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:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20221030T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20230326T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20231029T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20240331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20241027T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231102T120000 DTEND;TZID=Europe/Stockholm:20231102T130000 DTSTAMP:20260403T205612 CREATED:20230711T115341Z LAST-MODIFIED:20231012T084425Z UID:10000933-1698926400-1698930000@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Emilie Flaberg & Kiana Hosseinpour Moghaddam DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nEmilie Flaberg\n\n\n\nPäivi Östling – alpha 4 \n\n\n\n \n\n\n\n\n\nKiana Hosseinpour Moghaddam\n\n\n\nOla Larsson – gamma 5 \n\n\n\n \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-nov-2/ LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_124630107_HDR-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231106T090000 DTEND;TZID=Europe/Stockholm:20231110T170000 DTSTAMP:20260403T205612 CREATED:20230818T135627Z LAST-MODIFIED:20230915T130032Z UID:10000955-1699261200-1699635600@www.scilifelab.se SUMMARY:DDLS Population genomics in practice DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of hands-on and practical skills for the analyses of population genomics data. \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-08-17 \n\n\n\nApplication closes: 2023-09-30 \n\n\n\nConfirmation to accepted students: 2023-10-10 \n\n\n\nCourse Leader and teachers: Per Unneberg (CL)\, Nikolay Oskolkov\, Jason Hill\, André Soares \n\n\n\nIn case you miss information on any of the above dates\, please contact: edu.population-genomics-in-practice@nbis.se \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches\, coffee and snacks. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse content\n\n\n\nThe aim of this workshop is to provide an introduction to commonly used methods in population genomics. As the focus of the course is on hands-on work\, the topics have been designed to cover the fundamental analyses that are common in many population genomics studies. The course consists of lectures and exercises\, with a focus on the practical aspects of analyses. Whereas lectures introduce some background theory\, their primary aim is to set the stage for accompanying exercises. \n\n\n\nTopics covered will include: \n\n\n\n\nFoundations of population genetics\n\n\n\nIntroduction to simulation and the coalescent\n\n\n\nBasics of variant calling\n\n\n\nVariant filtering and sequence masks\n\n\n\nCharacterization and interpretation of DNA sequence variation\n\n\n\nCalculation and interpretation of summary statistics from variation data\n\n\n\nInvestigating population structure with admixture modelling and principal component analyses\n\n\n\nDemographic modelling using sequentially Markovian coalescent models and linkage disequilibrium\n\n\n\nSelection scans\n\n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\ndescribe the different forces of evolution and how they influence genetic variation\n\n\n\nunderstand and interpret genealogical trees and how they relate to genetic variation data\n\n\n\ndescribe the basics of the coalescent\n\n\n\nperform simple coalescent simulations with msprime\n\n\n\nrun simple SLiM forward simulation models\n\n\n\ndescribe and run the steps of a variant calling pipeline\, including quality control of raw reads\, read mapping\, and variant calling\n\n\n\nknow how and when to filter raw variant calls using manual coverage filters\n\n\n\ndescribe and calculate nucleotide diversity from variation data\n\n\n\nanalyse population structure with admixture modelling and dimensionality reduction methods\n\n\n\nperform demographic modelling with sequential Markovian coalescent models\n\n\n\ndescribe methods that identify regions undergoing adaptation and selection\n\n\n\nrun selection scans\, score identified regions and interpret findings in the context of genome annotations\n\n\n\n\n\n\n\n\n\n\nEntry Requirements\n\n\n\nThe following is a list of skills required for being able to follow the course and complete the exercises: \n\n\n\n\nBasic knowledge in R or Python\n\n\n\nBasic knowledge of variant calling\, or the equivalent of NBIS course “Introduction to Bioinformatics using NGS data”\n\n\n\nBasic knowledge of population genetics\n\n\n\nBasic understanding of frequentist statistics\n\n\n\nA computer\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nExperience with analysis of NGS and other omic data\n\n\n\n\nDue to limited space the course can accommodate a maximum of 25 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance. URL:https://www.scilifelab.se/event/population-genomics-in-practice/ LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231106T100000 DTEND;TZID=Europe/Stockholm:20231107T170000 DTSTAMP:20260403T205612 CREATED:20230509T092633Z LAST-MODIFIED:20231020T075809Z UID:10000882-1699264800-1699376400@www.scilifelab.se SUMMARY:21st Swedish Bioinformatics Workshop 2023 in Stockholm DESCRIPTION:We’re pleased to invite you to the 21st Swedish Bioinformatics Workshop (SBW) that will take place in Stockholm on November 6th – 7th (Mo-Tu). SBW is an annual event that is hosted by different universities across Sweden. This year\, the event will take place at Karolinska Sjukhuset Solna at the Sune Bergström’s Aula. \n\n\n\nAs is tradition\, SBW will be a chance for PhD students and postdocs as well as all researchers working with bioinformatics or computational biology to present their work\, discuss the latest developments in the field\, and improve their bioinformatic skills through different workshops. In addition\, the program includes lectures from invited speakers\, participant presentations\, and poster sessions. \n\n\n\nThis year SBW is part of the Nordic Computational Biology Week. It features SBW (6th-7th of Nov.\, Mo-Tu)\, the Danish Bioinformatics Symposium (8th-9th of Nov.\, We-Th) and the Finish Symposium on Computational Biology (10th of Nov.\, Fr). More information can be found under: bit.ly/ncb-week-2023 \n\n\n\nMore information regarding SBW will be updated on the website: sbw2023.eu. On-site registration is closed\, but you can still sign up for free for virtual attendance. There you can also sign up for the other events that are part of the Nordic Computational Biology Week. If you have any questions\, feel free to reach out to sbw2023@scilifelab.se. \n\n\n\nWelcome to the Swedish Bioinformatics Workshop 2023! URL:https://www.scilifelab.se/event/swedish-bioinformatics-workshop-2023/ LOCATION:Sune Bergström Aula\, BioClinicum\, New Karolinska University Hospital\, Solnavägen 30\, Stockholm\, 17164\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/05/SBW2023_logo_green_tb1-1024x327-1.png ORGANIZER;CN="Swedish Bioinformatics Workshop 2023":MAILTO:sbw2023@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231107T130000 DTEND;TZID=Europe/Stockholm:20231107T140000 DTSTAMP:20260403T205612 CREATED:20231030T125153Z LAST-MODIFIED:20231030T132952Z UID:10001009-1699362000-1699365600@www.scilifelab.se SUMMARY:Discovery of SARS-CoV-2 Main Protease inhibitors at the DDD platform DESCRIPTION:Pandemic preparedness and the generation of SARS-CoV-2 inhibitors – A new exit from SciLifeLab Drug Discovery and Development platform \n\n\n\nDDD Exit Event 2023-11-07\, zoomcast 13.00 \n\n\n\n \n\n\n\nPresenters\n\n\n\nDr. Ulf Ribacke. Dept. of Microbiology\, Tumor and Cell Biology\, Karolinska InstitutetTel: +46 70 497 5196\, Email: ulf.ribacke@ki.se \n\n\n\nProf. Jens Carlsson\, Dept. of Cell and Molecular Biology\, Uppsala UniversityTel: +46 72 227 7976\, Email: jens.carlsson@icm.uu.se \n\n\n\nAbstract\n\n\n\nSciLifeLab has been commissioned by the government to build laboratory capacity to assist in future pandemics through research and competence and technology development. Hear more about the SciLifeLab Pandemic Laboratory Preparedness program from Ulf Ribacke\, (SciLifeLab and Karolinska Institutet) and groundbreaking research performed by researchers at Uppsala University that led to discovery of potent main protease SARS-CoV-2 inhibitors. \n\n\n\nJens Carlsson\, Helena Danielson\, Anja Sandström and Lindon Moodie have recently signed an agreement for international partnering of a project focusing on development of drugs for treatment of COVID-19 (DP_JC_188). \n\n\n\nThe project was funded by the National COVID-19 Research Program initiated by the Knut and Alice Wallenberg Foundation. Hit compounds identified by virtual screening were published in 2022 by Luttens et al. (https://doi.org/10.1021/jacs.1c08402). Hit-to-lead generation was then performed together with the Drug Discovery and Development Platform in the DP_JC_188 project. Lead optimization and preclinical development of assets are now supported by an international pharmaceutical company. \n\n\n\nShort speakers biography:\n\n\n\nUlf Ribacke: Ulf is scientific co-director of the SciLifeLab Pandemic Laboratory Preparedness program and heads two research labs located at Karolinska Institutet and Uppsala University\, both dedicated to resolve how malaria parasites adapt to evade cellular stress with the ultimate goal to identify targets for new interventions. \n\n\n\nJens Carlsson: Jens is a Professor of Computational Biochemistry at Uppsala University\, where his group uses computational models to understand protein function at the molecular level and develops strategies for drug discovery.For more information\, visit http://www.carlssonlab.org/. \n\n\n\nUlf RibackeKarolinska InstitutetScientific Lead – Pandemic Laboratory Preparedness at SciLifeLabulf.ribacke@ki.se\n\n\n\nJens CarlssonUppsala Universityjens.carlsson@icm.uu.se URL:https://www.scilifelab.se/event/discovery-of-sars-cov2-mpro-inhibitors-at-the-ddd-platform/ CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231109T100000 DTEND;TZID=Europe/Stockholm:20231109T153000 DTSTAMP:20260403T205612 CREATED:20231009T132350Z LAST-MODIFIED:20231026T114542Z UID:10000995-1699524000-1699543800@www.scilifelab.se SUMMARY:The Spatial Biology Tour 2023 - the Spatial Proteomics Unit and Lunaphore DESCRIPTION:The Spatial Proteomics Unit at SciLifeLab hosts the Lunaphore Spatial Biology Tour at SciLifeLab Solna. \n\n\n\nTake the opportunity to learn more about the COMET platform for automated sequential immunofluorescence and how you can work with the Spatial