BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//SciLifeLab - ECPv6.16.2//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
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:20210910T130000
DTEND;TZID=Europe/Stockholm:20210910T135500
DTSTAMP:20260528T143753
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:20210909T090000
DTEND;TZID=Europe/Stockholm:20210909T093000
DTSTAMP:20260528T143753
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:20260528T143753
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:20260528T143753
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:20210907T090000
DTEND;TZID=Europe/Stockholm:20210907T110000
DTSTAMP:20260528T143753
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:20210903T090000
DTEND;TZID=Europe/Stockholm:20210903T093000
DTSTAMP:20260528T143753
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:20210823T151500
DTEND;TZID=Europe/Stockholm:20210823T163000
DTSTAMP:20260528T143753
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:20260528T143753
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:20210611T130000
DTEND;TZID=Europe/Stockholm:20210611T160000
DTSTAMP:20260528T143753
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:20210609T140000
DTEND;TZID=Europe/Stockholm:20210609T150000
DTSTAMP:20260528T143753
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:20260528T143753
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:20260528T143753
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:20210602T090000
DTEND;TZID=Europe/Stockholm:20210602T130000
DTSTAMP:20260528T143753
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:20260528T143753
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:20210526T150000
DTEND;TZID=Europe/Stockholm:20210526T160000
DTSTAMP:20260528T143753
CREATED:20210428T095007Z
LAST-MODIFIED:20210602T140817Z
UID:10000370-1622041200-1622044800@www.scilifelab.se
SUMMARY:Role of physiologically-based pharmacokinetics in regulatory submissions
DESCRIPTION:Fabienne Gaugaz Slides from the webinarDownload\n\n\n\nLuzon et al\, 2017Download\n\n\n\nAbstractPhysiologically based pharmacokinetic (PBPK) is an approach that help predict the absorption\, distribution\, metabolism and excretion (ADME) properties of candidate drugs in animal/human and evaluate the effects of intrinsic (e.g. organ dysfunction\, age\, genetics) and extrinsic (e.g. diet\, smoking habit\, drug-drug interactions) factors\, alone or in combinations\, on drug exposure\, during drug discovery and development process. Currently\, different software (i.e. SimCYP\, PK-Sim\, GastroPlus etc) are available to perform the PBPK simulations\, and the simulations are often part of regulatory submissions of small molecules and biologic new drug candidates (CD). \n\n\n\nIf successful\, the simulations may complement or replace the experimental study and/or help to explain different findings\, scenarios related to estimation of exposure and effect of new CDs. Therefore\, the regulatory authorities i.e. EMA and FDA provided guidelines\, which described how to report PBPK models and simulations in a regulatory context.Dr Gaugaz in her presentation will discuss role of PBPK simulations from small molecules and biologic CDs in submissions\, from regulatory point of view. \n\n\n\nPresenterDr Fabienne GaugazPharmacokinetics Assessor\,Medical Products Agency (Läkemedelsverket)Dag Hammarskjölds Väg 42\,752 37 Uppsala \n\n\n\nBiographyDr Fabienne Gaugaz is pharmacokinetics assessor at the Swedish Medical Product Agency (Läkemedelsverket)\, which entails the evaluation of the pharmacologically-based pharmacokinetics (PBPK) simulations related to small molecules and biologic drug candidates. Dr Gaugaz previously worked at Bayer (Wuppertal\, Germany) as lab head of research pharmacokinetics. Fabienne made her postdoc project at Karolinska Institutet (KI) and Uppsala University (UU). Dr Gaugaz obtained her Ph.D. in 2013 in pharmaceutical biology at the Institute of Pharmaceutical Sciences\, Swiss Federal Institute of Technology (ETH) in Zürich\, Switzerland and her M.Sc. in Pharmacy\, ETH\, Zürich\, Switzerland.
