes\, gene programs\, the physical location and interactions between cells\, the underlying regulatory circuits\, and even the possibility of predicting cell types and behaviors\, towards a “periodic table of our cells”. These\, in turn give us a new vocabulary for disease studies to determine the way in which cells do disease genes act\, which cells are disrupted in disease\, which programs change in them\, what mechanisms underlie their (dis)regulation\, how their cell-cell communications affected\, and what would be the impact of therapies. In this talk\, I will focus on how atlases help us to understand the relation between genotype to phenotype\, especially in the context of human genetics and disease\, from cells\, to programs\, to deciphering individual gene functions\, using single cell genomics as a conceptual and technical framework\, in complex disease\, cancer\, and COVID-19.Read more about Prof. Regev´s research HERE URL:https://www.scilifelab.se/event/the-svedberg-seminar-series-prof-regev-aviv/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210910T140000 DTEND;TZID=Europe/Stockholm:20210910T150000 DTSTAMP:20260403T230832 CREATED:20210827T111618Z LAST-MODIFIED:20210909T122507Z UID:10000418-1631282400-1631286000@www.scilifelab.se SUMMARY:BiG Talks - Network-based integration and visualization of large-scale data DESCRIPTION:BiG Talks: Integrative Omics\n\n\n\nArranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development \n\n\n\nThe Bioinformatics and Genomics seminar series (“BiG Talks”) is an initiative arranged by the SciLifeLab platforms for Bioinformatics (NBIS)\, Genomics (NGI) and Clinical Genomics platform. The seminar series aims to give inspiration to the SciLifeLab community and to create new networking possibilities. Each event will be broadcasted over Zoom where you will be able to interact with the speakers\, and live broadcasted at the SciLifeLab YouTube channel.  \n\n\n\nIn this seminar series\, run in parallel with the ELIXIR-SE / NBIS workshop in Omics Integration and Systems Biology\, we will be broadcasting three seminars about research and tools for integration of omics data through systems biology approaches\, in humans and model organisms. Please use the following link to register and access the Zoom link: \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nMetabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info: See below \n\n\n\n\n\n\n\n\n\n\nNetwork-based integration and visualization of large-scale data\n\n\n\nDr. Lars Juhl Jensen\, Group Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nAbstract \n\n\n\nNetworks are a powerful abstraction for modeling and visualizing the interplay between the many proteins within a cell. In this lecture\, I will first introduce the STRING database\, which uses the network abstraction to integrate a wide range of evidence types for physical protein interactions and functional association. This includes predicted interactions\, interactions from other public databases\, and automatic text mining of the biomedical literature. I will show a common use case of STRING\, namely network-based visualization of omics data via the Cytoscape stringApp. \n\n\n\nBiography \n\n\n\nDr. Lars Juhl Jensen started his research career in Søren Brunak’s group at the Technical University of Denmark (DTU)\, from where he in 2002 received the Ph.D. degree in bioinformatics for his work on non-homology-based protein function prediction. During this time\, he also developed methods for visualization of microbial genomes\, pattern recognition in promoter regions\, and microarray analysis. From 2003 to 2008\, he was at the European Molecular Biology Laboratory (EMBL) where he worked on literature mining\, integration of large-scale experimental datasets\, and analysis of biological interaction networks. Since 2009\, he has continued this line of research as a professor at the Novo Nordisk Foundation Center for Protein Research at the Panum Institute in Copenhagen and as a founder\, owner and scientific advisor of Intomics A/S. He is a co-author of more than 200 scientific publications that have in total received more than 40\,000 citations. He was awarded the Lundbeck Foundation Talent Prize in 2003\, his work on cell-cycle research was named “Break-through of the Year” in 2006 by the magazine Ingeniøren\, his work on text mining won the first prize in the “Elsevier Grand Challenge: Knowledge Enhancement in the Life Sciences” in 2009\, and he was awarded the Lundbeck Foundation Prize for Young Scientists in 2010. Homepage: https://jensenlab.org/ \n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nDate: September 10\, 14:00 – 15:00 CET online on Zoom \n\n\n\nBroadcast link (live event): SciLifeLab YouTube channel  \n\n\n\n \n\n\n\n \n\n\n\nRegistration form for zoom link URL:https://www.scilifelab.se/event/big-talks-3/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210910T130000 DTEND;TZID=Europe/Stockholm:20210910T150000 DTSTAMP:20260403T230832 CREATED:20210910T060532Z LAST-MODIFIED:20210910T081453Z UID:10000444-1631278800-1631286000@www.scilifelab.se SUMMARY:BiG Talks - Integrative Omics DESCRIPTION:Arranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development.\n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nThe Bioinformatics and Genomics seminar series (“BiG Talks”) is an initiative arranged by the SciLifeLab platforms for Bioinformatics (NBIS)\, Genomics (NGI) and Clinical Genomics platform. The seminar series aims to give inspiration to the SciLifeLab community and to create new networking possibilities. Each event will be broadcasted over Zoom where you will be able to interact with the speakers\, and live broadcasted at the SciLifeLab YouTube channel.  \n\n\n\nIn this seminar series\, run in parallel with the ELIXIR-SE / NBIS workshop in Omics Integration and Systems Biology\, we will be broadcasting three seminars about research and tools for integration of omics data through systems biology approaches\, in humans and model organisms. Please use the following link to register and access the Zoom link. \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nThe Metabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info\, see below \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info\, see below \n\n\n\n\n\n\nMetabolic Atlas: Genome-scale metabolic models for easy browsing and analysis\n\n\n\nMihail Anton\, Project Manager for Metabolic Atlas\, NBIS / Chalmers University of Technology\, Sweden \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 be centred on showcasing how Metabolic Atlas is aiding discovery of disease-related alterations of metabolism by contributing to this ecosystem. \n\n\n\nMetabolic Atlas integrates open-source GEMs of several model organisms\, and provides visualisations for these\, such as the Map Viewer via the manually curated 2D maps and the automatically generated 3D maps\, and the gene- and metabolite-centric Interaction Partners. In concert with other supporting features\, Metabolic Atlas is making open source genome-scale metabolic models easy to browse and analyse. \n\n\n\nThe talk will also promote a way to organise a model in a git repository\, the model test suite Memote\, and how this and other automations can be deployed on GitHub\, with the ultimate purpose of facilitating transparent community curation. \n\n\n\nBiography: In his role as project manager for Metabolic Atlas\, Mihail has been watching and contributing to the infrastructure supporting the development and community curation of genome scale metabolic models. Homepage: https://nbis.se/about/staff/mihail-anton/ \n\n\n\nDate: September 10\, 13:00 – 14:00 CET online on Zoom \n\n\n\nregistration for both talks\n\n\n\n\n\n\n\nNetwork-based integration and visualization of large-scale data\n\n\n\nDr. Lars Juhl Jensen\, Group Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nAbstract \n\n\n\nNetworks are a powerful abstraction for modeling and visualizing the interplay between the many proteins within a cell. In this lecture\, I will first introduce the STRING database\, which uses the network abstraction to integrate a wide range of evidence types for physical protein interactions and functional association. This includes predicted interactions\, interactions from other public databases\, and automatic text mining of the biomedical literature. I will show a common use case of STRING\, namely network-based visualization of omics data via the Cytoscape stringApp. \n\n\n\nBiography \n\n\n\nDr. Lars Juhl Jensen started his research career in Søren Brunak’s group at the Technical University of Denmark (DTU)\, from where he in 2002 received the Ph.D. degree in bioinformatics for his work on non-homology-based protein function prediction. During this time\, he also developed methods for visualization of microbial genomes\, pattern recognition in promoter regions\, and microarray analysis. From 2003 to 2008\, he was at the European Molecular Biology Laboratory (EMBL) where he worked on literature mining\, integration of large-scale experimental datasets\, and analysis of biological interaction networks. Since 2009\, he has continued this line of research as a professor at the Novo Nordisk Foundation Center for Protein Research at the Panum Institute in Copenhagen and as a founder\, owner and scientific advisor of Intomics A/S. He is a co-author of more than 200 scientific publications that have in total received more than 40\,000 citations. He was