Proteomics Unit to generate highly multiplexed imaging data for your research project. \n\n\n\nThe Spatial Proteomics Unit was an early beta tester of the COMET platform in 2021 and since 2022 offer the COMET platform as a service in their unit. You will also get the chance to see the instrument live in the Spatial Proteomics unit. \n\n\n\nRead more and register here\n\n\n\n\n\n\n\nMultiplexed image of a colon FFPE sample generated on the COMET platform\n\n\n\n \n\n\n\nProgram\n\n\n\n10:00Welcome and registration10.15Spatial cell profiling with hyperplex immunofluorescenceAngelo Da Rosa11.00COMET – opportunities in the Spatial Proteomics FacilityCharlotte Stadler11.45RNAscope™: Single-molecule RNA in situ hybridization. ANY Gene. ANY Species. ANY tissue.Joan Raouf12.15Lunch and networking13.00COMET™ on-site instrument demonstration14.15Refreshment and networking URL:https://www.scilifelab.se/event/the-spatial-biology-tour-2023-the-spatial-proteomics-unit-and-lunaphore/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/10/COMET-colon.png ORGANIZER;CN="Spatial Proteomics Unit":MAILTO:spatial.proteomics@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231109T120000 DTEND;TZID=Europe/Stockholm:20231109T130000 DTSTAMP:20260403T205612 CREATED:20230711T115453Z LAST-MODIFIED:20231107T105533Z UID:10000934-1699531200-1699534800@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Adelina Rabenius DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nAdelina Rabenius\n\n\n\nAnniina Vihervaara – alpha 3 \n\n\n\nTimers in genes: Introns define the order of heat-induced chaperone production \n\n\n\n\n\n\n\n\n\n \n\n\n\n \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-nov-9/ LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_120135408_HDR-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231113T090000 DTEND;TZID=Europe/Stockholm:20231117T170000 DTSTAMP:20260403T205612 CREATED:20230607T141335Z LAST-MODIFIED:20230607T141419Z UID:10000906-1699866000-1700240400@www.scilifelab.se SUMMARY:Introduction to bioinformatics using NGS data DESCRIPTION:National workshop for PhD students\, postdocs\, researchers\, and other employees within Swedish academia\, introducing the analysis of next generation sequencing data. \n\n\n\nThe course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI) \n\n\n\nResponsible teachers: Malin Larsson\, Martin Dahlö\, Roy Francis \n\n\n\nContact information: edu.intro-ngs@nbis.se  \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\n\n\n\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Jun 7\, 2023 \n\n\n\nApplication deadline: October 4\, 2023 \n\n\n\nConfirmation to accepted participants: Week 41 (October 9-12) \n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis on-site training event costs 3000 SEK for academic participants\, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee.  \n\n\n\n\n\n\n\nCourse description\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\n\n\n\n\nCourse content\n\n\n\nBriefly\, the workshop covers the followings major topics: \n\n\n\n\nWorking on the UNIX/LINUX command line\n\n\n\nBioinformatic/NGS data formats and QC\n\n\n\nDNA variant calling workflow essentials\n\n\n\nRNA sequence analysis workflow essentials\n\n\n\n\n\n\n\n\nLearning outcomes\n\n\n\nAfter this workshop you should be able to: \n\n\n\n\nDescribe the basic principles of next generation sequencing.\n\n\n\nUse the Linux command line interface to manage simple file processing operations\, and organise directory structures.\n\n\n\nConnect to and work on a remote high performance compute cluster.\n\n\n\nApply programs in Linux for analysis of NGS data.\n\n\n\nSummarise the applications of current NGS technologies\, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.\n\n\n\nExplain common NGS file formats.\n\n\n\nInterpret quality control of NGS reads.\n\n\n\nExplain the steps involved in variant calling using whole genome sequencing data.\n\n\n\nIndependently perform a basic variant calling workflow on example data.\n\n\n\nDemonstrate hands-on experience with handling raw RNA sequencing data\, QC and quantification of gene expression.\n\n\n\nExplain the steps involved in differential gene expression using RNA seq data.\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nTo be able to follow the workshop you need to: \n\n\n\n\nBYOL\, bring your own laptop configured according to precourse instructions.\n\n\n\nHave a background in genetics\, cell biology\, biomedicine\, biochemistry\, bioinformatics or comparable.\n\n\n\nTo get the maximum benefit from the workshop you should:\n\n\n\nHave a research project where you are currently using or are planning to use next generation sequencing.\n\n\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nDue to limited space the course can accommodate a maximum of 30 participants. If we receive more applications\, participants will be selected based on several criteria. Selection criteria include correct entry requirements\, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers\, and we will prioritise applications  from Swedish academia. URL:https://www.scilifelab.se/event/introduction-to-bioinformatics-using-ngs-data-3/ LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231115T123000 DTEND;TZID=Europe/Stockholm:20231116T123000 DTSTAMP:20260403T205612 CREATED:20230119T182051Z LAST-MODIFIED:20231114T233510Z UID:10000792-1700051400-1700137800@www.scilifelab.se SUMMARY:DDLS Annual Conference 2023; The emerging role of AI in data-driven life science DESCRIPTION:Image generated with DALL-E 3\n \n\n\n\n\n\n\n\n\nThis DDLS Annual Conference brings together the data-driven community in Life Science\, introduces newly appointed DDLS fellows\, and provides opportunities for networking across the research community and SciLifeLab infrastructures. The theme for 2023 is “the emerging role of AI in data-driven life science”\, and we are excited to welcome Prof. Dr. Fabian Theis\, Director of the Computational Health Center and Director of the Institute for Computational Biology and Rocio Mercado\, WASP Fellow\, Chalmers University of Technology as Keynote speakers. There will be presentations from DDLS fellows\, and invited speakers on how they use AI in their research and their future visions. The conference also features two pre-conference introductory lectures on AI for imaging and natural language processing and a post-conference workshop on AI model serving. \n\n\n\nTarget group: All scientists interested in data-driven research are welcome to join the 2-day lunch-to-lunch Conference in Stockholm. \n\n\n\nRegistration\n\n\n\nThe onsite event has reached total capacity. Please register as a Zoom participant to get access to the Zoom link. Feel free to add yourself to the waiting list\, and you will be notified by email if a place becomes available. \n\n\n\nRegistration for zoom link\n\n\n\n\n\n\n\nPoster session\n\n\n\nPoster session\, Flash Talk & Best Poster Award (click to open)\nPoster list \n\n\n\nPoster-List-DDLS-Annual-conference-2023Download\n\n\n\nPoster booklet\, including abstracts \n\n\n\nPoster-Booklet-DDLS-Annual-conference-2023Download\n\n\n\nThe DDLS Annual Conference Best Poster Award\, encourages the submission and exhibition of high-quality posters carried out by young scientists\, including Ph.D. students\, post-doctoral researchers\, etc. The poster should be on a topic related to data-driven life science. The Prize\, which is based upon the decision of a Scientific Committee-appointed Jury\, consists of a certificate and a travel grant of up to 5 000 SEK. The travel must be booked and ordered through the DDLS Support team and follow regular University travel policy. The trip should be completed before 2024-12-31. \n\n\n\nThe Best Poster Award winner for 2022 was Adelina Rabenius\, KTH\, and we are proud to support her attendance at an EMBO conference this summer. \n\n\n\nOrganizer: SciLifeLab\, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science\, on behalf of the DDLS Steering group. \n\n\n\n\nPre-conference introductory lectures \n\n\n\nIn the morning of the first conference day\, there will be two introductory lectures; one on AI within image analysis (by Anna Klemm from Bioimage Informatics Facility\, SciLifeLab) and one on large-language models (by Magnus Sahlgren from AI Sweden). The purpose of these lectures is to cover the basics and emerging role of AI within these two active fields. No prior knowledge of the fields is required. \n\n\n\nPost-conference activities\n\n\n\nNote! The Post-conference workshop and different DDLS stakeholder meetings will be handled separately and require separate registrations. \n\n\n\nWorkshop\n\n\n\nBuilding and sharing machine learning demo applications within life sciences: a practical tutorial. This event is now full\, you can register for the wait list only (in case we receive a cancellation). November 16\, at 13:30 – 15:30. SciLifeLab Campus Solna\, Tomtebodavägen 23. Meet-up in the Lobby. Room Gamma 2 Lunchroom. Participant list here \n\n\n\nStakeholder meetings\n\n\n\nDDLS Fellows meeting (DDLS Fellows only). November 16\, at 13:30 – 15:30. Biomedicum\, Solnavägen 9. Room B0317. Participant list here \n\n\n\nDDLS Fellows PhD & Postdocs meeting (for the PhD and Postdoc members of the DDLS Fellows research groups). November 16\, at 13:30 – 15:30. Biomedicum\, Solnavägen 9. Room B0313. Participant list here \n\n\n\nDDLS Cell and Molecular Biology Expert group meeting (for the CMB Expert group and the CMB Data Science Node). November 16\, at 15:30 – 17:30. SciLifeLab Campus Solna\, Tomtebodavägen 23. Room Earth \n\n\n\n\nDDLS Research area Cell and Molecular Biology Symposium\, Nov 17\n\n\n\nThe DDLS research area\, Cell and molecular biology\, invites you to the first in-person symposium on November 17 from 9 to 14. The day will be an introduction to the research area Fellows and Expert Group. \n\n\n\nMore information here\n\n\n\n\nProgram\n\n\n\nNovember 15\n\n\n\n09:30Venue: Jacob Berzeliussalen\, Berzelius väg 3\, SolnaRegistration is open from 09:30. Hang your poster from 09:30 to 12:30.10:00Pre-conference introductory lecture: AI in bioimage analysisAnna Klemm\, Uppsala University10:45Pre-conference introductory lecture: Large Language ModelsMagnus Sahlgren\, AI Sweden11:30Lunch12:30WelcomeOla Spjuth\, chair of Scientific Committee DDLS Annual ConferenceModerator: Ola Spjuth\, Uppsala University12:35Data-driven Life ScienceOlli Kallioniemi\, Director SciLifeLab13:00Blood proteome