URL:https://www.scilifelab.se/event/role-of-physiologically-based-pharmacokinetics-in-regulatory-submissions/
CATEGORIES:Event
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210526T100000
DTEND;TZID=Europe/Stockholm:20210526T120000
DTSTAMP:20260528T143753
CREATED:20210428T095940Z
LAST-MODIFIED:20210511T080725Z
UID:10000371-1622023200-1622030400@www.scilifelab.se
SUMMARY:NGI and NBIS webinar on de novo sequencing and analysis
DESCRIPTION:Welcome to a webinar on de novo sequencing and analysis\, a service that the National Genomics Infrastructure (NGI) and National Bioinformatics Infrastructure Sweden (NBIS) offers to its users. De novo\, which translates to “starting from the beginning”\, refers to the process of sequencing a novel genome from an organism where no previous reference sequence is available. \n\n\n\nThe de novo analysis strategy is divided into separate stages\, starting with (i) sequencing\, (ii) assembly\, and finally (iii) annotation.  \n\n\n\nDuring the sequencing stage\, short and/or long DNA/RNA reads are produced using several sequencing technologies\, such as Illumina\, PacBio and Nanopore. The obtained DNA reads are subsequently assembled into longer sequences\, called contigs during the assembly stage. The gaps between contigs can be linked by scaffolding using long read data and chromosome contact maps obtained by Hi-C.Assembled genomes are then annotated\, allowing for the structure and the function of the assembled sequences to be inferred. This includes protein-coding genes\, but also other features such as non-coding genes and regulatory elements. This webinar will focus on what one needs to consider while planning a de novo project. We are also proud to have Alexander Suh (Lecturer\, University of East Anglia and Uppsala University) describing one of his many projects on how to solve sex-specific and tissue-specific genome differences of birds by using de novo tools facilitated by NGI and NBIS.  \n\n\n\nAgenda\n\n\n\n10:00De novo analysis that NGI can offer youOlga Vinnere Pettersson\, PhD\, Project coordinator NGI10:20PacBio/Nanopore in de novo realmIgnas Bunikis\, PhD\, Bioinformatician NGI10:35Using Hi-C methods to generate chromosome-scaled assembly scaffoldsRemi-Andre Olsen\, PhD\, Bioinformatician NGI10:50The assembly and annotation support available at the SciLifeLab bioinformatics platform NBISHenrik Lantz\, PhD\, Joint Head of Unit Support and Infrastructure NBIS11:05Diving into the depths of sex-specific and tissue-specific genome differences of birdsAlexander Suh\, PhD\, Lecturer\, University of East Anglia and Uppsala University11:30Q&A session
URL:https://www.scilifelab.se/event/ngi-and-nbis-webinar-on-de-novo-sequencing-and-analysis/
CATEGORIES:Event
ORGANIZER;CN="National Genomics Infrastructure (NGI)":MAILTO:support@ngisweden.se
LOCATION:https://www.scilifelab.se/event/ngi-and-nbis-webinar-on-de-novo-sequencing-and-analysis/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210524T151500
DTEND;TZID=Europe/Stockholm:20210524T163000
DTSTAMP:20260528T143753
CREATED:20210521T083002Z
LAST-MODIFIED:20210521T094043Z
UID:10000390-1621869300-1621873800@www.scilifelab.se
SUMMARY:SciLifeLab The Svedberg seminar: Ehab Abouheif
DESCRIPTION:Prof. Ehab Abouheif\n\n\n\nDepartment of Biology\, McGill University\, Canada \n\n\n\nLINK TO SEMINAR \n\n\n\n\n\n\n\nAbouheif received a PhD in Biology from Duke University in 2002\, and from 2002 to 2004\, he completed his postdoctoral studies at the University of Chicago and at the University of California\, Berkeley. In 2004 Abouheif was appointed Assistant Professorship at McGill University as Canada Research Chair (tier 2) in Evolutionary Developmental Biology. Currently\, he is a James McGill Professor in the Department of Biology at McGill University. He is a pioneer of eco-evo-devo\, a field that integrates the concepts and technical tools of ecology\, evolutionary\, and developmental biology. Abouheif focuses on ant societies to understand the origins and evolution of complex biological systems. He served as founding President of the Pan-American Society for Evolutionary Developmental Biology and is currently Editor-in-Chief of JEZ-B: Molecular and Developmental Evolution\, one of the main journals in his field. \n\n\n\nDarwin’s invisible ink: The