awarded the Lundbeck Foundation Talent Prize in 2003\, his work on cell-cycle research was named “Break-through of the Year” in 2006 by the magazine Ingeniøren\, his work on text mining won the first prize in the “Elsevier Grand Challenge: Knowledge Enhancement in the Life Sciences” in 2009\, and he was awarded the Lundbeck Foundation Prize for Young Scientists in 2010. Homepage: https://jensenlab.org/ \n\n\n\nDate: September 10\, 14:00 – 15:00 CET online on Zoom \n\n\n\nregistration for both talks URL:https://www.scilifelab.se/event/big-talks/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210910T130000 DTEND;TZID=Europe/Stockholm:20210910T135500 DTSTAMP:20260403T230832 CREATED:20210827T111000Z LAST-MODIFIED:20210909T122434Z UID:10000417-1631278800-1631282100@www.scilifelab.se SUMMARY:BiG Talks - Metabolic Atlas: genome-scale metabolic models for easy browsing and analysis DESCRIPTION:BiG Talks: Integrative Omics\n\n\n\nArranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development \n\n\n\nThe Bioinformatics and Genomics seminar series (“BiG Talks”) is an initiative arranged by the SciLifeLab platforms for Bioinformatics (NBIS)\, Genomics (NGI) and Clinical Genomics platform. The seminar series aims to give inspiration to the SciLifeLab community and to create new networking possibilities. Each event will be broadcasted over Zoom where you will be able to interact with the speakers\, and live broadcasted at the SciLifeLab YouTube channel.  \n\n\n\nIn this seminar series\, run in parallel with the ELIXIR-SE / NBIS workshop in Omics Integration and Systems Biology\, we will be broadcasting three seminars about research and tools for integration of omics data through systems biology approaches\, in humans and model organisms. Please use the following link to register and access the Zoom link: \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nThe Metabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info\, see below \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info \n\n\n\n\n\n\n\n\n\n\nMetabolic Atlas: Genome-scale metabolic models for easy browsing and analysis\n\n\n\nMihail Anton\, Project Manager for Metabolic Atlas\, NBIS / Chalmers University of Technology\, Sweden \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 be centred on showcasing how Metabolic Atlas is aiding discovery of disease-related alterations of metabolism by contributing to this ecosystem. \n\n\n\nMetabolic Atlas integrates open-source GEMs of several model organisms\, and provides visualisations for these\, such as the Map Viewer via the manually curated 2D maps and the automatically generated 3D maps\, and the gene- and metabolite-centric Interaction Partners. In concert with other supporting features\, Metabolic Atlas is making open source genome-scale metabolic models easy to browse and analyse. \n\n\n\nThe talk will also promote a way to organise a model in a git repository\, the model test suite Memote\, and how this and other automations can be deployed on GitHub\, with the ultimate purpose of facilitating transparent community curation. \n\n\n\nBiography: In his role as project manager for Metabolic Atlas\, Mihail has been watching and contributing to the infrastructure supporting the development and community curation of genome scale metabolic models. Homepage: https://nbis.se/about/staff/mihail-anton/ \n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nDate: September 10\, 13:00 – 13:55 CET online on Zoom \n\n\n\nBroadcast link (live event): SciLifeLab YouTube channel \n\n\n\n \n\n\n\nRegistration form for zoom link URL:https://www.scilifelab.se/event/big-talks-2/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210909T130000 DTEND;TZID=Europe/Stockholm:20210909T140000 DTSTAMP:20260403T230832 CREATED:20210824T114020Z LAST-MODIFIED:20210824T114023Z UID:10000411-1631192400-1631196000@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Jaromir Mikes and Niklas Sandström DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 13:00-13:50 and following current regulations\, they will be broadcast via zoom. \n\n\n\n \n\n\n\nThis week\n\n\n\nMinimizing technical variance by improved whole blood sampling protocol leads to better data and more interesting scienceJaromir Mikes (Petter Brodin\, alpha 1)  \n\n\n\n \n\n\n\nLab-on-chip for drug toxicology and cell cytotoxicity assaysNiklas Sandström (Björn Önfelt\, gamma 3) \n\n\n\nRegistration\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. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-jaromir-mikes-and-niklas-sandstrom/ CATEGORIES:Community ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210909T090000 DTEND;TZID=Europe/Stockholm:20210909T093000 DTSTAMP:20260403T230832 CREATED:20210903T140828Z LAST-MODIFIED:20210906T140903Z UID:10000438-1631178000-1631179800@www.scilifelab.se SUMMARY:Clinical Talks: From BMC to Wall Street DESCRIPTION:After our recent planning hiatus\, we now have the great pleasure to announce that “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 until December 2021 with a total of seven 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. \n\n\n\nRead more about the clinical talk series here\n\n\n\n\n\n\n\n\n \n\n\n\n\n\nDr. Andrea Ballagi\, Olink Proteomics VP Sales and Marketing \n\n\n\nAndrea Ballagi has an MD from Semmelweis School of Medicine in Budapest\, a PhD in Cancer research from Ludwig Institute for Cancer Research in Uppsala and a MBA from Uppsala University. She started her industry career at IDEXX Laboratories located in Switzerland as a general manager and later moved back to Uppsala as a global technical service and product line manager in 2011. Andrea joined Olink in 2012 as director of commercial operations and has since been a major part of the company’s expansive growth phases. She currently serves as VP Sales and Marketing EMEA. \n\n\n\nAndrea has with her roots as an MD a real passion to change the way diagnostics is being conducted to in today’s clinical reality. By bringing in groundbreaking technological possibilities and unprecedented future treatment options made possible by the extensive Olink technological platform. \n\n\n\n\n\n\n\n\n\n\n\n\n\nDr. Simon Fredriksson\, Co-Founder Olink \n\n\n\nSimon Fredriksson has a PhD in Molecular Medicine from Uppsala University and conducted postdoctoral studies in biochemistry at Stanford University\, and most recently appointed Adjunct Professor at KTH. He is also the co-founder of Olink\, and both former CSO\, and CEO of the company in its formation and growth phases. His academic research resulted in multiple high impact publications and inventions that were commercialized into products. Most notably the Proximity-Ligation and -Extension assays for multiplex protein detection\, the main products of Olink Proteomics. \n\n\n\nIn 2015\, Simon co-founded and was the former CEO of Genagon Therapeutics\, a ground-breaking immuno-oncology company. Presently co-founder and CEO of Pixelgen Technologies\, and Partner in Colibri Ventures\, a premier life science business incubator\, that helps start-ups develop early ideas into successful companies faster and more efficient. Simon also has extensive board member experience from 9 years at Olink AB (partly exited to Nexttobe 2011)\, Biolamina AB (+6 years)\, Olink Proteomics AB (exited to Summa Equity 2019)\, and Cartana AB (exited to 10X Genomics 2020) and Genagon Therapeutics. \n\n\n\nAs an experienced life science entrepreneur\, researcher and inventor spanning from research tools to bio-therapeutics\, Simon has always been fascinated by technology innovation capable of pushing the frontiers of scientific discovery into new and unchartered territories. \n\n\n\n\n\n\n\n\n\n\n\n \n\n\n\nRegister to receive zoom link URL:https://www.scilifelab.se/event/clinical-talks-from-bmc-to-wall-street/ CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2021/09/ClinicalTalks_Season5_twitter_1024.jpg ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210909T090000 DTEND;TZID=Europe/Stockholm:20210909T093000 DTSTAMP:20260403T230832 CREATED:20210830T154920Z LAST-MODIFIED:20210903T142012Z UID:10000421-1631178000-1631179800@www.scilifelab.se SUMMARY:Clinical Talks: From BMC to Wall Street DESCRIPTION:After our recent planning hiatus\, we now have the great pleasure to announce that “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 until December 2021 with a total of seven 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. \n\n\n\nRead more about the clinical talk series here\n\n\n\n\n\n\n\n\n \n\n\n\n\n\nDr. Andrea Ballagi\, Olink Proteomics VP Sales and Marketing \n\n\n\nAndrea Ballagi has an MD from Semmelweis School of Medicine in Budapest\, a PhD in Cancer research from Ludwig Institute for Cancer Research in Uppsala and a MBA from Uppsala University. She started her industry career at IDEXX Laboratories located in Switzerland as a general manager and later moved back to Uppsala as a global technical service and product line manager in 2011. Andrea joined Olink in 2012 as director of commercial operations and has since been a major part of the company’s expansive growth phases. She currently serves as VP Sales and Marketing EMEA. \n\n\n\nAndrea has with her roots as an MD a real passion to change the way diagnostics is being conducted to in today’s clinical reality. By bringing in groundbreaking technological possibilities and unprecedented future treatment options made possible by the extensive Olink technological platform. \n\n\n\n\n\n\n\n\n\n\n\n\n\nDr. Simon