is a powerful tool to monitor human health and diseaseWen Zhong\, DDLS Fellow\, Linköping University 13:20Artificial intelligence-based computational pathology for precision diagnostics in breast cancerMattias Rantalainen\, KI13:40Coffee break 14:10Keynote: Generative AI for modeling single-cell state and responseFabian J. Theis\, Helmholtz Munich\, Technical University of Munich15:00Short breakModerator: Fredrik Johansson\, Chalmers15:155 x Flash Talks à 5 min per selected poster1. Gonzalo Uribarr2. Melisa Maidana Capitan3. Marcel Tarbier4. Sheng Joevenller5. Philipp Rentzsch 15:45Poster session with snacks and drinks17:30End of Day 117:30Speakers Dinner. Invited only. Speakers\, DDLS Steering Group\, DDLS Fellows\, Organizing committee\n\n\n\nNovember 16\n\n\n\n08:30CoffeeModerator: Laura Carroll\, Umeå University09:00From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processesJuliette Griffé\, DDLS Fellow\, Stockholm University09:20Multi-omics data integration with robust penalized regression identifies context-dependent signaling networksCemal Erdem\, DDLS Fellow\, Umeå University09:40AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell ModelingWei Ouyang\, DDLS Fellow\, KTH10:00Data Centre – capabilities and collaborationsJohan Rung\, SciLifeLab Data centre10:20Coffee break10:45Announcement of Best Poster Award10:50Keynote: Transforming Biomolecular Engineering Through AIRocio Mercado\, WASP Fellow\, Chalmers University of Technology Moderator: Johan Bengtsson-Palme\, Chalmers11:45Panel discussion about the emerging role of AI in DDLS12:30Lunch and end of DDLS Annual Conference13:30Post-Conference activities (separate registration)Building and sharing machine learning demo applications within life sciences: a practical tutorial. The event is fully booked.SciLifeLab Campus Solna\, Tomtebodavägen 23A. Room Gamma lunch room.DDLS Fellows meetingBiomedicum\, Solnavägen 9. Room B0317.DDLS Fellows PhD & Postdoc meetingBiomedicum\, Solnavägen 9. Room B0313.15:30End of Post-Conference activities15:30DDLS Cell and Molecular Biology Expert group meetingSciLifeLab Campus Solna\, Tomtebodavägen 23A. Room Earth.\n\n\n\nAbstracts\n\n\n\nPre-Conference Lectures\n\n\n\nAnna Klemm – AI in bioimage analysis\nIn this introductory lecture I will present how AI is used in bioimage analysis. The lecture will start with examples of “classical” image analysis to then explain the concepts of machine learning and AI-techniques in bioimage analysis. In the lecture I will give examples of life science projects in which we have trained convolutional neural networks to segment and classify structures of interest in the images\, or encode entire images. I will explain why we chose AI-based methods over classical image analysis and will also point to resources of the growing landscape of workflows\, pre-trained networks\, and repositories of freely available bioimage data + their annotations. \n\n\n\n\n\n\n\nExample of using a CNN for image segmentation on H&E-stained sections of mouse salivary glands. Segmentation starting from manually generated ground-truth\, using a Xception network model. Source: https://biifsweden.github.io/projects/2023/08/07/EduardoVillablanca2023-1/\, Xenia Tolstoy\, Christophe Avenel (BIIF) \n\n\n\n\nMagnus Sahlgren – Large Language Models\nThis presentation gives an introduction to and overview of the currently dominating trend in AI with Large Language Models (LLMs). We cover the theoretical background\, basic architectures\, training methodologies\, and capabilities of LLMs\, spotlighting models like the GPT series\, as well as Sweden’s national initiative GPT-SW3. We will touch upon diverse applications of LLMs in both the public and private sectors\, and address various considerations and challenges related to LLMs\, including biases\, transparency\, and societal implications. \n\n\n\n\nConference\n\n\n\nMartin Eklund – Prediction models and artificial intelligence for improving prostate cancer diagnostics and treatment\nProstate cancer diagnostics and treatment suffer from inefficient use of information for clinical decision making\, leading to high rates of overdiagnosis and overtreatment of indolent disease at the same time as prostate cancer is the leading cause of cancer death among men. We will in our presentation discuss how we are systematically trying to develop and clinically implement prediction models and artificial intelligence (AI) systems to address these inefficiencies. We will for example discuss the combination of the Stockholm3 test with MRI to improve prostate cancer diagnostics (Eklund et al. NEJM\, 2021; Nordström et al. Lancet Oncology\, 2021)\, and show results from the development of an AI-system for diagnosis and grading of prostate cancer in biopsies (Ström et al. Lancet Oncology\, 2020; Bulten et al. Nature Medicine\, 2022; Olsson et al. Nature Communications 2022)\, which we have demonstrated can performs on par with internationally leading uro-pathologist. We will also discuss the link between AI and clinical trials and how clinical trials can be transformed into continuous learning systems\, which we will exemplify with the ongoing ProBio trial for improving treatment for men with metastatic prostate cancer (Crippa et al. Trials\, 2020; De Laere et al. European Urology Focus\, 2022). \n\n\n\n\nCemal Erdem – Multi-omics data integration with robust penalized regression identifies context-dependent signaling networks\nCells integrate signals from different external stimuli to decide their fate\, such as growth or death. The “context” of a cell -the extracellular and intracellular environments- dictates the structure of signaling networks that determine such cellular responses. Identifying context-specific edges is vital for predicting and understanding cell decision-making logic. However\, robust identification of context-dependent network structures remains a broadly unsolved problem. Here\, I will talk about a pipeline we built previously to integrate multi-omics datasets using machine learning algorithms in a central-dogmatic view. Applying this pipeline to publicly available datasets\, we showed that it could pinpoint differentially activated pathways: (i) in response to two highly similar sister cytokines in breast epithelial cells and (ii) in breast tumor subtypes. I will conclude my talk with a vignette showing how such knowledge can further be utilized to explore new gene regulatory mechanisms. \n\n\n\n\nJuliette Griffié – From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processes\nSingle Molecule Localisation Microscopy (SMLM) is a fluorescence super-resolution microscopy technique which allows to image fluorophores in cells with unprecedented resolution (typically 10-30nm). It produces lists of localisations from which fundamental information about key cellular processes can be extracted. We will focus here on how SMLM data sets can be used as input to design dynamic models on cellular membrane biophysics. We will apply these data-driven models to reliably recapitulate and predict the nanoscale requirements for immune cells activation as well as to control and modify cellular signalling in the context of diseases. \n\n\n\n\nRocío Mercado – Transforming Biomolecular Engineering Through AI\nAI’s lightning-paced advancements are ushering in a new era of scientific research\, and the realm of molecular engineering stands as a prime beneficiary of this transformation. This talk explores the growing integration of AI in the life sciences\, with a primary emphasis on therapeutic discovery\, shedding light on the current state-of-the-art for molecular discovery and future prospects. We delve into the evolution of deep generative models and their practical applications in molecular engineering\, giving a few key examples of reinforcement learning and synthesizability-constrained design in this domain. Moreover\, we share recent progress in challenging application areas\, such as targeted protein degradation and synthesis prediction. With adaptive AI models\, capable of learning from vast datasets in real time\, we can streamline computational and experimental resources\, improving efficiency as we search through the complex chemical space. The talk will conclude with an overview of leading developments in AI which have yet to see widespread application in the life sciences\, offering new horizons for scientists exploring data-driven life science research. These innovative methodologies hold the potential to reshape conventional practices and bridge the gap between scientific exploration and AI-driven innovation. \n\n\n\n\nWei Ouyang – AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell Modeling\nAs part of the Data-Driven Life Science fellows program at SciLifeLab\, AICell Lab is actively laying the groundwork for a future powered by AI in cellular and molecular biology. With a focus on long-term strategic planning\, the lab is investing in state-of-the-art automated imaging farms\, complete with advanced microscopes\, robotic arms\, liquid handlers\, and automatic incubators. \n\n\n\nIn addition\, AICell Lab is developing specialized AI software to augment real-time microscopic imaging\, enable smart acquisition\, facilitate robotic control\, integrate multi-omics data\, and power AI-driven cell simulators\, among other functionalities. These preparatory steps align with the lab’s long-term vision to build large-scale\, comprehensive models of human cells\, utilizing both existing multi-omics datasets and new data generated in-house. \n\n\n\nThrough this focused preparation and investment\, AICell Lab aims to redefine in-silico cellular research and drug discovery\, contributing to a unified and systematic understanding of human cellular biology. \n\n\n\n\nFabian J. Theis – Generative AI for modeling single-cell state and response\nAdvances in single cell genomics nowadays allow the large scale construction of organ atlases. These can be used to study perturbations such as signaling\, drugs or diseases\, with large-scale access to state changes on the multi-omic and spatial level. This provides an ideal application area for machine learning methods to understand cellular response. With generative AI revolutionizing many fields of science by allowing researchers to explore uncharted territories\, generate novel hypotheses\, and simulate complex phenomena\, we ask how it has been enabling modeling single cell variation\, potentially towards a single cell foundation model. \n\n\n\nAfter reviewing deep generative representation learning approaches to identify the gene expression manifold\, I will shortly outline some applications on cell atlas building. Then I will discuss interpretable modeling of perturbations on this manifold\, in particular effect of drug responses as well as multiscale readouts such as disease state across patients\, and how to learn organism-wide cell type predictors. I will finish with extensions towards temporal and spatial observations. \n\n\n\n\nWen Zhong – Blood proteome is a powerful tool to monitor human health and disease\nThe rise of high throughput molecular technologies has shed lights on the development of next-generation molecular diagnostics and biomarkers for patient stratifications in the precision medicine era. There is an urgent need to develop new systematic tools to combine multi-omics data and link genotype to phenotype to expand our knowledge of complex traits of human diseases. Our research group mainly focuses on the integration of multi-omics\, the interplay between genetics and phenotypes\, and the development of data-driven strategies/tools for precision medicine. The aim is to investigate the molecular biomarkers for the estimation of disease risks\, early diagnosis of disease\, stratification of drug treatment response\, disease progression monitoring and the stratification of patients.  \n\n\n\n\nWorkshop \n\n\n\nBuilding and sharing machine learning demo applications within life sciences: a practical tutorial\nIt is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application\, prepare it for deployment\, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable within a couple of hours. \n\n\n\nThe workshop will last for 2 hours with a break in the middle. We have room to accept 30 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nNote that registration for the workshops is separate from the registration for the conference. Please see the workshop page for information on registration. \n\n\n\n \n\n\n\n\nScientific Committee\n\n\n\n\nChair: Ola Spjuth\, Uppsala University\n\n\n\nJohan Bengtsson-Palme\, Chalmers\n\n\n\nLaura Carroll\, Umeå University\n\n\n\nFredrik Johansson\, WASP\, Chalmers\n\n\n\n\nProject leader\n\n\n\n\nErika Erkstam\, Operations office URL:https://www.scilifelab.se/event/ddls-annual-conference-2023/ LOCATION:Jacob Berzelius salen\, KI\, Berzelius väg 3\, Solna\, 171 65\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/DDLS_cropped-Liten.jpeg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231116T093000 DTEND;TZID=Europe/Stockholm:20231116T170000 DTSTAMP:20260403T205612 CREATED:20231004T141040Z LAST-MODIFIED:20231109T155333Z UID:10000989-1700127000-1700154000@www.scilifelab.se SUMMARY:New Horizons for Swedish Sciences: World-unique (Bio)Solids Capabilities at the national UMU NMR facility DESCRIPTION:Inauguration of world-unique combined solid-state NMR equipment (MAS CryoNMR Probe + Ultrafast MAS NMR Probe) for the next application level in sciences ranging from bio and medical sciences to novel material and environment. Equipment is installed at the Umeå University KBC NMR core facility\, a national SciLifeLab and VR-RFI (SwedNMR) node. \n\n\n\nRead more\n\n\n\nProgram \n\n\n\nProgramInaugurationNMR20231116finalDownload URL:https://www.scilifelab.se/event/new-horizons-for-swedish-sciences-world-unique-biosolids-capabilities-at-the-national-umu-nmr-facility/ LOCATION:Carl Kempe-salen\, KBC Building\, Umeå University\, Umeå\, Sweden CATEGORIES:Event ORGANIZER;CN="Swedish NMR Centre":MAILTO:info@nmr.gu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231116T120000 DTEND;TZID=Europe/Stockholm:20231116T130000 DTSTAMP:20260403T205612 CREATED:20230711T115618Z LAST-MODIFIED:20231107T105923Z UID:10000935-1700136000-1700139600@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Greta Gudoityte & Stavros Azinas DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nGreta Gudoityte\n\n\n\nBrinton Seashore-Ludlow – alpha 4 \n\n\n\nInterplay between Cancer-Associated Fibroblasts and Ovarian Cancer. \n\n\n\n\n\nStavros Azinas\n\n\n\nMarta Carroni – gamma3 \n\n\n\nConfirmational insights of bacterial dissagregase CLPG. \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-nov-16/ LOCATION:Gamma-6-Pascal\, SciLifeLab\, Tomtebodavägen 23\, Solna\, 17165\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_123412496_HDR2-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231116T133000 DTEND;TZID=Europe/Stockholm:20231116T153000 DTSTAMP:20260403T205612 CREATED:20231017T130803Z LAST-MODIFIED:20231101T115949Z UID:10001003-1700141400-1700148600@www.scilifelab.se SUMMARY:Building and sharing machine learning demo applications within life sciences: a practical tutorial DESCRIPTION:This workshop is part of the DDLS Annual Conference 2023: The emerging role of AI in data-driven life science. This event is also part of Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre. \n\n\n\nTitle: Building and sharing machine learning demo applications within life sciences: a practical tutorial \n\n\n\nOrganizer: AI Data Engineers from the SciLifeLab Serve team. \n\n\n\nWhere and when: November 16\, 2023 at 13:30-15:30 at SciLifeLab Solna (Tomtebodavägen 23A\, Solna) \n\n\n\nAbstract: It is becoming increasingly popular to share machine learning models with the community as web applications with an easy-to-use interface. Users can then adjust parameters or submit their own input and see the predictions generated by the underlying model. This tutorial is aimed at researchers working within life sciences who work with machine learning models but do not have the skills to build applications for web. During the tutorial we will start from a trained model and demonstrate step by step how you can create a graphical user interface for your application\, prepare it for deployment\, and make it available on the web with a URL. We will demonstrate the use of specific tools which make this process easy and doable in under an hour. \n\n\n\nThe workshop will last for 2 hours with a break in the middle. We have room to accept 30 participants\, on the first come first served basis. Those registered after that will be placed on the waiting list. \n\n\n\nSince there is a limited number of spots in this workshop please sign up only if you intend to attend. \n\n\n\nThis event is now full\, you can register for the waiting list only (in case we received a cancellation). We will organize similar workshops in the future\, it will be announced in the same event series. \n\n\n\nRegister to join the event\n\n\n\nMore about the event series: \n\n\n\nTools for AI/ML research in life sciences is an event series by the SciLifeLab Data Centre aimed at life science researchers who use machine learning methods in their work. The goal of the events in this series is to provide introductions to different tools for ML research but also to foster discussions around our practices and how they can be improved. The events takes place virtually (over Zoom) and are open to researchers in Sweden and beyond. Each event is scheduled for 60 minutes\, consisting of a talk and an extended discussion. Follow the page of the event series to learn about future seminars. \n\n\n\nFor questions about the events please contact the organizing team by emailing serve@scilifelab.se \n\n\n\n \n\n\n\nScientific lead: Prof. Ola Spjuth\, SciLifeLab Data Centre and Uppsala University \n\n\n\nContact information: serve@scilifelab.se URL:https://www.scilifelab.se/event/building-and-sharing-machine-learning-demo-applications-within-life-sciences-a-practical-tutorial/ LOCATION:SciLifeLab Campus Solna\, Tomtebodavägen 23 A\, Solna\, Sweden CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231117T090000 DTEND;TZID=Europe/Stockholm:20231117T141000 DTSTAMP:20260403T205612 CREATED:20230830T210018Z LAST-MODIFIED:20231112T090520Z UID:10000962-1700211600-1700230200@www.scilifelab.se SUMMARY:Cell and Molecular Biology Symposium DESCRIPTION:The DDLS research area\, Cell and molecular biology\, invites you to the first in-person symposium. The day will be an introduction to the research area Fellows and Expert Group. \n\n\n\nRegistration\n\n\n\nWe have a limited number of seats (52p). All participants must register (including the speakers i.e.\, DDLS Fellows and research area Expert group). Participant list here If you register after Nov 7\, we offer fika and lunch but can’t accommodate food preferences. \n\n\n\nRegistration\n\n\n\nAgenda\n\n\n\n08:45Registration\, check-in and Coffee09:00Introduction to Data-driven Life Science program and the Cell and molecular biology research areaMargit Mahlapuu\, Chair of the DDLS CMB Expert groupPresentations of fellows\, Expert group members\, and Data science node09:15Title TBAJuliette Griffie\, DDLS Fellow09:40Making it work in reality – bridging the gap between curated proof of concept tests and real world deployment of biomedical image based deep learningIda-Maria Sintorn\, DDLS Expert group 09:55AICell Lab: Towards AI-powered Data-driven Whole-cell ModelingWei Ouyang\, DDLS Fellow10:20Title TBAErik Lindahl\, DDLS Expert group10:35Coffee break 10:50Time-resolved structural studies of photoactive proteinsSebastian Westenhoff\, DDLS Expert group11:05From model systems to global surveillance programs for infectious diseases: Some challenges and the road aheadJohan Bengtsson-Palme\, DDLS Fellow11:30The DDLS Data Science Node – status report towards supporting the national CMB research communityThomas Svensson\, Sverker Holmgren\, Data Science node12:00RNA insights from extinct animals and single cellsMarc Friedländer\, DDLS Expert group12:15Understanding intestinal diseases with spatial transcriptomicEduardo Villablanca\, DDLS Expert group12:30Lunch13:15“Weak\, noisy and uninteresting”: subtle features of macromolecular structuresNicholas Pearce\, DDLS Fellow13:40Metabolic Liver Disease: Molecular Mechanisms and Novel TargetsMargit Mahlapuu\, DDLS Expert group13:55Wrap-up and Action item summaryMargit Mahlapuu14:10End of the day URL:https://www.scilifelab.se/event/cell-and-molecular-biology-symposium/ LOCATION:Biomedicum\, room Peter Reichard\, Solnavägen 9\, Stockholm\, 171 65 CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/03/CMB_Icon-1.