storage and release of ancestral genetic potential in complex biological systems\n\n\n\nAncestral and dormant genetic potentials exist in all animals\, as reflected by the sporadic appearance of ancestral traits in individuals that normally should not have them\, such as teeth in a chicken or hindlimbs in a whale. Such individuals are traditionally thought to be “freaks” that contribute little to the evolutionary process. Abouheif’s lab\, using supersoldier ants as their model\, has changed this traditional view by demonstrating that evolution can harness dormant genetic potentials after they have been released by certain environmental triggers. His lab also demonstrated that rudimentary organs\, like the human appendix\, are not functionless. Rather\, they can play key regulatory functions during development and store this ancestral genetic  potential over millions of years. These discoveries open up future possibilities for harnessing dormant genetic potentials to advance medicine\, biodiversity conservation\, and animal/plant breeding. \n\n\n\nHost: Arild HusbyRead more about Ehab Abouheif´s research
URL:https://www.scilifelab.se/event/scilifelab-the-svedberg-seminar-ehab-abouheif/
CATEGORIES:Event
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210524T151500
DTEND;TZID=Europe/Stockholm:20210524T161500
DTSTAMP:20260528T143753
CREATED:20210518T081818Z
LAST-MODIFIED:20210524T113122Z
UID:10000386-1621869300-1621872900@www.scilifelab.se
SUMMARY:SciLifeLab The Svedberg seminar: Prof. Ehab Abouheif
DESCRIPTION:Ehab Abouheif\n\n\n\nDepartment of Biology\, McGill University\, Canada \n\n\n\nLINK TO SEMINAR \n\n\n\n Abouheif received a PhD in Biology from Duke University in 2002\, and from 2002 to 2004\, he completed his postdoctoral studies at the University of Chicago and at the University of California\, Berkeley. In 2004 Abouheif was appointed Assistant Professorship at McGill University as Canada Research Chair (tier 2) in Evolutionary Developmental Biology. Currently\, he is a James McGill Professor in the Department of Biology at McGill University. He is a pioneer of eco-evo-devo\, a field that integrates the concepts and technical tools of ecology\, evolutionary\, and developmental biology. Abouheif focuses on ant societies to understand the origins and evolution of complex biological systems. He served as founding President of the Pan-American Society for Evolutionary Developmental Biology and is currently Editor-in-Chief of JEZ-B: Molecular and Developmental Evolution\, one of the main journals in his field. \n\n\n\nDarwin’s invisible ink: The storage and release of ancestral genetic potential in complex biological systems\n\n\n\nAncestral and dormant genetic potentials exist in all animals\, as reflected by the sporadic appearance of ancestral traits in individuals that normally should not have them\, such as teeth in a chicken or hindlimbs in a whale. Such individuals are traditionally thought to be “freaks” that contribute little to the evolutionary process. Abouheif’s lab\, using supersoldier ants as their model\, has changed this traditional view by demonstrating that evolution can harness dormant genetic potentials after they have been released by certain environmental triggers. His lab also demonstrated that rudimentary organs\, like the human appendix\, are not functionless. Rather\, they can play key regulatory functions during development and store this ancestral genetic  potential over millions of years. These discoveries open up future possibilities for harnessing dormant genetic potentials to advance medicine\, biodiversity conservation\, and animal/plant breeding. \n\n\n\nHost: Arild Husby \n\n\n\nRead more about Ehab Abouheif´s research
URL:https://www.scilifelab.se/event/scilifelab-the-svedberg-seminars-prof-ehab-abouheif/
CATEGORIES:Event
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
LOCATION:https://www.scilifelab.se/event/scilifelab-the-svedberg-seminars-prof-ehab-abouheif/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210519T151500
DTEND;TZID=Europe/Stockholm:20210519T164500
DTSTAMP:20260528T143753
CREATED:20210507T142326Z
LAST-MODIFIED:20210511T080437Z
UID:10000385-1621437300-1621442700@www.scilifelab.se
SUMMARY:SciLifeLab COVID-19 seminars: Leen Delang and Jonas Klingström