Fredriksson\, Co-Founder Olink \n\n\n\nSimon Fredriksson has a PhD in Molecular Medicine from Uppsala University and conducted postdoctoral studies in biochemistry at Stanford University\, and most recently appointed Adjunct Professor at KTH. He is also the co-founder of Olink\, and both former CSO\, and CEO of the company in its formation and growth phases. His academic research resulted in multiple high impact publications and inventions that were commercialized into products. Most notably the Proximity-Ligation and -Extension assays for multiplex protein detection\, the main products of Olink Proteomics. \n\n\n\nIn 2015\, Simon co-founded and was the former CEO of Genagon Therapeutics\, a ground-breaking immuno-oncology company. Presently co-founder and CEO of Pixelgen Technologies\, and Partner in Colibri Ventures\, a premier life science business incubator\, that helps start-ups develop early ideas into successful companies faster and more efficient. Simon also has extensive board member experience from 9 years at Olink AB (partly exited to Nexttobe 2011)\, Biolamina AB (+6 years)\, Olink Proteomics AB (exited to Summa Equity 2019)\, and Cartana AB (exited to 10X Genomics 2020) and Genagon Therapeutics. \n\n\n\nAs an experienced life science entrepreneur\, researcher and inventor spanning from research tools to bio-therapeutics\, Simon has always been fascinated by technology innovation capable of pushing the frontiers of scientific discovery into new and unchartered territories. \n\n\n\n\n\n\n\n\n\n\n\n \n\n\n\nRegister to receive zoom link URL:https://www.scilifelab.se/event/from-bmc-to-wall-street-old/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2021/08/Clinical-Talks.png ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se LOCATION:https://www.scilifelab.se/event/from-bmc-to-wall-street-old/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210908T150000 DTEND;TZID=Europe/Stockholm:20210908T160000 DTSTAMP:20260403T230832 CREATED:20210827T090406Z LAST-MODIFIED:20210902T144342Z UID:10000416-1631113200-1631116800@www.scilifelab.se SUMMARY:BiG Talks - Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology DESCRIPTION:BiG Talks: Integrative Omics\n\n\n\nArranged by the SciLifeLab platforms for Bioinformatics\, Genomics and Diagnostics Development \n\n\n\nThe Bioinformatics and Genomics seminar series (“BiG Talks”) is an initiative arranged by the SciLifeLab platforms for Bioinformatics (NBIS)\, Genomics (NGI) and Clinical Genomics platform. The seminar series aims to give inspiration to the SciLifeLab community and to create new networking possibilities. Each event will be broadcasted over Zoom where you will be able to interact with the speakers\, and live broadcasted at the SciLifeLab YouTube channel.  \n\n\n\nIn this seminar series\, run in parallel with the ELIXIR-SE / NBIS workshop in Omics Integration and Systems Biology\, we will be broadcasting three seminars about research and tools for integration of omics data through systems biology approaches\, in humans and model organisms. Please use the following link to register and access the Zoom link: \n\n\n\nRegistration\n\n\n\n\n\n\n\n\n\n8th of September\, 15:00 – 16:00 CET \n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biologyDr. Pedro BeltraoGroup Leader\, EMBL-EBI\, United Kingdom \n\n\n\nMore info\, see below \n\n\n\n \n\n\n\n\n\n10th of September\, 13:00 – 13:55 CET \n\n\n\nMetabolic Atlas: genome-scale metabolic models for easy browsing and analysisMihail AntonProject Manager for Metabolic Atlas\, NBIS / Chalmers University\, Sweden \n\n\n\nMore info \n\n\n\n\n\n10th of September\, 14:00 – 15:00 CET \n\n\n\nNetwork-based integration and visualization of large-scale dataDr. Lars Juhl JensenGroup Leader\, Novo Nordisk Foundation Center for Protein Research\, Denmark \n\n\n\nMore info \n\n\n\n\n\n\n\n\n\n\nNetwork based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology\n\n\n\nDr. Pedro Beltrao\, Group Leader\, EMBL – EBI\, United Kingdom \n\n\n\nAbstract \n\n\n\nUnderstanding how genetic variation contributes to phenotypic differences is a central question in biology. This requires models that can describe how rare and common genetic variability impacts on different cellular components and traits. To study the impact of rare variants we develop and combine variant effect predictors for protein stability\, interaction affinity\, and gene expression regulation. We have applied these to study the impact of rare variants on trait variation in strains of micro-organisms\, including panels of 1000 strains of E. coli and S. cerevisiae.  For human we have used a network-based approach to study 1002 traits analysed by genome wide association studies (GWAS). Based on the principle that genes associated with the same phenotype tend to be involved in the same cellular processes\, we performed a network expansion and prioritization of trait associated genes. The network based gene-trait association scores allows for the identification of related traits and the biological processes that they share. Based on this we can identify pleiotropic biological processes that can influence a large number of human traits and identify opportunities for drug repurposing. Finally\, I will illustrate how this analysis can be combined with patient specific mRNA/protein data for further prioritization. I will focus on neurodegeneration diseases to illustrate the identification of shared aetiology and further integrate ALS SOD1 mutant patient mRNA/protein data to identify novel astrocyte candidate ALS linked genes. As a future perspective I will briefly discuss the need for approaches that can jointly integrate common and rare genetic variation to improve our understanding of trait variation. \n\n\n\nBiography \n\n\n\nDr. Pedro Beltrao is a group leader at EMBL – EBI where his research group seeks to understand how cellular functions have diverged during evolution as well as how they are altered in disease. He employs systems biology techniques to analyse GWAS\, post-translational modifications (PTMs) data from mass-spectrometry experiments\, among other omics\, to study the molecular sources of phenotypic novelties\, exploring how DNA changes are propagated through molecular structures and interaction networks to give rise to phenotypic variability. Dr. Beltrao has a PhD in Biology from the University of Aveiro (research conducted at EMBL-Heidelberg)\, after which he conducted his postdoctoral research at the University of California San Francisco. Dr. Beltrao is a group leader at EMBL-EBI since 2013\, and will join ETH Zurich in 2022.  Homepage: https://www.ebi.ac.uk/research-beta/beltrao/ \n\n\n\nHost: Rui Benfeitas\, NBIS Stockholm (rui.benfeitas@scilifelab.se) \n\n\n\nDate: September 8\, 15:00 – 16:00 CET online on Zoom \n\n\n\nBroadcast link (live event): SciLifeLab YouTube channel  \n\n\n\nRegistration form for zoom link URL:https://www.scilifelab.se/event/big-talks-1/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="BiG Talks":MAILTO:info@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210908T080000 DTEND;TZID=Europe/Stockholm:20210910T170000 DTSTAMP:20260403T230832 CREATED:20210527T110708Z LAST-MODIFIED:20210906T135301Z UID:10000393-1631088000-1631293200@www.scilifelab.se SUMMARY:Workshop on Plotting in R - ONLINE 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.The course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Lokeshwaran Manoharan\, Louella Vasquez\, Markus RingnerContact information: edu.plotting.r@nbis.se \n\n\n\n\n\n\n\n\nApplication\n\n\n\nCourse website\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: June 01Application deadline: July 30Confirmation to accepted participants: August 06 \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 1700 SEK.*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.In particular\, you will learn: \n\n\n\n·          how to format the data necessary for ggplot·          how to make bar-charts\, box-plots and others using ggplot·          how to make PCA plots in ggplot·          how to use R packages for heatmaps·          how to plot data on maps using R (optional)·          how to plot and handle phylogenetic trees in R (optional)·          how to make interactive plots in R using Rshiny·          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·          apply the grammar efficiently in ggplot to get the desired plot·          combine different data and/or different plots that are of publication-grade·          write your own simple Rshiny app·          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 a webcam running R and Rstudio You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseyou 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-plotting-in-r-online/ CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210907T090000 DTEND;TZID=Europe/Stockholm:20210907T110000 DTSTAMP:20260403T230832 CREATED:20210902T060222Z LAST-MODIFIED:20210902T060229Z UID:10000423-1631005200-1631012400@www.scilifelab.se SUMMARY:BioImage Informatics 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\, September 7\, 2021\, 9.00-11.00. \n\n\n\nDeadline for application: Friday\, September 3\, 2021. URL:https://www.scilifelab.se/event/bioimage-informatics-call4help-3/ CATEGORIES:Event ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210906T080000 DTEND;TZID=Europe/Stockholm:20210910T170000 DTSTAMP:20260403T230832 CREATED:20210603T124622Z LAST-MODIFIED:20210615T135807Z