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231120T090000 DTEND;TZID=Europe/Stockholm:20231124T160000 DTSTAMP:20260403T205612 CREATED:20230911T091422Z LAST-MODIFIED:20230911T091932Z UID:10000970-1700470800-1700841600@www.scilifelab.se SUMMARY:NBIS/ELIXIR-SE Tools for Reproducible Research DESCRIPTION:NBIS / ELIXIR-SE course is open for PhD students\, postdocs\, group leaders and core facility staff interested in making their computational analysis more reproducible. International applications are welcome\, but we will give approximately half of the participant slots to applicants from Swedish universities at minimum\, due to the national role NBIS plays in Sweden. \n\n\n\nThe course is organized by NBIS (ELIXIR-SE). \n\n\n\nResponsible teachers: Erik Fasterius\, John SundhContact information: edu.trr@nbis.se \n\n\n\n\n\n\n\n\n\nApply here\n\n\n\n\n\nCourse website\n\n\n\n\n\nImportant dates\n\n\n\nApplication open: Sep 11\, 2023 \n\n\n\nApplication deadline: Oct 20\, 2023 \n\n\n\nConfirmation to accepted participants: Oct 27\, 2023 \n\n\n\n\n\n\n\nCourse fee\n\n\n\nA course fee of 3000 SEK will be invoiced to accepted participants. This includes lunches\, coffee and snacks\, and course dinner. Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse description\n\n\n\nOne of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis\, e.g. bioinformatics or computational biology\, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete\, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study\, all the code and/or computational notebooks needed to produce results from the raw data\, and the computational environment or a complete description thereof. \n\n\n\nReproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly\, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self! \n\n\n\n\n\n\n\nCourse content\n\n\n\nTopics covered \n\n\n\n\nGood practices for data analysis\n\n\n\nVersion control and collaborative code development\n\n\n\nPackage and environment management\n\n\n\nWorkflow management\n\n\n\nDocumentation and reporting\n\n\n\nContainerized computational environments\n\n\n\n\nLearning outcomes \n\n\n\nBy the end of the course the student will be able to: \n\n\n\n\nOrganize and structure computational projects\n\n\n\nTrack changes and collaborate on code using Git\n\n\n\nInstall packages and manage software environments using Conda\n\n\n\nStructure computational steps into workflows with Snakemake and Nextflow\n\n\n\nCreate automated reports and document their analyses with RMarkdown and Jupyter\n\n\n\nPackage and distribute computational environments using Docker and Singularity\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nRequired for being able to follow the course and to complete computer exercises: \n\n\n\n\nFamiliarity with using the terminal (e.g. be familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.)\n\n\n\nSome knowledge in R and/or python is beneficial but not strictly required\n\n\n\n\n\n\n\n\nSelection criteria\n\n\n\nThe course can accommodate 20 participants. Selection criteria include correct entry requirements\, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.  \n\n\n\nPlease note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits\, however the estimated credits are just guidelines. If formal credits are crucial\, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not. URL:https://www.scilifelab.se/event/nbis-elixir-se-tools-for-reproducible-research/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231121T150000 DTEND;TZID=Europe/Stockholm:20231121T160000 DTSTAMP:20260403T205612 CREATED:20220829T115023Z LAST-MODIFIED:20231120T151621Z UID:10000656-1700578800-1700582400@www.scilifelab.se SUMMARY:SciLifeLab Data Platform- how we support data-driven life science research DESCRIPTION:The SciLifeLab Data Management seminar series next event is focused on the SciLifeLab Data Platform which is a hub for data-driven life science research. The SciLifeLab Data Platform aims to act as a ‘one-stop shop’ for data-driven life science in Sweden. It includes services (e.g. tools and databases)\, materials related to community building (e.g. jobs and events pages)\, and resources aimed at promoting data-driven life science research (e.g. data highlights). Presentations from the Liane Hughes\, SciLifeLab Data Centre Platform team lead\, will give you an overview of about the services\, resources\, and community building of the Platform\, suggestions on how you can contribute\, as well as a quick guide to hosting your data on the Platform.  \n\n\n\nWhen: Nov 21\, 3.00-4.00 PM CET.Where: Zoom \n\n\n\nRegister before Nov 21 at 3PM ( Zoom link will be sent out to registered participants.) \n\n\n\n\nRegister\n\n\n\n\nSciLifeLab Data Management seminar series is an event series by the SciLifeLab Data Centre and NBIS joint Data Management team aimed at both the life science research community and infrastructure\, and others with an interest in research data management in life sciences. The events will showcase how to put the FAIR principles\, and good data management into practice. The goal of the events in this seminar series is to provide interesting seminars around topics related to research data management in general but also to foster discussions around best practices and how they can be improved. The events takes place virtually (over Zoom) and are open to everyone\, (researchers\, staff\, RDM professionals etc.) working at or affiliated with a Swedish research institute or university. Each event is scheduled for 60 minutes\, consisting of a presentation and an also gives time to discussion and questions from the participants. The videos will be published openly after the seminars at the SciLifeLab YouTube channel. \n\n\n\nMore information about  SciLifeLab Data Centre and NBIS joint Data Management team: https://data-guidelines.scilifelab.se/ \n\n\n\nWelcome! \n\n\n\nOrganisers: SciLifeLab Data Centre and NBIS National Bioinformatics Infrastructure Sweden \n\n\n\nContact us\, data-management@scilifelab.se URL:https://www.scilifelab.se/event/data-platform-how-we-support-data-driven-life-science/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/05/prickar-1-edited-1.png LOCATION:https://www.scilifelab.se/event/data-platform-how-we-support-data-driven-life-science/ END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231122T100000 DTEND;TZID=Europe/Stockholm:20231122T120000 DTSTAMP:20260403T205612 CREATED:20230921T093726Z LAST-MODIFIED:20231120T152126Z UID:10000974-1700647200-1700654400@www.scilifelab.se SUMMARY:Data Management Plans in practise - research funder perspectives and practical demos DESCRIPTION:Join SciLifeLab Data Centre and NBIS in collaboration with Uppsala University Library and Umeå University Library for a joint virtual event “Data Management Plans in practise – research funder perspectives and practical demos“. The first hour is focused on Data Management Plans (DMPs) from the perspective of Swedish research funders. \n\n\n\nPart 1 – Data Management Plans (DMPs) from the perspective of Swedish research fundersToday\, many research funders require or recommend that researchers write DMPs for the research projects that they fund. What is the purpose of DMPs from the research funder´ s perspective? What would the funder like to achieve with the DMPs? Major Swedish research funders present their perspective as stakeholders\, followed by a panel discussion about how DMPs can help researchers and funders conduct research more effectively and to improve the quality of the research outputs. \n\n\n\nPart 2 – Demonstration of DMPonline and Data Stewardship WizardMany researchers and PhD students perceive writing a DMPs as a difficult task. A common mistake that researchers make when they write their first DMPs is copying content from their research plan. This is usually not going to work well because data management plans address different questions than research plans. A data management plan is not about scientific questions but about work with information and how this information can be preserved and shared with other stake holders. This webinar offers interested participants an opportunity to see how tools for writing DMPs look like\, what guidance they give and how one can use question-based templates to write a data management plan in a short time. The demonstrations cover the tools DMPonline and Data Stewardship Wizard. DMPonline is a general tool that researchers can use to write DMPs or all disciplines. Data Stewardship Wizard has a different design and SciLifeLab offers an instance focused on research in life sciences. \n\n\n\nWhen: Nov 22nd 2023. 10.00-12.00 (Stockholm time) on Zoom \n\n\n\nTarget group: Researchers and PhD students from all research fields and everybody else who works with research data. \n\n\n\nRegister by Nov 22\, at 10.00 \n\n\n\n\nRegister\n\n\n\n\n \n\n\n\nPart 1: Data Management Plans – the perspective of Swedish research funders \n\n\n\n10:00 – 10:05 Welcome\, Christer Lagvik\, Uppsala University Library \n\n\n\n10:05 – 10:35 Presentations from Sanja Halling\, Swedish Research Council\, Eva Stensköld\, Riksbankens Jubileumsfond and Andreas Björke\, Forte. \n\n\n\n10:35 – 10:55 Panel discussion Sanja Halling\, Swedish Research Council\, Eva Stensköld\, Riksbankens Jubileumsfond\, Andreas Björke\, Forte and Siv Andersson\, Knut and Alice Wallenberg Foundation. Moderator: Niclas Jareborg\, NBIS \n\n\n\nPart 2. Demos of tools for writing DMPs \n\n\n\n11:05 – 11:35 Demonstration of DMPonline using a question-based template\, Theresa Kieselbach\, Umeå University Library. \n\n\n\n11:35 – 12:00 Demonstration of Data Stewardship Wizard at SciLifeLab\, Elin Kronanser\, NBIS. \n\n\n\nWelcome! \n\n\n\nThis event is a collaboration between SciLifeLab Data Centre\, NBIS\, Uppsala University Library and Umeå University Library. For questions please contact SciLifeLab Data Centre datacentre@scilifelab.se URL:https://www.scilifelab.se/event/data-management-plans-in-practise/ CATEGORIES:Event LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231122T140000 DTEND;TZID=Europe/Stockholm:20231122T143000 DTSTAMP:20260403T205612 CREATED:20231108T102002Z LAST-MODIFIED:20231108T102034Z UID:10001015-1700661600-1700663400@www.scilifelab.se SUMMARY:CSI Seminar: ‘Movement Snacks’ DESCRIPTION:We at the Coaching in Science Initiative (CSI) are excited to host our first invited speakers talk titled: ‘Movement Snacks’ \n\n\n\nIn this seminar Movement Snacks will raise awareness about integrating movement into our day\, and providing simple exercises we all can do\, regardless of where we sit and work! \n\n\n\nA snack is a small meal that bridges the gap between larger ones\, providing