DESCRIPTION:This first seminar starts with Leen Delang\, Assistant Professor in Virology at KU Leuven\, Belgium\, who will talk about Antiviral therapies for emerging RNA viruses: combatting arboviruses and SARS-CoV-2. Jonas Klingström\, Associate Professor at the Department of Medicine\, Karolinska Institutet\, then continues the seminar by talking about SARS-CoV-2 transmission and pathogenesis. \n\n\n\nHost:  Dr. Marjo-Riitta Puumalainen\, Karolinska Institutet \n\n\n\n\n\n\n\nProgram\n\n\n\n15:15-16:00Antiviral therapies for emerging RNA viruses: combatting arboviruses and SARS-CoV-2Leen Delang\, Assistant Professor in Virology at KU Leuven16:00-16:45SARS-CoV-2 transmission and pathogenesisJonas Klingström\, Associate Professor at the Department of Medicine\, KI\n\n\n\n\nZoom link to seminar\n\n\n\n\n\n\n\n\n\n\nLeen Delang – Bio & abstractDownload\n\n\n\n\n\n\n\n\n\nJonas Klingström – Bio & abstractDownload
URL:https://www.scilifelab.se/event/scilifelab-covid-19-seminars/
CATEGORIES:Event
ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2020/09/covid_3d_model-min-edited-e1620399232105.jpg
LOCATION:https://www.scilifelab.se/event/scilifelab-covid-19-seminars/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210518T151500
DTEND;TZID=Europe/Stockholm:20210518T161500
DTSTAMP:20260528T143753
CREATED:20210428T094603Z
LAST-MODIFIED:20210512T085641Z
UID:10000369-1621350900-1621354500@www.scilifelab.se
SUMMARY:Statistical and machine learning techniques in microbiome research
DESCRIPTION:Leo Lahti\n\n\n\nDepartment of Computing\, University of Turku\, Turku\, Finland \n\n\n\nLINK TO SEMINAR \n\n\n\nLeo Lahti is associate professor in data science in University of Turku\, Finland. After completing his PhD in Aalto University\, Finland\, in 2010 he carried out several years of postdoctoral research in The Netherlands and Belgium on population studies of the human microbiome. Lahti has organized various international training events in microbiome bioinformatics\, and he is the Finnish coordinator of the COST action on statistical and machine learning methods in microbiome studies. \n\n\n\nStatistical and machine learning techniques in microbiome research\n\n\n\nThe diverse microbial communities living in human body have a profound influence on our well-being. Human microbiome research has expanded rapidly following the recent advances in high-throughput DNA sequencing and other omics’ technologies. Consequently\, the demand for targeted computational methods has increased significantly in the recent years. We have a limited understanding of the overall mechanisms that control the observed variation and activity of these microbial ecosystems. Our observations have contributed to the systematic characterization of the individual dynamics and population variation of the human microbiome. I will discuss contemporary topics in statistical analysis and machine learning related to microbiome research\, with a specific emphasis on probabilistic latent variable models in understanding the individual and dynamic variation across the landscape of microbiome composition. \n\n\n\nHost: Anders Andersson \n\n\n\nRead more about Leo Lahti´s research
URL:https://www.scilifelab.se/event/statistical-and-machine-learning-techniques-in-microbiome-research/
CATEGORIES:Event
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
LOCATION:https://www.scilifelab.se/event/statistical-and-machine-learning-techniques-in-microbiome-research/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210510T131500
DTEND;TZID=Europe/Stockholm:20210510T140000
DTSTAMP:20260528T143753
CREATED:20210428T092922Z
LAST-MODIFIED:20210507T075745Z
UID:10000367-1620652500-1620655200@www.scilifelab.se
SUMMARY:A more sustainable chemistry with elemental sulfur