UID:10000396-1630915200-1631293200@www.scilifelab.se SUMMARY:ELIXIR Omics Integration and Systems Biology - Online DESCRIPTION:The National Bioinformatics Infrastructure Sweden (NBIS) / ELIXIR Sweden is pleased to announce the workshop in Omics Integration and Systems Biology. This workshop is open for PhD students\, postdocs\, group leaders and core unit staff from European institutions looking for an introduction to multi-omics integration and systems biology approaches. \n\n\n\nThis workshop will include lectures and hands-on exercises from NBIS / Scilifelab experts from Stockholm\, Lund and Gothenburg\, as well as guest sessions from: \n\n\n\nRicard Argelaguet\, PhD\, Babraham Institute\, United KingdomKim-Anh Lê Cao\, PhD\, Melbourne University\, AustraliaPedro Beltrao\, PhD\, EMBL-EBI\, United KingdomNikolaus Sonnenschein\, PhD\, DTU Technical University of Denmark\, Denmark\n\n\n\n More information to come on the course website. \n\n\n\nImportant Dates \n\n\n\n\nApplication opens: 3 JuneApplication closes: 9 AugustConfirmation to accepted students: 16 August\n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\nFee \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. \n\n\n\n* Please note that NBIS cannot invoice individuals. \n\n\n\nContent \n\n\n\nThe aim of this workshop is to provide an integrated view of data-driven hypothesis generation through biological network analysis\, constraint-based modelling\, and supervised and unsupervised integration methods. A general description of different methods for analysing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods and pitfalls in their integration. The techniques will be discussed in terms of their rationale and applicability. The course will also include hands-on sessions and several seminars by invited speakers. \n\n\n\nSome of the covered topics include: \n\n\n\nData pre-processing and cleaning prior to integration\n\n\n\nApplication of key machine learning methods for multi-omics analysis including deep learning\n\n\n\nMulti-omics integration\, clustering and dimensionality reduction\n\n\n\nBiological network inference\, community and topology analysis and visualization\n\n\n\nCondition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic\, proteomic\, metabolomic and fluxomig data\n\n\n\nIdentification of key biological functions and pathways\n\n\n\nIdentification of potential biomarkers and targetable genes through modeling and biological network analysis\n\n\n\nApplication of network approaches in meta-analyses\n\n\n\nSimilarity network fusion and matrix factorization techniques\n\n\n\nIntegrated data visualization techniques\n\n\n\nFurther details about the course content may be found on the course website. \n\n\n\nEntry requirements \n\n\n\nThis is a course is open for PhD students\, postdocs\, group leaders and core unit staff from European institutions. Please note that NBIS training events do not provide any formal university credits. 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. \n\n\n\nPractical exercises can be performed using R or Python\, so we only accept students with previous experience in one of those programming languages. We will not discuss how to process specific omics\, and the students are referred to other NBIS courses for this matter. \n\n\n\nRequired: \n\n\n\nBasic knowledge in R or Python;Basic understanding of frequentist statistics;A computer with web camera\, Zoom\, and permissions for installing software.\n\n\n\nDesirable: \n\n\n\nExperience with analysis of NGS and other omic data;Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “Introduction to biostatistics and machine learning”Basic conda and git knowledge\n\n\n\nThis workshop can accommodate a maximum of 25 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\nContact information \n\n\n\nFor questions about this workshop please contact: edu.omics-integration@nbis.se URL:https://www.scilifelab.se/event/elixir-omics-integration-and-systems-biology-online/ CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210903T090000 DTEND;TZID=Europe/Stockholm:20210903T093000 DTSTAMP:20260403T230832 CREATED:20210820T082759Z LAST-MODIFIED:20220914T085524Z UID:10000409-1630659600-1630661400@www.scilifelab.se SUMMARY:Clinical Talks: Combining the power of nature with the efficiency of the chemical industry DESCRIPTION:After our recent planning hiatus\, we now have the great pleasure to announce that “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 until December 2021 with a total of seven 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. \n\n\n\nRead more about the clinical talk series here\n\n\n\n\n\n\n\n \n\n\n\n\n\nCombining the power of nature with the efficiency of the chemical industry\n\n\n\nKarim E. Cassimjee\, CEO & co-Founder EnginZyme \n\n\n\nRegister to receive zoom link\n\n\n\n\n\n\n\n\n\n\n\nKarim has a PhD in biotechnology from Royal Institute of Technology (KTH) and conducted postdoctoral studies in organic chemistry and quantum mechanics at Arrhenius laboratory (Stockholm University). He early found a passion for enzymes and their potential for solving the commonly unsustainable production of the chemical products used in our everyday lives and that modern society relies upon. He co-founded EnginZyme in 2014 – a company dedicated to replacing the incumbent chemical transformations that rely on heavy metal catalysts and high energy consumption\, and produce a lot of bi-products. This is accomplished by developing production processes based on a proprietary and general enzyme immobilization technology applied in flow chemistry set-ups. In 2021 Karim was selected as the KTH Alumnus of the Year\, and EnginZyme as Technology Pioneer by the World Economic Forum. \n\n\n\nDuring the first Clinical Talks of the season\, Karim will share his passion and insights for his work\, technology aspirations\, and experiences in pharmaceutical production\, and how EnginZyme will “make the impossible possible” for a sustainable industrial large-scale production for future generations.” URL:https://www.scilifelab.se/event/clinical-talks-combining-the-power-of-nature-with-the-efficiency-of-the-chemical-industry/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2021/08/Clinical-Talks.png ORGANIZER;CN="Clinical Talks":MAILTO:precisionmedicine@scilifelab.se LOCATION:https://www.scilifelab.se/event/clinical-talks-combining-the-power-of-nature-with-the-efficiency-of-the-chemical-industry/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210902T130000 DTEND;TZID=Europe/Stockholm:20210902T140000 DTSTAMP:20260403T230832 CREATED:20210824T112822Z LAST-MODIFIED:20210825T082041Z UID:10000410-1630587600-1630591200@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Banushree Kumar and Vivek Singh DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 13:00-13:50 and following current regulations\, they will be broadcast via zoom. \n\n\n\n \n\n\n\nThis week\n\n\n\nPolycomb Repressive Complex 2 shields naive human pluripotent cells from trophectoderm differentiation. Banushree Kumar (Simon Elsässer\, alpha 4)  \n\n\n\n \n\n\n\nTowards high-resolution structures of the human mitoribosomeVivek Singh (Alexey Amunts\, gamma 6) \n\n\n\nRegistration\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. URL:https://www.scilifelab.se/event/a-campus-solna-seminar-series-banushree-kumar-and-vivek-singh/ CATEGORIES:Community ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210830T080000 DTEND;TZID=Europe/Stockholm:20210903T170000 DTSTAMP:20260403T230832 CREATED:20210607T141128Z LAST-MODIFIED:20210608T125759Z UID:10000398-1630310400-1630688400@www.scilifelab.se SUMMARY:Summer School Advanced topics in single cell Transcriptomics - Online DESCRIPTION:Overview\n\n\n\nNBIS (SciLifeLab Bioinformatics Platform) and SIB (Swiss Institute of Bioinformatics) are pleased to co-organize this online course in Advanced topics in single cell Transcriptomics. \n\n\n\nThis jointly collaborative effort between the SIB and NBIS (SciLifeLab Bioinformatics Platform) was launched in 2019 as an every-second-year seasonal school where the thematic topic mirrors the life science demand of knowledge up-skilling. In 2019 we did a seasonal school on the topic of single-cell omics analysis and this year we are repeating this theme as the demand is still extremely high. \n\n\n\nIn recent years\, single-cell transcriptomics has become a widely used technology to study heterogeneous and dynamic biological systems. A large number of new tools and approaches have been developed for analyzing this new type of data. The goal of this joint School is to provide PhD students and postdocs with theoretical and mostly hands-on knowledge on selected advanced topics in Single Cell analysis. In particular\, the participants will be split into small groups to develop mini projects (more details provided later to accepted students. \n\n\n\nFor this one week course in single-cell transcriptomic we are delighted to have several excellent researchers and experts from both the Swedish and the Swiss Life Science community such as teachers such as Alma Andersson\, Åsa Björklund\, Volker Bergen\, Paulo Czarnewski\, Emma Dann\, Charlotte Soneson\, Panagiotis Papasaikas\, Geert van Geest and others. \n\n\n\nTarget audience\n\n\n\nThis course is designed for intermediate users and we consider the knowledge of basic steps in single-cell analysis as a prerequisite. \n\n\n\nCourse and Application details\n\n\n\nApplication is now open at SIB announcement Summer School