relief from hunger. Similarly\, a movement snack involves a brief burst of physical activity to give your body a break from inactivity. If you find yourself sitting for extended periods\, don’t be overly concerned – it’s a common situation for most of us. Introducing short bursts of movement\, or “movement snacks\,” throughout the day can help enhance blood circulation\, alleviate joint stiffness\, increase your energy levels\, sharpen your focus\, and contribute to your overall well-being. \n\n\n\nBut what exactly is the Movement Snacks initiative? It’s more than just a concept – it’s a peer-led active break initiative. Using a “train the trainer” model\, it aims to train instructors in guiding active breaks among their group of peers\, co-workers. The idea isn’t just to provide knowledge but to move from theory to actual practice. In this seminar\, Movement Snacks will provide practical examples and inspire everyone to prioritize their health and well-being\, regardless of where they are. Thereby we want to ‘Practice what we preach’ and contribute to the Sustainable Development Goals (SDG 3\,11). \n\n\n\nDate: 22/11/2023Time: 14:00 – 14:30Zoom link: https://kth-se.zoom.us/j/63988892680On-site location: Gamma 2 lunch room \n\n\n\nWe will begin with a ~ 20 min talk\, held in Solna and over zoom. After the talk\, there will be a short Q&A opportunity for people participating over zoom. Then we will proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties\, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI. \n\n\n\nTo help facilitate discussion and reflection\, consider the follow starter questions: \n\n\n\nAwareness: where do we experience Movements Snacks in our lives already?Analysis: how well do I currently integrate Movements Snacks into my life?Alternative: what alternatives for sedentary behavior are there\, for ourselves and others?Action: how will knowledge of Movements Snacks change my decisions going forward? \n\n\n\nPlease forward this to friends and colleagues! \n\n\n\nYours sincerely\,The CSI Team URL:https://www.scilifelab.se/event/csi-seminar-movement-snacks/ LOCATION:Hybrid event in Gamma 2 lunchroom and zoom\, Tomtebodavägen 23 B\, Solna\, 17165\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/11/CSI_logo_text.png ORGANIZER;CN="Coaching in Science Initiative (CSI)":MAILTO:sami.saarenpaa@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231122T141500 DTEND;TZID=Europe/Stockholm:20231122T150000 DTSTAMP:20260403T205612 CREATED:20231115T101836Z LAST-MODIFIED:20231115T150503Z UID:10001028-1700662500-1700665200@www.scilifelab.se SUMMARY:Launch of calls for DDLS PhD projects DESCRIPTION:The SciLifeLab & Wallenberg National Program for Data-Driven Life Science announces calls for PhD projects within academia and industry. The calls will be open for researchers in Sweden who are interested to act as supervisor for a PhD student. The aim is to fund 20 projects for academic PhD students and 7 for industrial. Join this online event for detailed information about the calls and the possibility to ask questions. \n\n\n\nAGENDA \n\n\n\nInformation about calls – Olli Kallioniemi\, DDLS director \n\n\n\nQ & A session \n\n\n\n\nRegister here\n\n\n\n\nWebpage: https://www.scilifelab.se/data-driven/ddls-research-school/ URL:https://www.scilifelab.se/event/call-for-ddls-phd-projects/ LOCATION:Online event via Zoom CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/11/Academy_call.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231122T150000 DTEND;TZID=Europe/Stockholm:20231122T160000 DTSTAMP:20260403T205612 CREATED:20231107T071615Z LAST-MODIFIED:20231115T100612Z UID:10001019-1700665200-1700668800@www.scilifelab.se SUMMARY:BAM-seminar; From PhD-student to patent attorney at Potter Clarkson DESCRIPTION:The PhD and PostDoc council is excited to host Dr. Tomasz Wirt\, who currently serves as a trainee patent lawyer at Potter Clarkson\, a European law firm specialised in intellectual property. \n\n\n\nTomasz pursued his doctoral studies at Stockholm University and is a SciLifeLab Campus Solna alumni. He will offer valuable insights into his career journey and provide an in-depth look at his current role as a patent lawyer. \n\n\n\n\n\n\n\nThis seminar is tailored specifically to address the unique challenges faced by PhD students and PostDocs in navigating a transition to jobs in industry. Join us as we highlight real-life success stories and provide valuable insights into professions outside academia. \n\n\n\nEveryone welcome! Fika for registered participants. Register by November 19th! \n\n\n\n\n\n\n\n\n\n\n\nRegister URL:https://www.scilifelab.se/event/bam-seminar-from-phd-student-to-patent-attorney-at-potter-clarkson/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/11/BAM-seminar.png ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231123T120000 DTEND;TZID=Europe/Stockholm:20231123T130000 DTSTAMP:20260403T205612 CREATED:20230711T115744Z LAST-MODIFIED:20231107T110518Z UID:10000936-1700740800-1700744400@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Femke Hormann & Maianna Tampere DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nFemke Hormann\n\n\n\nSean Rudd – alpha 5 \n\n\n\nDeciphering the molecular mechanisms of purine analogue nelarabine in the treatment of leukemia. \n\n\n\n\n\nMarianna Tampere\n\n\n\nPäivi Östling – alpha 4 \n\n\n\nExploring the morphology of the host cell to open new possibilities for drug repurposing in viral infections. \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-nov-23/ LOCATION:Milkyway SciLifeLab Solna\, Tomtebodavägen 23\, Solna CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/12/IMG_4110-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231124T100000 DTEND;TZID=Europe/Stockholm:20231124T160000 DTSTAMP:20260403T205612 CREATED:20231019T124448Z LAST-MODIFIED:20231122T105255Z UID:10001004-1700820000-1700841600@www.scilifelab.se SUMMARY:SciLifeLab Bioinformatics Platform NBIS celebrates 15 years DESCRIPTION:NBIS celebrates 15 years and organises an Anniversary Symposium on Friday 24 November at 10:00 – 16:00 with mingle afterwards in Uppsala\, SciLifeLab Trippelrummet.On the agenda so far:KeynotesPresentation of Human Protein Atlas (HPA) by Mathias UhlénPresentation of Bigpicture by Jeroen van der LaakUser presentations2–3 user presentations (users of the national bioinformatics infrastructure NBIS)NBIS presentationsPresentation of NBIS 15 years and ELIXIR 10 years by Bengt PerssonPresentation of WABI 10 years by Björn NystedtHuman data — 1+MG och GDI (Anna Hagwall/Johan Viklund)Presentation of our Training activities by Jessica LindvallPresentation of computational support by Jonas SöderbergData management – enable FAIR data for Swedish research (Niclas Jareborg)Mingle afterwards with drinks and finger food.Preliminary programme and link to registration available \n\n\n\nRead more URL:https://www.scilifelab.se/event/scilifelab-bioinformatics-platform-nbis-celebrates-15-years/ LOCATION:Navet\, SciLifeLab Uppsala\, SciLifeLab Uppsala\, BMC C11\, Husargatan 3\, Uppsala\, 75237\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/10/nbis-eventlogo-nb.png ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231127T151500 DTEND;TZID=Europe/Stockholm:20231127T161500 DTSTAMP:20260403T205612 CREATED:20231113T153444Z LAST-MODIFIED:20231113T153447Z UID:10001029-1701098100-1701101700@www.scilifelab.se SUMMARY:[The Svedberg seminar] - Brain-wide hierarchical and multiplexed encoding of behaviour in C. elegans DESCRIPTION:Manuel Zimmer \n\n\n\nProfessor Department of Neuroscience and Developmental Biology\, The University of Vienna \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\n\n\n\n\nManuel Zimmer studied biochemistry at the Free University of Berlin and performed his undergraduate thesis in 1998 on neuromuscular synapse formation with Steve Burden at the Skirball Institute of Biomolecular Medicine\, New York University Medical School\, New York. Afterward\, he moved back to Germany to perform his Ph.D. work with Rüdiger Klein at the European Molecular Biology Laboratory in Heidelberg and the Max Planck Institute of Neurobiology in Munich\, until 2003. Here\, he focused on the molecular mechanisms that wire up the nervous system during development. From 2004 to 2010\, he performed his postdoctoral studies with Cori Bargmann at the University of California\, San Francisco\, and Rockefeller University\, New York. Here\, he developed lab-on-a-chip and calcium-imaging techniques to investigate the chemosensory mechanisms by which animals sense oxygen in the environment. Since 2010\, he has lived in Austria\, where he works as an independent group leader at the Research Institute of Molecular Pathology in Vienna. Dr. Zimmer’s current research is focused on how neuronal network dynamics in the brain of C. elegans arise from sleep to wakefulness to engage in processing the sensory world and to produce competent behaviors\, like foraging and navigation. \n\n\n\n \n\n\n\nBrain-wide hierarchical and multiplexed encoding of behaviour in C. elegans\n\n\n\nLarge-scale neuronal recordings in the brains of different species have revealed brain-wide\, highly coordinated patterns of neuronal activity associated with the animals’ ongoing behaviours. It is not known why behaviour is represented in the brain on such a global scale. In the nematode C. elegans\, the activity of such neuronal populations recorded from immobilised animals was suggested to correlate with brain-wide motor commands orchestrating a major action sequence. Direct confirmation of this conclusion in freely crawling animals has been lacking. I will present unpublished data from a new imaging pipeline to record brain-wide activity at single cell resolution in freely crawling animals performing a variety of motor behaviours.Extending our previous findings\, we observe population-wide neural activity in the form of a structured low-dimensional manifold from which the major motor programmes\, arranged as an action sequence\, can be decoded. However\, the brain-wide activity appears to be much richer than just encoding the identity of the main actions: while all behaviourally relevant neuronal activity patterns we detect in our recordings are modulated by the global population modes\, many individual neurons show multiplexed activity\, i.e. they carry additional residual signals. These can represent a variety of behaviourally relevant information\, such as graded movement metrics\, the animal’s