DESCRIPTION:Thanh Binh Nguyen\n\n\n\nUniversité Paris-Saclay\, France\n\n\n\nLINK TO THE SEMINAR\n\n\n\nAbstract\n\n\n\nFacing a more and more rapid depletion of natural resources\, one of the most challenging problems to be solved of modern organic chemistry is to develop reactions enabling access to target molecules from simple and readily available starting materials with higher efficiency in number of atoms while reducing the number of steps\, unnecessary redox changes and waste. With this idea in mind\, we have been concentrating on the use of elemental sulfur – an abundant waste of oil and gas industry with annual product up to 70 MT –  as a polyvalent synthetic tool. This lecture will focus on organic redox reactions developed in our laboratory involving this element as a new synthetic strategy that satisfies most of the requirements of a more sustainable chemistry. \n\n\n\nBiography\n\n\n\nThanh Binh Nguyen received his BS degree (2004) from the University of Natural Sciences in Hochiminh city\, Vietnam and subsequently his MS (2005) and PhD degrees (2008) from the the Université du Maine – Le Mans -France. After a two-year postdoctoral stay at the Institut de Chimie des Substances Naturelles – Gif-sur-Yvette – France\, he obtained a permanent research associate position (Chargé de Recherche) of the Centre National de la Recherche Scientifique (CNRS) in 2011\, working in the same institute. His main research interest is the development of new synthetic methods for carbon-nitrogen bond formation with a strong emphasis on using elemental sulfur\, molecular iodine and iron–sulfur catalysts. \n\n\n\nHost\n\n\n\nDuc Duy Vo\, Uppsala University
URL:https://www.scilifelab.se/event/a-more-sustainable-chemistry-with-elemental-sulfur/
CATEGORIES:Event
ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se
LOCATION:https://uu-se.zoom.us/j/65768822626
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210507T100000
DTEND;TZID=Europe/Stockholm:20210507T120000
DTSTAMP:20260528T143753
CREATED:20210428T092256Z
LAST-MODIFIED:20210428T092313Z
UID:10000366-1620381600-1620388800@www.scilifelab.se
SUMMARY:SciLifeLab Data Repository Launch
DESCRIPTION:SciLifeLab Data Centre invites you to join the launch of the SciLifeLab Data Repository! The event will feature presentations of the repository by representatives from Data Centre and Figshare\, presentation of the user perspective of the repository and opportunities to ask questions.   \n\n\n\nRegister to the launch event to learn more about the SciLifeLab Data Repository and how it can be of use to you! \n\n\n\n \n\n\n\nIntroductionJohan Rung – Head of Data Centre\, SciLifeLabStoring\, sharing\, and citing your data with SciLifeLab’s FigshareMegan Hardeman – Head of Engagement at FigshareUser perspectives:Vicent Pelechano – Researcher at the Department of Microbiology\, Tumor and Cell Biology\, Karolinska Institutet and SciLifeLab FellowJonne Rietdijk – PhD student at the Department of Pharmaceutical Biosciences\, Uppsala UniversityMikael Sellin – Senior lecturer/Associate Professor at the Departement of Medical Biochemistry and Microbiology\, Uppsala University and SciLifeLab FellowFAIR as a factor for bigger research impactWolmar Nyberg Åkerström – Data Steward at NBISQ&A sessionModerated by Data Centre\n\n\n\n\n\n\n\n\nAbout the SciLifeLab Data Repository\n\n\n\nThe SciLifeLab Data Repository\, powered by Figshare\, is a repository for publishing any kind of research-related data\, e.g. documents\, figures\, or presentations. Figshare is an open data repository used by researchers in numerous disciplines. Through an agreement with Figshare\, SciLifeLab offers researchers and units the opportunity to upload and publish their research data through a dedicated portal. The purpose of the SciLifeLab Data Repository is to serve publishing of data.  \n\n\n\n\nContact: datacentre@scilifelab.se
URL:https://www.scilifelab.se/event/scilifelab-data-repository-launch/
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210504T090000
DTEND;TZID=Europe/Stockholm:20210504T100000
DTSTAMP:20260528T143753
CREATED:20210428T091829Z
LAST-MODIFIED:20210428T091856Z
UID:10000365-1620118800-1620122400@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:The April version of the Call4Help session will be a “special edition”. We will present ZeroCostDL4Mic. ZeroCostDL4Mic is a toolbox for the training and implementation of common Deep Learning approaches to microscopy imaging. It exploits the ease-of-use and access to GPU provided by Google Colab. https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki \n\n\n\nPresenter:Petter Ranefall\, BIIF \n\n\n\nTime and location:4 May 2021 (Tuesday)\, 09:00 – 10:00 AMzoom (link will be sent to registered users)
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210426T120000
DTEND;TZID=Europe/Stockholm:20210426T130000