Advanced topics in single cell Transcriptomics. The SIB page will be regularly updated with more detailed information. \n\n\n\nAny questions please contact Jessica Lindvall (Training coordination\, NBIS)\, jessica.lindvall@nbis.se and Grégoire Rossier (Training coordination\, SIB)\, Gregoire.Rossier@sib.swiss        \n\n\n\nImportant dates\n\n\n\nDeadline for free-of-charge cancellation is set to 28/07/2021. Cancellation after this date will not be reimbursed. \n\n\n\nCourse fee\n\n\n\nThe registration fees for academics are 300 CHF (appriximately 270 Euro) and 1500 CHF (approximately 1370 Euro) for for-profit companies. URL:https://www.scilifelab.se/event/summer-school-advanced-topics-in-single-cell-transcriptomics-online/ CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210823T151500 DTEND;TZID=Europe/Stockholm:20210823T163000 DTSTAMP:20260403T230832 CREATED:20210816T071003Z LAST-MODIFIED:20210816T093408Z UID:10000406-1629731700-1629736200@www.scilifelab.se SUMMARY:SciLifeLab The Svedberg seminar: Prof. Athula Attygalle DESCRIPTION: Stevens Institute of Technology\, USA \n\n\n\n\n\n\n\n\n\nLINK TO SEMINAR \n\n\n\n Prof. Athula Attygalle obtained a PhD in Chemistry from Keele University in 1983. After his doctorate\, Attygalle was awarded a Fellowship by the Humboldt Foundation to conduct research at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) under late Prof\, Hans Jürgen Bestmann\, a pioneer in the field of insect pheromone synthesis. Four years at FAU\, provided the impetus for Attygalle to become an expert in high-resolution mass spectrometry and micro-chemical techniques for structure elucidation of natural compounds at nanogram level. At FAU\, Attygalle championed in the area of lepidopteran sex pheromone identification. Attygalle was a visiting professor at University of Houston\, Texas and he has served as the Director of Mass Spectrometry facility at Cornell University. He has completed work there in GC-MS regarding insect substances and their identifications.  Currently Attygalle is attached to the Stevens Institute of Technology as a Research Professor in the Department of Chemistry and head of the mass spectrometry laboratory. Attygalle was the recipient of the 2014 ‘Inventor of the Year’ award presented by the New Jersey Inventors Hall of Fame for his patented work in Mass Spectrometric Analysis utilizing Helium Plasma and charge exchange ionization techniques. Attygalle co-authored the 1999 article “Single-Site Catalysts for Ring-Opening Polymerization:  Synthesis of Heterotactic Poly(lactic acid) from rac-Lactide” in the Journal of the American Chemical Society\, which has been widely cited. \n\n\n\nMultiple Personalities of Gaseous Ions \n\n\n\nFor mass spectrometry\, neutral molecules are converted to gaseous ions.   A mass spectrum is recorded by determining the mass-to-charge ratios and intensities of fragment ions generated by activating a specific ion. Many textbooks provide rules to identify molecules by interpreting their mass spectra.  All recommended interpretations start by presuming a specific structure for the initial ion.  However\, recent advances in ion-mobility methods demonstrate that an ensemble of ions with different structures are produced upon ionization. For example\, the most widely used electrospray ionization technique often generates a mixture of tautomeric forms of a precursor molecule.  Because fragmentation spectra of individual tautomers are often different from each other\, the spectra recorded without separating the isomeric mixtures are composites.  Although large collections of spectra are available as libraries\, the time has come to for us query of the quality of these compilations.                    \n\n\n\nHost: Kumari Ubhayasekera URL:https://www.scilifelab.se/event/scilifelab-the-svedberg-seminar-prof-athula-attygalle/ LOCATION:Online event via Zoom CATEGORIES:Event ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210623T130000 DTEND;TZID=Europe/Stockholm:20210623T160000 DTSTAMP:20260403T230832 CREATED:20210601T073659Z LAST-MODIFIED:20210601T075456Z UID:10000394-1624453200-1624464000@www.scilifelab.se SUMMARY:SciLifeLab Workshop on Federated Machine Learning DESCRIPTION:Location: Online via Zoom\n\n\n\nProgram:\n\n\n\n13.00 – 13.45  Presentation: Introduction to Federated Machine Learning \n\n\n\n14.00 – 16.00  Hands-on workshop: How to set up\, run and deploy a federated learning project using the FEDn open source solution \n\n\n\nNote that it is possible to attend the first presentation only\, or both presentation and workshop. \n\n\n\nWhat is Federated Machine Learning?\n\n\n\n\nFederated learning enables several organizations / groups to collaborate on machine learning models without needing to directly share sensitive or confidential data with each other.It is a distributed machine learning approach which enables training on decentralised data. A server coordinates a network of nodes\, each of which has local\, private training data. These nodes contribute to the construction of a global model by training on local data\, and the server combines non-sensitive node model contributions into the global model. \n\n\n\nFor a short (10min ) introduction see: https://www.youtube.com/watch?v=jbLHRtGWPL8 \n\n\n\n\nWho should attend?\n\n\n\n1.Researchers who are interested in learning more about FedML \n\n\n\n2.Researchers who are interested in testing FedML hands-on in the FEDn solution \n\n\n\nAbout the organizers\n\n\n\nScaleout consists of a team of data scientists\, machine learning engineers\, software engineers\, and entrepreneurs with experience from both industry and academic research in AI and applied machine learning\, cloud and fog computing\, and scientific computing from Uppsala University. We’re working on a platform for end-to-end privacy-preserving machine learning with a focus on helping organisations put advanced machine learning and DevOps technologies into production. \n\n\n\nRegistration\n\n\n\nThe presentation and the workshop is free of charge but requires registration. The number of seats for the hands-on part of the workshop is limited to 20 people so only register for the workshop if you are interested in actively participating in the tutorial. \n\n\n\nContact: Prof. Ola Spjuth\, AI coordinator\, SciLifeLab Data Centre. \n\n\n\nRegister here URL:https://www.scilifelab.se/event/fedml/ LOCATION:Online event via Zoom CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210617T130000 DTEND;TZID=Europe/Stockholm:20210617T140000 DTSTAMP:20260403T230832 CREATED:20210503T143813Z LAST-MODIFIED:20210601T093048Z UID:10000378-1623934800-1623938400@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Woonghee Kim and Markus Hilscher 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\nWoonghee Kim\n\n\n\nDrug discovery: Disease modeling and assessment of new small molecules for Non Alcoholic Fatty Liver Disease (NAFLD) \n\n\n\nAdil Mardinoglu\, Alpha 6 \n\n\n\n\n\nMarkus Hilscher\n\n\n\nBeyond a cell atlas – applications of in situ sequencing to models of disease \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-woonghee-kim-and-markus-hilscher/ CATEGORIES:Community ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210614T080000 DTEND;TZID=Europe/Stockholm:20210624T170000 DTSTAMP:20260403T230832 CREATED:20210503T140254Z LAST-MODIFIED:20210503T141941Z UID:10000375-1623657600-1624554000@www.scilifelab.se SUMMARY:RaukR\, Advanced R for Bioinformatics\, Summer course DESCRIPTION:International course. The course is open for researchers at university or in industry such as PhD students\, postdocs\, group leaders\, core unit staff and analysts.Apply hereCourse website \n\n\n\ncourse website\n\n\n\nThe course is organised by NBIS \n\n\n\nResponsible teachers: Marcin Kierczak\, Sebastian DiLorenzoContact: RaukR@NBIS.se \n\n\n\nImportant dates\n\n\n\nApplication deadline: Friday\, 23.04.2021\, 24:00 GMTNotification of acceptance/decline: Friday\, 30.04.2021 \n\n\n\nCourse fee\n\n\n\nAcademic: No fee this year. However\, if you register and will be admitted but you will not attend the event without a valid reason\, you will be charged a no-show fee (3000 SEK).Participants from outside of academia should contact us for a fee quote. \n\n\n\nCourse description\n\n\n\nJoin us online this June to improve your R skills and have a nice time!In Life Science and Bioinformatics\, R is increasingly being used to transform and analyse data\, perform statistical analysis and produce publication-ready visualisations. This Summer course will focus on advanced R functionality\, to increase the participants skillset and understanding of what is possible to do today. \n\n\n\nBig part of RaukR experience was coding and exchanging knowledge in a unique environment provided by Campus Visby in Gotland. Sadly\, due to COVID-19 outbreak\, RaukR 2020 did not happen. This year\, we still have to obey a number of restrictions and guidelines due to the outbreak. While we still cannot gather in Visby\, we decided to go online and we hope this year we will also learn a lot and have fun coding together! We wish you all the best. See you online! Stay safe and healthy! \n\n\n\nYou are very welcome to apply or see the homepage for more information. Please\, help us spread the word to interested participants! \n\n\n\nGuest speaker\n\n\n\nMax Kuhn (software engineer at RStudio) \n\n\n\nCourse content\n\n\n\nreproducible research in R (rmarkdown\, knitr)\,collaborative work using git and GitHub\, CD/CI\,R