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: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
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210527T130000
DTEND;TZID=Europe/Stockholm:20210527T140000
DTSTAMP:20260403T230832
CREATED:20210503T144307Z
LAST-MODIFIED:20210503T144310Z
UID:10000381-1622120400-1622124000@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series:  Saman Hosseini Ashtiani and Valentina Carannante
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\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\n\n\n\n\nSaman Hosseini Ashtiani\n\n\n\n \n\n\n\nArne Elofsson – Alpha 6 \n\n\n\n\n\nValentina Carannante\n\n\n\n \n\n\n\nBjörn Önfelt – Gamma 3 \n\n\n\n\n\nPlease select a valid form
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-saman-hosseini-ashtiani-and-valentina-carannante/
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210526T150000
DTEND;TZID=Europe/Stockholm:20210526T160000
DTSTAMP:20260403T230832
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:20260403T230832
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:20260403T230832
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:20260403T230832
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:20210520T130000
DTEND;TZID=Europe/Stockholm:20210520T140000
DTSTAMP:20260403T230832
CREATED:20210503T144432Z
LAST-MODIFIED:20210510T070134Z
UID:10000382-1621515600-1621519200@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Alma Andersson and Alexander Muhleip
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\nAlma Andersson\n\n\n\nExploring the cell type topography by integration of single cell and spatial transcriptomics data  \n\n\n\nJoakim Lundeberg – Alpha 3 \n\n\n\n\n\nAlexander Muhleip\n\n\n\nThe molecular basis for cristae maintenance in Toxoplasma mitochondria \n\n\n\nAlexey Amunts – Gamma 3 \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-alma-andersson-and-alexander-muhleip/
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210519T151500
DTEND;TZID=Europe/Stockholm:20210519T164500
DTSTAMP:20260403T230832
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:20260403T230832
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:20210517T080000
DTEND;TZID=Europe/Stockholm:20210521T170000
DTSTAMP:20260403T230832
CREATED:20210428T093317Z
LAST-MODIFIED:20210428T093423Z
UID:10000368-1621238400-1621616400@www.scilifelab.se
SUMMARY:Introduction to bioinformatics using NGS data (Online)
DESCRIPTION:National workshop for PhD students\, postdocs\, researchers and other employees within Swedish academia. This workshop is run by the National Bioinformatics Infrastructure Sweden(NBIS) and National Genomics Infrastructure (NGI). \n\n\n\nDue to the Covid-19 situation\, this workshop will be held online. \n\n\n\nIf you have questions regarding the workshop\, please email: edu.intro-ngs@nbis.se \n\n\n\nImportant dates \n\n\n\nApplication opens:  February 01\, 2021 Application closes: April 11\, 2021Confirmation to accepted students:  April 16\, 2021\n\n\n\nResponsible teachers:  Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\n \n\n\n\n \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 a 2000 SEK workshop fee**Please note that NBIS cannot invoice individuals \n\n\n\nCourse content \n\n\n\nThis intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform\, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures. \n\n\n\nAfter this workshop you should be able to: \n\n\n\nDescribe the basic principles of next generation sequencing.Use the Linux command line interface to manage simple file processing operations\, and organize directory structures.Connect to and work on a remote high performance compute cluster.Apply programs in Linux for analysis of NGS data.Summarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.Explain common NGS file formats.Interpret quality control of NGS reads.Explain the steps involved in variant calling using whole genome sequencing data.Independently perform a basic variant calling workflow on example data.Explain the steps involved in differential gene expression using RNA seq data.Independently perform differential gene expression analysis on example data.\n\n\n\nEntry requirements \n\n\n\nA background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to \n\n\n\nHave relevant previous experience in sequencing or analysis.Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.\n\n\n\nSelection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance.
URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-online/
CATEGORIES:Course
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210512T130000
DTEND;TZID=Europe/Stockholm:20210512T140000
DTSTAMP:20260403T230832
CREATED:20210503T144526Z
LAST-MODIFIED:20210503T144529Z
UID:10000383-1620824400-1620828000@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Rui Shao and Yerma Pareja Sanchez
DESCRIPTION:Introducing the new Campus Solna Seminar Series – a new initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 13:00-13:50 and following current regulations\, they will be broadcast via zoom. \n\n\n\n\n\n\nRui Shao\n\n\n\nEstimating RNA transcription speed with multi-omics \n\n\n\nSimon Elsässer Group – Alpha 4 \n\n\n\n\n\nYerma Pareja Sanchez\n\n\n\nDiscovering new factors involved in transcriptional memory \n\n\n\nVincent Pelechano Group – Gamma 5 \n\n\n\n\n\n\nRegister to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series\, i.e. only one registration is necessary. \n\n\nPlease select a valid form
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-rui-shao-and-yerma-pareja-sanchez/
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210510T131500
DTEND;TZID=Europe/Stockholm:20210510T140000
DTSTAMP:20260403T230832
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:20260403T230832
CREATED:20210428T092256Z
LAST-MODIFIED:20210428T092313Z
UID:10000366-1620381600-1620388800@www.scilifelab.se
SUMMARY:SciLifeLab Data Repository Launch
DESCRIPTION:SciLifeLab Data Centre invites you to join the launch of the SciLifeLab Data Repository! The event will feature presentations of the repository by representatives from Data Centre and Figshare\, presentation of the user perspective of the repository and opportunities to ask questions.   \n\n\n\nRegister to the launch event to learn more about the SciLifeLab Data Repository and how it can be of use to you! \n\n\n\n \n\n\n\nIntroductionJohan Rung – Head of Data Centre\, SciLifeLabStoring\, sharing\, and citing your data with SciLifeLab’s FigshareMegan Hardeman – Head of Engagement at FigshareUser perspectives:Vicent Pelechano – Researcher at the Department of Microbiology\, Tumor and Cell Biology\, Karolinska Institutet and SciLifeLab FellowJonne Rietdijk – PhD student at the Department of Pharmaceutical Biosciences\, Uppsala UniversityMikael Sellin – Senior lecturer/Associate Professor at the Departement of Medical Biochemistry and Microbiology\, Uppsala University and SciLifeLab FellowFAIR as a factor for bigger research impactWolmar Nyberg Åkerström – Data Steward at NBISQ&A sessionModerated by Data Centre\n\n\n\n\n\n\n\n\nAbout the SciLifeLab Data Repository\n\n\n\nThe SciLifeLab Data Repository\, powered by Figshare\, is a repository for publishing any kind of research-related data\, e.g. documents\, figures\, or presentations. Figshare is an open data repository used by researchers in numerous disciplines. Through an agreement with Figshare\, SciLifeLab offers researchers and units the opportunity to upload and publish their research data through a dedicated portal. The purpose of the SciLifeLab Data Repository is to serve publishing of data.  \n\n\n\n\nContact: datacentre@scilifelab.se
URL:https://www.scilifelab.se/event/scilifelab-data-repository-launch/
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210506T130000
DTEND;TZID=Europe/Stockholm:20210506T140000
DTSTAMP:20260403T230832
CREATED:20210503T144618Z
LAST-MODIFIED:20220202T083122Z
UID:10000384-1620306000-1620309600@www.scilifelab.se
SUMMARY:Campus Solna Seminar Series: Meike Latz and Daniel Gyllborg
DESCRIPTION:Introducing the new Campus Solna Seminar Series – a new initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 13:00-13:50 and following current regulations\, they will be broadcast via zoom. \n\n\n\n\n\n\nVesna Grujcic\n\n\n\nCombined imaging and single cell transcriptomics of eukaryotic plankton \n\n\n\nAnders Andersson – Alpha 3 \n\n\n\n\n\nDaniel Gyllborg\n\n\n\nApplications and advancements of in situ sequencing for cell atlas projects \n\n\n\nMats Nilsson – Gamma 4 \n\n\n\n\n\n\nRegister to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series\, i.e. only one registration is necessary. \n\n\nPlease select a valid form
URL:https://www.scilifelab.se/event/campus-solna-seminar-series-meike-latz-and-daniel-gyllborg/
CATEGORIES:Community
ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210504T090000
DTEND;TZID=Europe/Stockholm:20210504T100000
DTSTAMP:20260403T230832
CREATED:20210428T091829Z
LAST-MODIFIED:20210428T091856Z
UID:10000365-1620118800-1620122400@www.scilifelab.se
SUMMARY:BioImage Informatics Call4Help
DESCRIPTION:The April version of the Call4Help session will be a “special edition”. We will present ZeroCostDL4Mic. ZeroCostDL4Mic is a toolbox for the training and implementation of common Deep Learning approaches to microscopy imaging. It exploits the ease-of-use and access to GPU provided by Google Colab. https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki \n\n\n\nPresenter:Petter Ranefall\, BIIF \n\n\n\nTime and location:4 May 2021 (Tuesday)\, 09:00 – 10:00 AMzoom (link will be sent to registered users)
URL:https://www.scilifelab.se/event/bioimage-informatics-call4help/
CATEGORIES:Event
ORGANIZER;CN="Bioimage Informatics Unit":MAILTO:biif@scilifelab.se
LOCATION:
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260403T230832
CREATED:20210414T092540Z
LAST-MODIFIED:20210506T225135Z
UID:10000364-1620028800-1620406800@www.scilifelab.se
SUMMARY:Quick and clean: advanced Python for data science in biology - ONLINE
DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in need of Advanced Python skills within all Swedish universities. \n\n\n\nImportant dates\n\n\n\nApplication is open!Application closes: April 15\, 2021Confirmation to accepted students: April 21\, 2021For questions about the course\, please contact Ashfaq Ali (ashfaq.ali@nbis.se)\, Sergiu Netotea (sergiu.netotea@nbis.se)\n\n\n\nCourse fee\n\n\n\nThe course is free of charge but a no show fee course fee of 2000 SEK will be invoiced to accepted participants who failed to attend the course after accepting to participate. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\nThe main aim of this course is to introduce students to the so-called Zen of Python for quick and clean application of python in data science. The workshop is structured around  based on the industry way of classifying big data jobs: data analytics\, data science\, data engineering.  \n\n\n\nParticipants will have an opportunity to learn the following topics \n\n\n\nGeneral overview of computer choke points for various architectures together with a fast paced tutorial on advanced language concepts.Scientific computing\, statistics\, visualization and data mining\, via libraries such as numpy\, pandas\, statmodels and several other “science stack” libraries.Programming with focus on how to perform machine learning\, deep learning\, statistical learning and pattern recognition using python\, via scikit-learn\, tensorflow\, pymc3 and other more exotic libraries.Engineering the computing infrastructure and Python’s role in it. How to run Python on clouds and GPU machinesLearning how Python can be used to organize your workflow with efficiency and reproducibility in mind.Application to research themes where you will either pick one real ‘omics subject from a given task list or you will use Python in your project under our assistance. This is a great time to solidify your knowledge by applying it to your own research scope!\n\n\n\nLearning Outcomes\n\n\n\nAt the end of the course the course participants will have achieved following objectives \n\n\n\nGeneral knowledge about computational workflow using pythonHave knowledge about computer architecture and use of python for efficient computingKnowledge about python libraries for machine learning\, deep learning and statistical learning and their applicationsAbility to apply advanced python libraries in own research field\n\n\n\nWorkshop organization\n\n\n\nWe aim for a balance between lecturing and exercise in Jupyter notebooks (jupyter.org) which is used for taking notes\, self study\, hands on tasks and interaction. Considering that the course is online\, lectures will be delivered via zoom links and exercises will be carried out in zoom breakout rooms with the help of teaching assistants. Course session leaders will be available to answer theoretical and practical questions. Questions are welcome at any time. \n\n\n\nYou will be asked to prepare your laptop a week before the course starts. We will also use a slack channel for communication\, posting links or code tips. \n\n\n\nImportant to Know\n\n\n\nThe workshop covers some of the basic concepts of python programming and each session will have advanced material on the topic that may test the limits of the participant’s knowledge of python and computers. Difficulties during learning are expected and are part of the course design. \n\n\n\nFor the sessions on analyses of your own data\, students are encouraged to send their topic of interest before the start of the course.   \n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises \n\n\n\nA computer with any OS.           Python\, R or any other computer language basic knowledge.Basic skills handling your own computer.For those interested in tasks involving cloud computing\, access to Amazon AWS is required. (user configuration)\n\n\n\nDesirable to have \n\n\n\nYou have bioinformatics or systems biology background\, statistical and machine learning skills.Have Linux on your laptop\, or access to a Linux server.You did programming before (not just courses) and can handle the command line.Have a good idea for a task you want to achieve on the fourth day.\n\n\n\nDue to limited space the course can accommodate a maximum of 20 participants. If we receive more applications\, participants will be selected based on several criteria including entry requirements\, motivation to attend the course as well as gender and geographical balance. \n\n\n\nGithub page (older version)
URL:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
CATEGORIES:Course
LOCATION:https://www.scilifelab.se/event/quick-and-clean-advanced-python-for-data-science-in-biology-online/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20210503T080000
DTEND;TZID=Europe/Stockholm:20210507T170000
DTSTAMP:20260403T230832
CREATED:20210414T092106Z
LAST-MODIFIED:20210414T093012Z
UID:10000363-1620028800-1620406800@www.scilifelab.se
SUMMARY:Genome Assembly and Annotation 2021 – Online
DESCRIPTION:Elixir course open for PhD students\, postdocs\, researchers and other employees in need of Genome assembly and annotation skills. \n\n\n\nImportant dates\n\n\n\nApplication opens: 30th of March Application closes:19th of AprilConfirmation to accepted students: 26th of April \n\n\n\nResponsible teachers:  Christophe Klopp (FR)\, Lucile Soler (SE)\, Mahesh Binzer-Panchal (SE)\, Nima Rafati (SE)\, Tomas Larsson (SE)\, Henrik Lantz (SE)\, Brane Leskosek (SI)\, Marko Vidak (SI) and Erik Hjerde (NO) \n\n\n\nIf you do not receive information according to the above dates please contact:  Erik Hjerde \n\n\n\nCourse fee\n\n\n\nThe course is free of charge. \n\n\n\nCourse content\n\n\n\nThis course will introduce the best practice bioinformatics methods to assemble and annotate genomes via a series of lectures\, group work and computer practicals. Topics covered will include: \n\n\n\nQuality Assessment of sequencing dataLong read technologies and assemblies and assembly polishingAssembly ValidationHi-C sequencingMethod in Structural AnnotationAbinitio annotationAnnotation with makerAbinitio trainingFunctional annotationSubmission to DBBacterial annotation\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and complete the computer exercises: \n\n\n\nMandatory to complete a short command line course prior to the event. This will be made available to enrolled participants\n\n\n\nThe course is limited to 25 people\, and maximum 2 participants per national ELIXIR node (except Norway). The course is an advanced course. Based on the information collected upon registration\, the course organizers will enroll participants.
URL:https://www.scilifelab.se/event/genome-assembly-and-annotation-2021-online/
CATEGORIES:Course
ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se
END:VEVENT
END:VCALENDAR