DTSTAMP:20260528T143753
CREATED:20210414T085430Z
LAST-MODIFIED:20210414T085517Z
UID:10000362-1619438400-1619442000@www.scilifelab.se
SUMMARY:Nationella studier av värdet av breda genpaneler och helgenomsekvensering för patienter med hematologiska maligniteter
DESCRIPTION:Flera internationella studier tyder på att storskalig sekvensering kan förbättra diagnostik och behandling av patienter med hematologiska maligniteter. Arbetsutskottet för hematologi inom Genomic Medicine Sweden har initierat två nationella studier för att utvärderat potentialen av breda genpaneler och helgenomsekvenserig i svensk sjukvård. I det här webbinariet kommer vi informera om upplägget för studierna och diskutera detaljer kring patientrekrytering och genomförande. \n\n\n\nMålgrupp: Vi vänder oss till hematologer\, forskningssjuksköterskor\, diagnostiker\, laboratoriepersonal och bioinformatiker som arbetar med hematologiska maligniteter i Sverige\, samt alla andra professioner med intresse av frågan. \n\n\n\nDag och tid: 13 och 26 april\, kl 12-13 (samma webbinarium ges vid två tillfällen)Plats: Digitalt via Zoom https://uu-se.zoom.us/j/61739315319 \n\n\n\nVid webbinariet kommer följande nyckelfrågor att tas upp: \n\n\n\nHur ser etikansökan för studierna ut?Hur är studieupplägget för genpaneler?Hur är studieupplägget för helgenomsekvensering?\n\n\n\nMedverkande: \n\n\n\nRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppenLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi\n\n\n\nAnmälan: Ingen formell anmälan behövs. Anslut bara till länken på utsatt tid. \n\n\n\n\n\n\n\nProgram \n\n\n\n12.00-12.10Välkomna\, Introduktion till GMS och GMS hematologiRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS Hematologi \n\n\n\n12.10-12.20Upplägg för etikansökan och samtyckesblankettThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppen \n\n\n\n12.20-12-30Studieupplägg för genpanelerLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi \n\n\n\n12.30-12.40Studieupplägg för helgenomsekvenseringRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMS \n\n\n\n12.40-13.00Frågor\, diskussion \n\n\n\n\n\n\n\nOm du har frågor om webbinariet är du välkommen att kontakta Eva Berglund\, eva.berglund@scilifelab.uu.se
URL:https://www.scilifelab.se/event/nationella-studier-av-vardet-av-breda-genpaneler-och-helgenomsekvensering-for-patienter-med-hematologiska-maligniteter/2021-04-26/
CATEGORIES:Event
LOCATION:https://uu-se.zoom.us/j/61739315319
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210423T131000
DTEND;TZID=Europe/Stockholm:20210423T140000
DTSTAMP:20260528T143753
CREATED:20210414T084939Z
LAST-MODIFIED:20210414T084942Z
UID:10000359-1619183400-1619186400@www.scilifelab.se
SUMMARY:The open source ecosystem for genome-scale metabolic models
DESCRIPTION:Mihail Anton\, National Bioinformatics Infrastructure Sweden \n\n\n\nWhen: April 23\, 13:10  \n\n\n\nZoom link to the seminar: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nAs science is advancing towards full reproducibility\, the ecosystem of tools and resources for genome-scale metabolic modelling is increasingly open-source. The talk will showcase how Metabolic Atlas is contributing to this ecosystem by integrating several open-source GEMs\, and providing visualisations for these\, with the aim of aiding discovery of disease-related alterations of metabolism.
URL:https://www.scilifelab.se/event/the-open-source-ecosystem-for-genome-scale-metabolic-models/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210423T110000
DTEND;TZID=Europe/Stockholm:20210423T120000
DTSTAMP:20260528T143753
CREATED:20210414T085113Z
LAST-MODIFIED:20210414T085116Z
UID:10000360-1619175600-1619179200@www.scilifelab.se
SUMMARY:Systems biology approaches for translational cancer research
DESCRIPTION:Francesco Gatto\, CSO Elypta\, Sweden \n\n\n\nWhen: April 23\, 11:00  \n\n\n\nZoom: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nIn this seminar\, I will illustrate how we investigated regulation of cancer metabolism using systems biology approaches and leading to the discovery of potential disease biomarkers. The talk will further focus on the challenge to translate fundamental discoveries in clinical practice and the foundation of Elypta – a start-up university spin-off that is executing this transition.