code style guidelines\,parallelization and vectorization in R\,writing own functions – best practices\,understanding and using the system of R classes: S3\, S4\, R6 and RC\,anatomy of an R package: writing your own package from scratch\,code debugging\, profiling and optimization\,tidy data flow with tidyverse\,efficient use of magrittr pipes\,using the language of graphics\, ggplot2\,developing simple web applications using shiny\,efficient modelingthe second week will be devoted to collaborative project workthe last day\, all groups will present their project work\n\n\n\nEntry requirements\n\n\n\nThe course is aimed at both Ph.D. students and researchers within Life Sciences who are already using R for basic bioinformatics analyses and who would like to start using R at a more advanced level. In order for you and other participants to benefit the most\, you should consider yourself eligible if you are comfortable with reading and transforming data\, installing and using third-party packages and plotting using standard R graphics. \n\n\n\nWe offer places for participants from all over the world\, but there is a number of places reserved for participants from Sweden. \n\n\n\nSelection criteria\n\n\n\nThis year\, the school can accommodate ~30 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. This year\, we will also give priority to students who have already been admitted to RaukR 2020 (which had been cancelled). URL:https://www.scilifelab.se/event/raukr-advanced-r-for-bioinformatics-summer-course/ CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se LOCATION:https://www.scilifelab.se/event/raukr-advanced-r-for-bioinformatics-summer-course/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210614T080000 DTEND;TZID=Europe/Stockholm:20210616T170000 DTSTAMP:20260403T230832 CREATED:20210503T143343Z LAST-MODIFIED:20210608T152652Z UID:10000377-1623657600-1623862800@www.scilifelab.se SUMMARY:Campus Solna Science talks 2021 DESCRIPTION:SciLifeLab Campus Solna symposium is designed to inform the community about recent work\, provide an opportunity for scientists to present ongoing research\, and introduce new fellows.  \n\n\n\nTo create an open environment that encourages the unrestrained sharing of ongoing research and unpublished work\, the taking of screen shots\, video or audio recording is not allowed during the presentations. Of course\, taking written notes is fine. \n\n\n\nFor details please email science.talks@scilifelab.se \n\n\n\nRegister to Science Talks\n\n\n\n\n\n\n\nProgram\n\n\n\nProgram Science Talks 2021Download\n\n\n\nMonday\, June 14\n\n\n\n09:00Opening note – Welcome to Science Talks\, Per Ljungdahl\, SciLifeLab Campus Solna DirectorBioimagingChair: Per Ljungdahl09:05Ilaria Testa (KTH)\, A new observable window into living cells at high spatio-temporal resolution09:15Taras Sych (KI)\, Biophysical characterization of nano-sized physiological lipid particles with fluorescence flucutuometry09:25Linnea Nordahl (KTH)\, Interactions within the Na/K-ATPase09:35Hans Blom (KTH)\, Diagnosis of kidney diseases with all scale optical microscopy09:45Q&A with speakers10:00BreakCellular and Molecular BiologyChair: Marcel Tarbier10:10Lucie Delemotte (KTH)\, Elucidation of G protein-coupled receptor activation via data-driven modeling10:20Alexey Amunts (SU)\, Structural studies of bioenergetic complexes10:30Fitz Gerald S. Silao (SU)\, Proline assimilation is intrinsic to the opportunistic ecophagy of Candida albicans-infected hosts10:40Paul Hudson (KTH)\, Engineering the microbial Calvin cycle for bio-sustainability applications10:50Q&A with speakers11:05BreakCellular and Molecular BiologyChair: Vicent Pelechano11:15Eleni Gelali (KI)\, Deconwolf: a free deconvolution software that can facilitate imaging-based spatially resolved omics11:25Lukas Käll (KTH)\, Survival Analysis Based on Cancers’ Pathway Activity11:35Maurice Grube (KI)\, Small molecule activation of OGG1 increases base excision repair by gaining a new enzymatic function11:45Banushree Kumar (KI)\, Function of PRC2 in naïve and primed human pluripotency11:55Q&A with speakers12:10End of day\n\n\n\n\n\n\n\n\n\nTuesday\, June 15\n\n\n\nNucleic Acids and Multi-omicsChair: Alexey Amunts09:00Opening note09:05Stefania Giacomello (KTH)\, Understanding the impact of spaceflight on mouse brain and heart by using spatial multiomics methods09:15Marc Friedländer (SU)\, Ancient RNA – possibilities and challenges09:25Christian Sommerauer (KI)\, Are female sex hormones the key to preventing liver diseases?09:35Claudia Kutter (KI)\, High resolution RAPseq identifies functional propensities of RNA binding proteins in diseases and species evolution09:45Q&A with speakers10:00Break10:10Paula Pierozan (SU)\, re common per- and polyfluoroalkyl substances linked to breast cancer? -mechanistic studies by high-content screening and DNA methylation analysis10:20Kristoffer Sahlin (SU)\, Strobemers: an alternative to k-mers for sequence comparison\, clustering\, and alignment10:30Alisa Alekseenko (KI)\, OPUS-seq: One Pot Double Stranded UMI Sequencing10:40Lilit Nersisyan (KI)\, RNA degradation analysis reveals ribosome dynamics in complex microbiome samples10:50Q&A with speakers11:05BreakNucleic Acids and Multi-omicsChair: Vaishnovi Sekar11:15Cecilia Williams (KTH)\, Colorectal cancer development: sex differences and impact of estrogen11:25Erik Sonnhammer (SU)\, Network-based pathway analysis and drug repurposing\, with application to COVID-1911:35Jean Hausser (KI)\, Quantitative principles of tumor micro-architecture11:45Boyang Guo (KTH)\, The perfect fit: enzyme and substrate conformations in plastic degradation11:55Q&A with speakers12:10End of day\n\n\n\n\n\n\n\n\n\nWednesday\, June 16\n\n\n\nEpidemiology and DiagnosticsChair: Lucie Rodriguez09:00Opening note09:05Petter Brodin (KI)\, Human systems immunology09:15Ludvig Larsson (KTH)\, Molecular characterization of the mouse intestine09:25Jochen Schwenk (KTH)\, Decoding clinical heterogenity with the circulating proteome09:35Tea Dodig-Crnkovic (KTH)\, Multiplexed analysis of the GPCR-RAMP interactome09:45Q&A with speakers10:00BreakEpidemiology and DiagnosticsChair: Aditi Shenoy10:10Peter Nilsson (KTH)\, Development of a multiplex COVID-19 serology10:20Mats Nilsson (SU)\, The single sell- and spatial biology platform10:30Isabelle Leo (KI)\, Using proteomics to guide translational study of biology and biomarkers in childhood ALL10:40Aman Russom (KTH)\, Life at the micro- and nanoscale: microfluidics for clinical applications10:50Q&A with speakers11:05BreakNew RecruitmentsChair: Disa Hammarlöf11:15Iskra Pollak Dorocic (SU)\, Deciphering the molecular\, anatomical and functional diversity of neuromodulatory neurons11:25Anniina Vihervaara (KTH)\, Coordinating transcription at physically-linked genes and enhancers in stress and development11:35Saeed Shoaie (KTH)\, Global and temporal state of human microbiome11:45Tuuli Lappalainen (KTH)\, Functional variation in the human genome: lessons from the transcriptome11:55Q&A with speakers12:10Science communication AwardsOlli Kallioniemi\, Director SciLifeLab12:15Closing noteOlli Kallioniemi\, Director SciLifeLab URL:https://www.scilifelab.se/event/campus-solna-science-talks-2021/ CATEGORIES:Community LOCATION:https://www.scilifelab.se/event/campus-solna-science-talks-2021/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210611T130000 DTEND;TZID=Europe/Stockholm:20210611T160000 DTSTAMP:20260403T230832 CREATED:20210503T135955Z LAST-MODIFIED:20210609T083612Z UID:10000374-1623416400-1623427200@www.scilifelab.se SUMMARY:DDLS and WASP join forces for research within a data-driven future DESCRIPTION:Welcome to the official launch of the DDLS-WASP collaboration! \n\n\n\nThe two largest research programs in Sweden\, the Wallenberg AI\, Autonomous Systems and Software Program (WASP) and the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS)\, will team up in a new collaborative effort\, with the ultimate goal of solving groundbreaking research questions and to create synergies across disciplines. \n\n\n\nThis Zoom meeting will combine inspirational talks and discuss possible ways to initiate formations of strong collaborations that can bridge  the gap between the scientific disciplines. We welcome WASP researchers and life scientists to take part in the webinar and to actively engage in new alliances.  \n\n\n\nThe first part of the meeting will be recorded and published on WASP and SciLifeLab YouTube channels. \n\n\n\n\n\n\n\nRegistration\n\n\n\n\n\n\n\n\nMatchmaking: submit an abstract! \n\n\n\nPrepare for the joint call! To find potential collaborators\, common topics\, exchange ideas and opportunities\, and raise awareness of competencies on each side\, we invite you to submit an abstract. The Abstracts will be published in a PDF\, updated every Monday (except during July) until the Call closes. \n\n\n\nMatchmaking: Submit an Abstract\n\n\n\n\n\n\n\n\nProgram\n\n\n\nProgram WASP-DDLS June 11 (PDF)Download\n\n\n\n\n\n\n\nSession 1Hosts: Danica Kragic and Erik Lindahl13:00Welcome wordsSiv Andersson\, KAW\, Sara Mazur\, KAW\, Chair of WASP board\, Carl-Henrik Heldin\, Chair of SciLifeLab board13:15WASP\, Introducing WASP and bringing awareness of WASP to the DDLS communityAnders Ynnerman \, Director of WASP13:35DDLS\, Introducing DDLS and bringing awareness of DDLS to the WASP communityOlli Kallioniemi\, Director of SciLifeLab and DDLS13:55Joined forces for an increasingly data-driven futureInformation about our new collaboration and purpose of bridging WASP and DDLS research programs. Information about joint call.Danica Kragic\, Professor of Computer Science\, KTH\, Erik Lindahl\, Professor of Biophysics\, Stockholm University14:15Q&A session about the joint callModerators Danica Kragic and Erik LindahlPanel Anders Ynnerman\, Olli Kallioniemi and the joint WASP-DDLS working group14:35Short breakSession 2Host: Carolina Wählby14:45Inspirational TalksModerator Carolina Wählby\, Professor of Quantitative Microscopy\, Uppsala university Deep learning in drug discovery\, a WASP/AstraZeneca/KTH collaboration (8+2)Kevin Smith\, Associate Professor\, Division of Computational Science and Technology\, KTHFinding connections: how deep learning can help with COVID-19 and other major health challenges (8+2)Sonja Aits\, Associate Senior Lecturer\, Lund UniversityThe automation of Biology (16+4)Ross King\, Wallenberg Chair in AI\, Professor of Machine Intelligence\, Chalmers University of Technology15:25SummaryAnders Ynnerman\, Olli Kallioniemi15:30Informal breakout room discussions16:00End of day URL:https://www.scilifelab.se/event/ddls-and-wasp-join-forces-for-research-within-a-data-driven-future/ CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2021/04/DDLS_WASP_WP.jpg LOCATION:https://www.scilifelab.se/event/ddls-and-wasp-join-forces-for-research-within-a-data-driven-future/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210610T130000 DTEND;TZID=Europe/Stockholm:20210610T140000 DTSTAMP:20260403T230832 CREATED:20210503T144024Z LAST-MODIFIED:20210524T135338Z UID:10000379-1623330000-1623333600@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Gabriele Girelli and Ximena Lopez 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\nGabriele Girelli\n\n\n\nGPSeq – controlled diffusion to study radiality \n\n\n\nMagda Bienko – Alpha 4 \n\n\n\n\n\nXimena Lopez\n\n\n\nChemoenzymatic degradation of PET plastic \n\n\n\nPer-Olof Syrén – 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-gabriele-girelli-and-ximena-lopez/ CATEGORIES:Community ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210609T140000 DTEND;TZID=Europe/Stockholm:20210609T150000 DTSTAMP:20260403T230832 CREATED:20210519T132532Z LAST-MODIFIED:20210519T133127Z UID:10000389-1623247200-1623250800@www.scilifelab.se SUMMARY:SciLifeLab AI Seminar Series: Arne Elofsson DESCRIPTION:SciLifeLab Data Centre hosts a seminar series on the topic of applied AI in life science research. SciLifeLab AI Seminar Series combines scientific highlights from SciLifeLab-affiliated researchers and invited experts on the general topic of AI applications in Life Science. The SciLifeLab AI Seminar Series will be held virtually on Zoom and videos will be published openly after the seminars at the SciLifeLab YouTube channel. \n\n\n\nContact: Prof. Ola Spjuth\, AI coordinator\, SciLifeLab Data Center. \n\n\n\nUsing deep learning and coevolution to predict protein-protein interactions\n\n\n\nArne ElofssonStockholm University and Science for Life Laboratory \n\n\n\nAbstract \n\n\n\nIn the last decade de novo protein structure prediction accuracy for individual proteins\, by the use of co-evolution and deep learning harvesting the information from large multiple sequence alignments. In Casp14 it was shown that the best method can predict the structure for basically all proteins. This information can\, in principle\, also be used to extract information about protein-protein interaction\, but the success has so far been limited to a handful of proteins. However\, most of the earlier studies have not used the latest improvements achieved in contact-based predictions using deep learning to predict the distances between residue pairs. Here\, we first show that using one of the best residue-residue contact prediction methods (trRosetta) it is possible to simultaneously predict the structure of two proteins and their interaction for some proteins\, even when the structure of the monomers are not known. \n\n\n\nSecondly\, we apply this method to a standard dataset for protein-protein docking and find that the majority of the protein pairs are not docked correctly. By using alternative alignment methods to generate the multiple sequence alignments it is possible to accurately dock more proteins. The average performance is comparable to the use of alternative docking methods\, either template based or methods used by shape-complementarity\, although no structural information is needed for the individual proteins in a fold-and-dock pipeline. However\, the results are complementary as some methods work on some pairs and some on others.  \n\n\n\nWhen estimating differences between successful and unsuccessful fold-and-docked protein pairs.  We identify that the current method produces artefacts when there exists homology between the interacting proteins.  This bottleneck affects approximately one-third of the proteins pairs in our benchmark set. Further\, we find that one-third (?) of the proteins have too few sequences in the joint alignment. However\, for the remaining third (?) we can not find a good explanation why the docking was not successful. \n\n\n\nFinally\, we introduce a novel scoring function\, PconsDock\, that can be used to evaluate the quality of a protein-protein pair. This simple scoring scheme is very accurate as it can separate 98% of the correct and incorrect proteins.  \n\n\n\nRegister here URL:https://www.scilifelab.se/event/scilifelab-ai-seminar-series-arne-elofsson/ CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210608T140000 DTEND;TZID=Europe/Stockholm:20210609T120000 DTSTAMP:20260403T230832 CREATED:20210503T135818Z LAST-MODIFIED:20210607T152505Z UID:10000373-1623160800-1623240000@www.scilifelab.se SUMMARY:CryoEM in Drug Discovery DESCRIPTION:CryoEM has quickly become an essential tool in academic research\, with more than 1200 cryoEM structures deposited in the PDB in 2019. CryoEM is now also showing a significant impact on drug discovery in industry and academia. \n\n\n\nThis symposium\, co-arranged by the Drug Discovery and Development platform and the CryoEM unit at SciLifeLab\, highlights some of the recent advances in the field and familiarises the audience with the requirements\, opportunities\, and limitations of the technique. Speakers include leading scientists from both major pharma companies and academia. \n\n\n\nBy attending this symposium\, you learn what cryoEM can bring to your research\, what resources are available to Swedish researchers\, and how to get started. We welcome both Swedish and international participants. \n\n\n\n \n\n\n\n \n\n\n\n\nregister here to receive zoom link\n\n\n\n\n\n\n\nSession 1\n\n\n\nAll time slots below are in UTC+2 / CEST Time zone [Stockholm\, Sweden]. \n\n\n\nJune 8th – Afternoon\n\n\n\n14:00Welcome wordsAnnika Jenmalm-Jensen\, Infrastructure Director\, SciLifeLab14:05Introduction to the cryo-EM Unit at SciLifelabMarta Carroni\, SciLifeLab/Stockholm University\, Sweden14:15From Concept to Reality: CryoEM as an Integral Part of Drug Discovery and Development Corey Strickland; Merck\, Kenilworth\, United States14:55CryoEM at AstraZenecaChris Phillips; Astra Zeneca\, UK15:25Short break15:30An integrated cryo-EM and AI based approach for new vaccine identificationIlaria Ferlenghi\, GSK\, UK16:00Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 1.68 Å resolution Hartmut Luecke\, University of Oslo\, Norway16:30CryoEM in industry\, with an artisanal touchAlexis Rohou\, Genentech\, United States17:00Wrap upMarta Carroni\, SciLifeLab/Stockholm University\, Sweden\n\n\n\nSession 2\n\n\n\nAll time slots below are in UTC+2 / CEST Time zone [Stockholm\, Sweden]. \n\n\n\nJune 9th – Morning\n\n\n\n09:00Session 2 WelcomeMarta Carroni\, SciLifeLab/Stockholm University\, Sweden09:00Cryo-EM and crystal structure of the emerging cancer target PAICS incomplex with a low-nanomolar inhibitorJana Skerlova\, Stockholm University\, Sweden09:15Using Cryo-EM for GPCR Drug Discovery and Development Patrick M. Sexton\, Monash University\, Parkville\, Australia09:55Short break10:00Cryo-EM at NovartisMaryam Khoshouei\, Novartis\, Switzerland10:30CryoEM of SARM1 reveals a trigger of axon degenerationKatie Cunnea\, Evotec\, UK11:00Concluding RemarksMarta Carroni\, SciLifeLab/Stockholm University\, SwedenPer Arvidsson\, SciLifeLab/Karolinska Institutet\, SwedenAnders Olsson\, SciLifeLab/KTH Royal Institute of Technology\, Sweden\n\n\n\n\n\n\n\nScientific committee\n\n\n\nMarta Carroni\, Head of Cryo-EM unit\, SciLifeLabPer Arvidsson\, Director Drug Discovery and Development platform\, SciLifeLabAnders Olsson\, Head of Protein Expression and Characterization unit\, SciLifeLab URL:https://www.scilifelab.se/event/cryoem-in-drug-discovery/ CATEGORIES:Event LOCATION:https://www.scilifelab.se/event/cryoem-in-drug-discovery/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210604T130000 DTEND;TZID=Europe/Stockholm:20210604T134500 DTSTAMP:20260403T230832 CREATED:20210518T091847Z LAST-MODIFIED:20210520T115320Z UID:10000387-1622811600-1622814300@www.scilifelab.se SUMMARY:Drug Discovery Seminars: An adaptable Drug Affinity Conjugate (ADAC) targeting CD40 DESCRIPTION:Proof of Concept and Pharmaceutical profiling\n\n\n\nSara Mangsbo\, Uppsala University\n\n\n\nAbstract: \n\n\n\nMuch attention has focused on developing CD40 directed agonistic monoclonal antibody therapy. Monoclonal antibodies targeting CD40 have been profiled for their epitope specificity and isotype in relation to their agonistic potential. Still\, clinical impact relies on a well-balanced clinical efficacy versus target-mediated toxicity. As CD40-mediated immune activation must rely on a combination of stimulation of antigen-presenting cells alongside antigen-presentation\, for efficient T cell priming\, alternative approaches to improve the therapeutic outcome of CD40-targeting strategies should focus on providing optimal antigen presentation together with CD40 stimulation. We have developed a bispecific antibody targeting CD40 as a means to carry in cargo (herein synthetic peptides) into antigen-presenting cells through a non-covalent\, high-affinity interaction between the antibody and the cargo peptide\, further referred to as the Antibody Drug Affinity Conjugate (ADAC) technology. The ADAC can improve both CD4+ and CD8+ T cell expansion in vitro and significantly improve CD8+ T cell proliferation in vivo. In addition\, the strategy leads to a stabilization of the half-life of the synthetic peptide. Future applications of ADAC involve pandemic preparedness to viral genetic drift as well as neoepitope vaccination strategies where the bispecific antibody is an off-the-shelve product\, and the peptide antigen is synthesized based on next-generation sequencing data mining.  \n\n\n\nA short speaker biography: \n\n\n\nSara Mangsbo (PhD) is Associate senior lecturer in antibody drugs and Associate professor in Experimental clinical immunology at Uppsala University. Dr Mangsbo earned her PhD in 2010 in cancer immunotherapy at Uppsala University and has since then focused her research on antibody-based drug delivery and synthetic long peptides and was recently awarded the SITC team award within the SLP stream. She is a serial entrepreneur and has founded Immuneed AB\, a service provider of immunotoxicity measurements in human whole blood. She is the Chief Development Officer of Ultimovacs and the co-founder of Vivologica AB and STRIKE pharma AB.  She drives a translational research project with the ambition and track-record of taking research projects into clinical trial testing.   \n\n\n\nRegistration URL:https://www.scilifelab.se/event/an-adaptable-drug-affinity-conjugate-adac-targeting-cd40-proof-of-concept-and-pharmaceutical-profiling/ CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2020/02/pills_600x200px.jpg LOCATION:https://www.scilifelab.se/event/an-adaptable-drug-affinity-conjugate-adac-targeting-cd40-proof-of-concept-and-pharmaceutical-profiling/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210603T130000 DTEND;TZID=Europe/Stockholm:20210603T140000 DTSTAMP:20260403T230832 CREATED:20210503T144211Z LAST-MODIFIED:20210518T122326Z UID:10000380-1622725200-1622728800@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Trang Le and Aswathy Kallazhi 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\nTrang Le\n\n\n\nModelling the spatial cell cycle with deep learning \n\n\n\nEmma Lundberg – Alpha 2 \n\n\n\n\n\nAswathy Kallazhi\n\n\n\nLon-mediated proteolysis in Pseudomonas aeruginosa pathogenicity \n\n\n\nKristina Jonas – 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-trang-le-and-aswathy-kallazhi/ CATEGORIES:Community ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210602T090000 DTEND;TZID=Europe/Stockholm:20210602T130000 DTSTAMP:20260403T230832 CREATED:20210503T135504Z LAST-MODIFIED:20210528T132452Z UID:10000372-1622624400-1622638800@www.scilifelab.se SUMMARY:Using the national infrastructures to solve antimicrobial resistance DESCRIPTION:The first InfraLife workshop gathers stakeholders in the field of antimicrobial resistance (AMR) for a joint discussion on June 2nd\, 2021.  \n\n\n\nThe AMR workshop in June will be followed up by activities during Fall to focus and expand initiatives of relevance identified during initial discussions and the first workshop.  \n\n\n\nAs with other InfraLife initiatives – we invite all interested to reach out and be in touch if you want to hear more and see potential to get involved in activities! \n\n\n\nNew collaborations advancing science are about gathering cross sectorial experts and stakeholders around a grand challenge\, taking a thematic approach and engaging the infrastructures and available technologies in how they can help address the question and be part of the solution to the research challenge at hand. And showing the complementarities of the research infrastructures in this setting. \n\n\n\nWe plan for other future themes besides AMR\, such as lifestyle diseases/ cancer and clean water/ the Baltic Sea\, considering life sciences beyond human health including environmental challenges. If you are active in these areas within your organization and see potential for joint efforts\, please be in touch. We would love to hear from you and learn about the scientific questions and challenges of particular interest\, where you would like to get engaged to jointly explore the potential of the national research infrastructures. \n\n\n\nRegister to receive zoom link\n\n\n\n   \n\n\n\nProgram\n\n\n\n09:00Welcome remarksPia Kinhult\, moderator Olli Kallioniemi\, SciLifeLab Marjolein Thunnissen\, MAX IV Andreas Schreyer\, ESS09:20Current State of Affairs –  What have we learnt and where are we going?Anders Karlén Uppsala University09:40 SciLifeLab units and capabilitiesAnnika Jenmalm-Jensen\, SciLifeLab10:00Large-scale DNA sequencing and the AMR challenge: examples from CAReJoakim Larsson\, Göteborgs universitet10:15Short break10:20Life Science opportunities at MAXIVSelma Maric MAX IV10:40A taste of bio-imaging at MAX IVKarina Thånell\, MAX IV10:55Structural Biology at the European Spallation SourceEsko Oksanen\, ESS11:15Short break11:20Industry perspective Susanna Abrahmsén-Alami\, AstraZeneca11:40Round table discussion   Discussion topics: What are the most urgent needs for different stakeholders? How can different funding streams be utilized for AMR? How do we ensure a steady flow through all stages of development? How can the infrastructures be of use in the scientific\, diagnostic\, regulatory challenges of AMR?    12:50Conclusions and actionable projects  to address gaps in AMRPia Kinhult13:00End of Meeting URL:https://www.scilifelab.se/event/using-the-national-infrastructures-to-solve-antimicrobial-resistance/ CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2021/05/Infralife-square.jpg ORGANIZER;CN="InfraLife":MAILTO:events@scilifelab.se LOCATION:https://www.scilifelab.se/event/using-the-national-infrastructures-to-solve-antimicrobial-resistance/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210531T090000 DTEND;TZID=Europe/Stockholm:20210531T130000 DTSTAMP:20260403T230832 CREATED:20210518T122622Z LAST-MODIFIED:20210527T160117Z UID:10000388-1622451600-1622466000@www.scilifelab.se SUMMARY:SciLifeLab-EMBL: Building new collaborative links DESCRIPTION:Welcome to SciLifeLab-EMBL: Building new collaborative links\, a webinar on May 31st 9-13 to launch intensified collaboration between the organizations under the joint Memorandum of Understanding (MoU). The event is open to the community at large\, and we welcome all interested to join and hear about the organisations as well as plans ahead. \n\n\n\nThe MoU declares a joint ambition to stimulate mutually beneficial scientific and academic exchange and collaboration in various areas of life science research in order to ensure greater connectivity\, availability of scientific data\, use of shared key technologies and circulation of talent. Specific topics of research interest have been identified based on already existing ties and may be jointly developed in the future\, in particular in the context of EMBL’s Programme for 2022- 2026 “Molecules to Ecosystems” and the SciLifeLab Roadmap 2020-2030. \n\n\n\nRegistration form\n\n\n\n\n\n\n\nProgram\n\n\n\nPDF download below! \n\n\n\nProgram EMBL SciLifeLabDownload URL:https://www.scilifelab.se/event/scilifelab-embl-building-new-collaborative-links/ CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2021/05/image001.jpg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20210531T080000 DTEND;TZID=Europe/Stockholm:20210611T170000 DTSTAMP:20260403T230832 CREATED:20210413T071434Z LAST-MODIFIED:20210526T120645Z UID:10000355-1622448000-1623430800@www.scilifelab.se SUMMARY:Super-Resolution\, Light-Sheet\, STED-FCS and FRET-FCS DESCRIPTION:The Advanced Light Microscopy Unit\, ALM\, at Scilifelab gives a two-week course focusing on four new imaging and fluorescence spectroscopy techniques: \n\n\n\nLight-Sheet Imaging\n\n\n\nLong time-lapse imaging of live model organisms with low phototoxicityUltrafast volumetric imaging of cells with lattice light-sheet microscopy\n\n\n\nSuper-Resolution Imaging in Living Cells – MoNaLISA\n\n\n\nSmart probes. 50 nm resolution at 1-2 Hz. 100 x 100 mm field of view. Time lapse imaging\n\n\n\nSTED-FCS\n\n\n\nFluctuation spectroscopy with 30 nm resolutionSub-diffraction dynamics in living cells\n\n\n\nFRET-FCS\n\n\n\nEasy detection of protein-protein interactions in living cellsHighly sensitive detection of rare oligomers in living cells\n\n\n\nLecturers\n\n\n\nSteven EdwardsErdinc SezginIlaria TestaStefan Wennmalm\n\n\n\nCredits: 3 hp for PhD students\, but open for anyone \n\n\n\nLocation: Web-based \n\n\n\nRegistration: stewen@kth.se URL:https://www.scilifelab.se/event/super-resolution-light-sheet-sted-fcs-and-fret-fcs/ CATEGORIES:Course ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2019/10/microscope.png ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se END:VEVENT END:VCALENDAR