undulatory gate\, or even re-afferent sensation of movement-triggered external signals.In summary\, we discover a brain-wide hierarchical organisation of behaviour in which information about the current slow time-scale behavioural state is broadcast across the brain via a low-dimensional population mode\, providing a context for the encoding of fine-tuned fast movement patterns and even sensory perception. We propose this as an organising principle that may apply to animals with larger brains. \n\n\n\nhttps://neurodevbio.univie.ac.at/zimmer-research/ \n\n\n\n\n\n\n\nHost: Klas Kullander\, UU URL:https://www.scilifelab.se/event/the-svedberg-seminar-manuel-zimmer/ LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231128T090000 DTEND;TZID=Europe/Stockholm:20231128T130000 DTSTAMP:20260403T205612 CREATED:20230922T152232Z LAST-MODIFIED:20230929T114808Z UID:10000976-1701162000-1701176400@www.scilifelab.se SUMMARY:Science visualisation workshop DESCRIPTION:How to effectively communicate your research through visualisations\n\n\n\nThis workshop consists of lectures and short practical exercises on how to create scientific visualisations that clearly communicate your message. We will draw from Graphic Design knowledge on layout\, typography and colour\, define the steps in the design process of a visualisation that you can directly apply\, discuss common visual formats used in science communication (eg posters\, graphical abstracts)\, compare software options for creating your visualisations\, and learn about concepts from cognitive psychology and visual perception that explain what makes a visualisation effective.  \n\n\n\nRegister your interest to participate before November 1. \n\n\n\nRegistration\n\n\n\nThe content will be adjusted to the interest of the participants. Everyone within the SciLifeLab Community is invited to attend\, priority will be given to PhD students and postdocs. URL:https://www.scilifelab.se/event/science-visualisation-workshop/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2023/09/SciVisWorkshop-scaled.jpg ORGANIZER;CN="Meike Latz":MAILTO:meike.latz@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231129T080000 DTEND;TZID=Europe/Stockholm:20231201T170000 DTSTAMP:20260403T205612 CREATED:20230413T132104Z LAST-MODIFIED:20230508T131425Z UID:10000858-1701244800-1701450000@www.scilifelab.se SUMMARY:Correlated Array Tomography Workshop DESCRIPTION:Array Tomography workflow: Fixation of the specimen and embedding in a suitable matrix; Serial sectioning of the specimen\, and collection of the sections to create a ribbon; Staining of the sections; Sections are identified and imaged at low resolution to find ROIs\, which are later imaged at high-resolution to create a 3D view of the specimen.\n\n\n\n \n\n\n\nThe Centre for Cellular Imaging\, which is the national SciLifeLab facility for Correlative Array Tomography in Sweden\, has the great pleasure to welcome you to the first Cellular 3D volume – Correlative Array Tomography (CAT) Workshop! The workshop will take place from November 29th to December 1st. The lectures will take place at the Wallenberg Centre\, located at Medicinareberget\, above the Sahlgrenska Hospital in Gothenburg. The hands-on sessions will take place in the Centre for Cellular Imaging\, Core Facilities\, at Medicinareberget. \n\n\n\nIt is a great pleasure to welcome you to first Cellular 3D volume – Correlative Array Tomography (CAT) Workshop 2023 – Centre for Cellular Imaging the National SciLifeLab Facility in Correlative Array Tomography in Sweden \n\n\n\nMany biological functions depend critically upon fine details of tissue molecular architecture that have resisted exploration by existing imaging techniques. Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures of large samples in extremely fine structural and molecular detail\, including neural circuits\, organs (e.g. brain\, pancreas\, kidney\, heart)\, small model organisms and subcellular organelle networks. Based on methods for constructing and repeatedly staining and imaging ordered arrays of ultrathin resin-embedded serial sections on glass slides\, silicon wafers or tapes\, array tomography allows for quantitative\, high-resolution\, large-field volumetric imaging of large numbers of antigens\, fluorescent proteins\, and ultrastructure in individual tissue specimens. This will contribute further to the understanding of the complex 3D architecture of tissues in their natural context\, which is crucial for gaining understanding of the structure function correlation in biological systems\, and especially to resolve questions not possible to dissect with conventional scanning or transmission electron microscopy techniques. \n\n\n\nThe CAT 2023 Workshop is designed to bring experts\, researchers and industry together interested in Cellular 3D volume – Correlative Array Tomography to introduce this new technology\, stimulate knowledge exchange and the formation of collaborations. No matter where you are in your career\, participating at this Workshop will allow you to stay abreast of this new imaging technology\, learn new sample preparation and image analysis methods\, and most importantly\, network with colleagues and make new connections.  \n\n\n\nThe program will offer an attractive combination of lectures and hands-on demonstrations from electron and light microscopy to image analysis. It will also provide excellent opportunities for discussions and informal gatherings. The sessions will cover the following topics within cellular 3D volume-array tomography research: Volume electron/light microscopy-array tomography; Sample preparation for Array Tomography; Image processing and analysis for Array Tomography; Correlative array tomography; Multibeam scanning electron microscopy. Take the opportunity to challenge your brain and create a new network!  \n\n\n\nJulia Fernandez-Rodriguez \n\n\n\nChair of the Cellular 3D volume – Correlative Array Tomography Workshop \n\n\n\nread more\n\n\n\nregistration\n\n\n\nCLEM example: Correlative light and electron microscopy to identify cells of interest in skin equivalent. The image represents only a small example of the CAT dataset. URL:https://www.scilifelab.se/event/correlated-array-tomography-workshop/ LOCATION:Centre for Cellular Imaging\, Medicinaregatan 7A\, Göteborg CATEGORIES:Event END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231130T100000 DTEND;TZID=Europe/Stockholm:20231130T113000 DTSTAMP:20260403T205612 CREATED:20231116T081613Z LAST-MODIFIED:20231129T160528Z UID:10001030-1701338400-1701343800@www.scilifelab.se SUMMARY:SciLifeLab FAIR storage - how to apply for storage resources DESCRIPTION:SAVE THE DATE \n\n\n\nIn order to support data-driven life science research\, SciLifeLab offers storage resources for data sharing in accordance with the FAIR principles for projects that advance scientific knowledge and discovery within the field of Swedish data-driven life science. SciLifeLab Data Centre is responsible for allocating these resources and for the application process. The applications to use FAIRstorage is now open through the Swedish User and Project Repository (SUPR) Portal (call open Nov 16 -Dec 31). Following the recent launch of FAIRstorage\, this is an event where the FAIRstorage applications process\, along with Research Data Management resources needed for the application\, will be presented. The target group for this call is researchers\, research groups\, and organisations. \n\n\n\nAdhering to Open Science and FAIR principles the applicants will be required to submit a Data Management Plan (DMP) already at the time of application and should be actively maintained\, as DMP is a living document\, during the project. Awarded applicants are also expected to openly publish data output from the project. SciLifeLab Data Centre and NBIS are offering a support event where the FAIRstorage applications process\, along with Research Data Management resources needed for the application\, will be presented. \n\n\n\nWhen: Nov 30\, 10-11.30 AM \n\n\n\nWhere: Virtual event on Zoom \n\n\n\nRegister: before Nov 30\, at 9 AM \n\n\n\n10.00-10.20 Introduction to FAIRstorage and an overview of processes for applying for FAIRstorage using SUPR\, Jonas Svensson\, IT manager\, and Elisabeth Sundström\, Project leader\, SciLifeLab Data Centre \n\n\n\n10.20-10.50 Data Stewardship Wizard-a DMP tool- as a resource for your SUPR application\, Wolmar Nyberg Åkerström\, Data steward\, NBIS \n\n\n\n10.50-11.00  SciLifeLab Data Repository- publishing your data- as a resource for your SUPR application\, Angela Fuentes Pardo\, Data steward\, SciLifeLab Data Centre \n\n\n\n11.00-11.30 Q & A \n\n\n\n \n\n\n\n\nRegister \n\n\n\n\nThis is an event in the SciLifeLab Data Centre and NBIS  SciLifeLab Data Management seminar series.  \n\n\n\nLearn more about FAIRstorage and the call here: https://data.scilifelab.se/services/fairstorage/ \n\n\n\nMail: FAIRstorage@scilifelab.se Contact the SciLifeLab Data Centre and NBIS joint Data Management support team data-management@scilifelab.se URL:https://www.scilifelab.se/event/fairstorage/ CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/11/Skarmavbild-2023-11-16-kl.-09.23.09.png LOCATION: END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231130T120000 DTEND;TZID=Europe/Stockholm:20231130T130000 DTSTAMP:20260403T205612 CREATED:20230711T115852Z LAST-MODIFIED:20231127T100435Z UID:10000937-1701345600-1701349200@www.scilifelab.se SUMMARY:Campus Solna Seminar Series: Carmen Navarro & Elisabeth Söderberg DESCRIPTION:Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively)\, with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged. \n\n\n\nThe seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar. \n\n\n\nThis week:\n\n\n\n\n\n\nCarmen Navarro\n\n\n\nSimon Elsässer – alpha 4 \n\n\n\nThe role of Polycomb Repressive Complex 2 in early human development \n\n\n\n\n\nElisabeth Söderberg\n\n\n\nPer-olof Syren – gamma 5 \n\n\n\nA safer and more sustainable by design perspective in biocatalytic amide-bond coupling of in-silico controlled chemical space \n\n\n\n\n\n\nThis seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page. URL:https://www.scilifelab.se/event/campus-solna-seminar-series-nov-30/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Community ATTACH;FMTTYPE=image/jpeg:https://www.scilifelab.se/wp-content/uploads/2022/09/IMG_20221103_124630107_HDR-scaled.jpg ORGANIZER;CN="SciLifeLab Solna PhD & Postdoc Council":MAILTO:phd-council@scilifelab.