URL:https://www.scilifelab.se/event/systems-biology-approaches-for-translational-cancer-research/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210422T150000
DTEND;TZID=Europe/Stockholm:20210422T160000
DTSTAMP:20260528T143753
CREATED:20210414T084404Z
LAST-MODIFIED:20210414T084407Z
UID:10000358-1619103600-1619107200@www.scilifelab.se
SUMMARY:The evolution of human Genome Scale Metabolic models
DESCRIPTION:Jonathan Robinson\, Scientific Data Developer Bioinnovation Institute\, Denmark \n\n\n\nWhen: April 22\, 15:00 \n\n\n\nZoom: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nMetabolism provides the energy and building blocks necessary to support life\, but the complexity of the metabolic network presents a challenge when trying to determine how changes to one component affects the system as a whole. Genome-scale metabolic models (GEMs) were developed to address this challenge by providing computational reconstructions of metabolic networks. GEMs have been developed for hundreds of species including humans\, supporting new approaches to study human health and disease.In my talk\, I will present our work in developing the most recent human GEM\, Human1\, and the different ways in which the model can be used to interpret omics data in a metabolic context. I will also share the challenges that we faced while developing Human1\, and the challenges that we still face over a year after its initial release in 2020. Finally\, I will discuss how we envision the future of GEMs\, and our efforts to make them more accessible and useful for bioinformaticians.
URL:https://www.scilifelab.se/event/the-evolution-of-human-genome-scale-metabolic-models/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210421T131500
DTEND;TZID=Europe/Stockholm:20210421T140000
DTSTAMP:20260528T143753
CREATED:20210414T084108Z
LAST-MODIFIED:20210414T084111Z
UID:10000357-1619010900-1619013600@www.scilifelab.se
SUMMARY:Data-driven approaches towards studying context-specific cell signalling
DESCRIPTION:Evangelia Petsalaki\, Group Leader EMBL/EBI\, United Kingdom \n\n\n\nWhen: April 21\, 13:15 \n\n\n\nZoom: https://stockholmuniversity.zoom.us/j/68215564760 \n\n\n\nHost: Rui Benfeitas\, Stockholm University \n\n\n\nAbstract\n\n\n\nOur group aims to understand and describe the organisation principles of cell signalling that allow the diverse and context-specific cell responses and phenotypes.It is well established that signalling responses happen through complex networks. However\, most signalling research still uses linear pathways as the ground truth. Moreover\, signalling responses are highly dependent on context\, such as tissue type\, genetic background etc and therefore these static pathways are not always suitable. There is also a high bias in the literature towards kinases and pathways for which reagents and prior knowledge is readily available. This leaves a huge dark space in our understanding of cell signalling and significantly hinders studies of its general principles.In this talk I will present two projects where we try to mitigate some of the above issues. For the first one I will present CEN-tools\, an integrative webserver and python package\, that allows users to navigate the contexts of different gene essentialities. I will demonstrate examples of its use in discovering new gene-gene relationships and important putative signalling targets for different cancers. For the second one I will present a method that combines paired transcriptomics and imaging data to extract context-specific signalling networks\, with the context in this case cell shape in breast cancer. The method is generalisable to any paired transcriptomics/phenotype data.
URL:https://www.scilifelab.se/event/data-driven-approaches-towards-studying-context-specific-cell-signalling/
CATEGORIES:Event
ORGANIZER;CN="Rui Benfeitas%2C SciLifeLab/Stockholm University":MAILTO:rui.benfeitas@scilifelab.se
LOCATION:https://stockholmuniversity.zoom.us/j/68215564760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210420T100000
DTEND;TZID=Europe/Stockholm:20210420T120000
DTSTAMP:20260528T143753
CREATED:20210414T081421Z
LAST-MODIFIED:20210414T083002Z
UID:10000356-1618912800-1618920000@www.scilifelab.se
SUMMARY:NGI webinar on Spatial Transcriptomics 10X Visium
DESCRIPTION:The National Genomics Infrastructure (NGI) at SciLifeLab invites you to participate in a webinar on the Spatial Transcriptomics 10X Visium technology.  \n\n\n\nSpatially resolved transcriptomics\, recently pronounced Method of the Year by Nature Methods\, has undoubtedly changed the way we understand complex tissues.  With the recent launch of the 10X Genomics Visium assay\, we can now offer spatially resolved transcriptome-wide analysis in tissue sections\, right here at NGI!  \n\n\n\nThis webinar will serve as a guide through how the technology has evolved\, how the protocol is run\, and how spatial transcriptomics data can be analysed.  \n\n\n\nOur line-up of talks include speakers from NGI and the Spatial Research lab\, as well as two keynote speakers; Dr. Alessondra Speidel\, who will present how Spatial Transcriptomics has helped her understand how wound healing responds to different hydrogel materials\, and Dr. James Chell\, a Senior Scientist at 10X Genomics who will update us on the Visium spatial platform and its FFPE application.  \n\n\n\nInterested? Find out more how NGI can support projects that can benefit from 10X Genomics Visium.
URL:https://www.scilifelab.se/event/ngi-webinar-on-spatial-transcriptomics-10x-visium/
CATEGORIES:Event
ORGANIZER;CN="National Genomics Infrastructure (NGI)":MAILTO:support@ngisweden.se
LOCATION:https://www.scilifelab.se/event/ngi-webinar-on-spatial-transcriptomics-10x-visium/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210413T120000
DTEND;TZID=Europe/Stockholm:20210413T130000
DTSTAMP:20260528T143753
CREATED:20210414T085430Z
LAST-MODIFIED:20210414T085517Z
UID:10000361-1618315200-1618318800@www.scilifelab.se
SUMMARY:Nationella studier av värdet av breda genpaneler och helgenomsekvensering för patienter med hematologiska maligniteter
DESCRIPTION:Flera internationella studier tyder på att storskalig sekvensering kan förbättra diagnostik och behandling av patienter med hematologiska maligniteter. Arbetsutskottet för hematologi inom Genomic Medicine Sweden har initierat två nationella studier för att utvärderat potentialen av breda genpaneler och helgenomsekvenserig i svensk sjukvård. I det här webbinariet kommer vi informera om upplägget för studierna och diskutera detaljer kring patientrekrytering och genomförande. \n\n\n\nMålgrupp: Vi vänder oss till hematologer\, forskningssjuksköterskor\, diagnostiker\, laboratoriepersonal och bioinformatiker som arbetar med hematologiska maligniteter i Sverige\, samt alla andra professioner med intresse av frågan. \n\n\n\nDag och tid: 13 och 26 april\, kl 12-13 (samma webbinarium ges vid två tillfällen)Plats: Digitalt via Zoom https://uu-se.zoom.us/j/61739315319 \n\n\n\nVid webbinariet kommer följande nyckelfrågor att tas upp: \n\n\n\nHur ser etikansökan för studierna ut?Hur är studieupplägget för genpaneler?Hur är studieupplägget för helgenomsekvensering?\n\n\n\nMedverkande: \n\n\n\nRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppenLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi\n\n\n\nAnmälan: Ingen formell anmälan behövs. Anslut bara till länken på utsatt tid. \n\n\n\n\n\n\n\nProgram \n\n\n\n12.00-12.10Välkomna\, Introduktion till GMS och GMS hematologiRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMSThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS Hematologi \n\n\n\n12.10-12.20Upplägg för etikansökan och samtyckesblankettThoas Fioretos\, överläkare i klinisk genetik och co-chair GMS HematologiMartin Höglund\, överläkare i hematologi och f.d. ordförande Svenska AML-gruppen \n\n\n\n12.20-12-30Studieupplägg för genpanelerLucia Cavelier\, sjukhusgenetiker och co-chair GMS Hematologi \n\n\n\n12.30-12.40Studieupplägg för helgenomsekvenseringRichard Rosenquist Brandell\, överläkare i klinisk genetik och föreståndare GMS \n\n\n\n12.40-13.00Frågor\, diskussion \n\n\n\n\n\n\n\nOm du har frågor om webbinariet är du välkommen att kontakta Eva Berglund\, eva.berglund@scilifelab.uu.se
URL:https://www.scilifelab.se/event/nationella-studier-av-vardet-av-breda-genpaneler-och-helgenomsekvensering-for-patienter-med-hematologiska-maligniteter/2021-04-13/
CATEGORIES:Event
LOCATION:https://uu-se.zoom.us/j/61739315319
END:VEVENT
END:VCALENDAR