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231204T080000 DTEND;TZID=Europe/Stockholm:20231204T170000 DTSTAMP:20260403T205612 CREATED:20231205T091920Z LAST-MODIFIED:20231206T095226Z UID:10001059-1701676800-1701709200@www.scilifelab.se SUMMARY:SciLifeLab workshop on dynamical microscopy DESCRIPTION:Welcome to a SciLifeLab workshop on dynamical microscopy covering modalities AIRY\, lattice lightsheet and FCS/DP\, including quality control and image analysis. \n\n\n\nAgenda \n\n\n\n12:00 Introduction – Hans Blom\, ALM/SciLifeLab \n\n\n\n12:05 AIRY scan imaging – Eric Murén ZEISS & Hjalmar Brismar\, ALM/SciLifeLab \n\n\n\n12:35 Quality Control  – Chris Lagerholm\, Turku Bioimaging Center \n\n\n\n13:05 Lattice light-sheet imaging – Steven Edwards\, ALM/SciLifeLab & Jan Schlegel Karolinska Institutet \n\n\n\n13:35 Coffee break \n\n\n\n13:50 Dynamical analysis with FCS – Stefan Wennmalm\, ALM/SciLifeLab \n\n\n\n14:15 Multiplexed dynamical analysis with DP – Maria Trulsson ZEISS \n\n\n\n14:40 Advanced image analysis support – Molly McQuilken\, ZEISS arivis \n\n\n\n15:20 – 16:20   3x Demo sessions (project discussions) \n\n\n\nFast AIRY scan microscopy & FCS/DP; Lattice light-sheet imaging; Image analysis support \n\n\n\nRegistration: hans.blom@scilifelab.se URL:https://www.scilifelab.se/event/scilifelab-workshop-on-dynamical-microscopy/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2023/12/March-6th.png ORGANIZER;CN="Advanced Light Microscopy Unit":MAILTO:stewen@kth.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231204T090000 DTEND;TZID=Europe/Stockholm:20231206T170000 DTSTAMP:20260403T205612 CREATED:20230906T082705Z LAST-MODIFIED:20231106T132742Z UID:10000967-1701680400-1701882000@www.scilifelab.se SUMMARY:Snakemake “bring-your-own-code” (BYOC) workshop - Cancelled DESCRIPTION:National course open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of skills to write Snakemake workflows for reproducible and scalable bioinformatics data analyses. CANCELLED! \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-09-11 \n\n\n\nApplication closes: 2023-10-29 \n\n\n\nConfirmation to accepted students: 2023-11-06 \n\n\n\nCourse Leader and teachers: Verena Kutschera (CL)\, Marcel Martin\, John Sundh. In case you have any workshop-specific questions\, please contact: edu.byoc-snakemake@nbis.se \n\n\n\n\n\n\n\n\n\nApplication\n\n\n\n\n\nCourse Website\n\n\n\n\n\n\n\n\n\nCourse fee\n\n\n\nThis online training event has no fee. However\, if you confirm your participation but do not do so (no-show) you will be invoiced 2\,000 SEK*.*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nCourse content\n\n\n\nAs data analysis projects grow and change over time\, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up\, perform and monitor defined sequences of computational tasks (“workflows”)\, thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows. \n\n\n\nThe NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake. \n\n\n\nThis Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here\, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash\, R or python into a Snakemake workflow\, or B) apply more advanced techniques to their existing Snakemake workflows. \n\n\n\n\n\n\n\nLearning Outcomes\n\n\n\nUpon completion of this course\, you will be able to: \n\n\n\n\nBe able to create Snakemake workflows for bioinformatics data analysis\n\n\n\nDemonstrate knowledge of the structure and syntax of different types of Snakemake workflows\n\n\n\nDemonstrate knowledge of advanced features of the Snakemake workflow language\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required for being able to follow the course: \n\n\n\n\nPrevious participation in the NBIS Tools for reproducible research course. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflows and with at least basic Unix/bash knowledge (e.g. being familiar with commands such as ls\, cd\, touch\, mkdir\, pwd\, wget\, man\, etc.).\n\n\n\nYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improve. \n\n\n\nA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant\, additional setup will be required).\n\n\n\n\nDue to limited space the course can accommodate a maximum of 12 participants. If we receive more applications\, participants will be selected based on selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance. URL:https://www.scilifelab.se/event/snakemake-bring-your-own-code-byoc-workshop-online/ LOCATION:Online event via Zoom CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231204T151500 DTEND;TZID=Europe/Stockholm:20231204T161500 DTSTAMP:20260403T205612 CREATED:20231123T132908Z LAST-MODIFIED:20231124T082227Z UID:10001037-1701702900-1701706500@www.scilifelab.se SUMMARY:[The Svedberg seminar] - Intersecting population genetics\, stem cell biology\, and cellular genomics to study complex human disease DESCRIPTION:Joseph Powell \n\n\n\nProfessor Garvan Institute of Medical Research\, Sydney Australia \n\n\n\n \n\n\n\n\n\n\n\nBio\n\n\n\nProfessor Powell is the Director of Translational Genomics at the Garvan Institute and Director of the UNSW Cellular Genomics Futures Institute. He received his PhD from the University of Edinburgh. Subsequently\, he undertook postdoctoral training with Professor Peter Visscher’s FAA FRS and started his lab in 2016. In 2018\, he was recruited as the inaugural Director of the Garvan-Weizmann Centre for Cellular Genomics and developed a multidisciplinary program in translational genomics research. \n\n\n\n\n\n\n\nAbstract: Genetic variants can contribute to disease in many ways. In complex diseases\, hundreds to thousands of variants independently contribute to disease risk\, and an accumulation of risk alleles – often combined with specific environmental exposures –is required to develop the disease phenotype. The overwhelming evidence showing enrichment of disease-associated variants in regulatory regions suggests that regulation of gene expression is likely a dominant mediator for disease risk. Expression quantitative trait loci (eQTL) analysis links disease risk-SNPs to downstream expression effects. An essential next step is defining the cellular contexts in which disease risk-SNPs affect gene expression levels. This will help better understand the molecular and cellular mechanisms by which disease risk is conferred and inform therapeutic strategies. This talk will cover a body of work on how single-cell sequencing technology can be scaled to enable the type of population genetics studies required to address these biological questions. I will present recent research on how we have resolved how genetic variation acts at the level of individual cells in immune cell and stem cell systems and outline the next steps in translating these findings into clinical impact. \n\n\n\n \n\n\n\n\n\n\n\nHost: Weronica Ek\, UU URL:https://www.scilifelab.se/event/the-svedberg-seminar-joseph-powell/ LOCATION:BMC Room C8:301\, Husargatan 3\, Uppsala\, Sweden CATEGORIES:Event ATTACH;FMTTYPE=image/png:https://www.scilifelab.se/wp-content/uploads/2022/02/Picture1-The-Svedberg.png ORGANIZER;CN="The Svedberg Seminar Series":MAILTO:thesvedberg@scilifelab.uu.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231206T080000 DTEND;TZID=Europe/Stockholm:20231208T170000 DTSTAMP:20260403T205612 CREATED:20231002T115541Z LAST-MODIFIED:20231002T115646Z UID:10000980-1701849600-1702054800@www.scilifelab.se SUMMARY:DDLS Biomarker Discovery: from theory to real world examples DESCRIPTION:National workshop open for PhD students\, postdocs\, researchers and other employees in all Swedish universities\, in need of understanding biomarker research and methods. \n\n\n\nWorkshop location:  SciLifeLab\, Tomtebodavägen 23A\, Solna \n\n\n\nVenue:  Air&Fire (G2690) and Milky Way (A2631) \n\n\n\n\n\n\n\nImportant dates and information\n\n\n\nApplication opens: 2023-10-01 \n\n\n\nApplication closes: 2023-10-30 \n\n\n\nConfirmation to accepted students: 2023-11-15 \n\n\n\n \n\n\n\nCourse Leaders and teachers: Animesh Acharjee\, Clemens Wittenbecher\, Markus Mayrhofer\, Mun-Gwan Hong\, Paul Pyl\, Prasoon Agarwal \n\n\n\nplease contact edu.biomarkers@nbis.se for course-specific questions \n\n\n\n\n\n\n\nApplication\n\n\n\n\n\n\n\nWorkshop fee\n\n\n\nA course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunch and coffee. \n\n\n\n*Please note that NBIS cannot invoice individuals \n\n\n\n\n\n\n\nWorkshop content\n\n\n\nThe main purpose of this workshop is to provide a good overview of biomarkers and biomarker studies. This workshop will explore recent research\, showcasing diverse biomarker applications within clinical trials. Methods employed to identify biomarkers through various omics datasets will be reviewed. Participants will engage in discussion on biomarker studies and data analysis exercises that encompass approaches like machine learning methods and other integrative omics strategies used in biomarker discovery. \n\n\n\nTopics covered will include: \n\n\n\n\nBiomarker study design for “context of use”\n\n\n\nTypes of biomarkers\, diagnostic\, prognostic\, and wellness\n\n\n\nBiomarkers are in use for various diseases such as cancer\, cardiovascular diseases\n\n\n\nBiomarker discovery from various omics data including proteome\, microbiome\n\n\n\nBiomarker and multi-omics data integration\n\n\n\nMachine learning methods\, lasso logistic regression and random forest\, to identify biomarkers\n\n\n\nPerformance indicators\, e.g. sensitivity and specificity\n\n\n\nInternal/external validation\n\n\n\n\n\n\n\n\nEntry requirements\n\n\n\nThe following is a list of skills required to be able to follow the workshop and complete the exercises: \n\n\n\n\nAbility to bring your own laptop with R installed for the practical exercises\n\n\n\nBasic Programming/scripting experience in R\n\n\n\nor took an R course NBIS prepared.\n\n\n\n\nDesirable\, but not essential\, skills increasing the output of the course\, include: \n\n\n\n\nSome basic knowledge of biostatistics\n\n\n\nPrevious experience in biomarker-related studies\n\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 selection criteria\, including (but not limited to) correct entry requirements\, motivation to attend the course\, as well as gender and geographical balance. URL:https://www.scilifelab.se/event/ddls-biomarker-discovery-from-theory-to-real-world-examples/ LOCATION:Air&Fire\, SciLifeLab Stockholm\, Tomtebodavägen 23A\, Solna\, Sweden CATEGORIES:Course ORGANIZER;CN="NBIS - National Bioinformatics Infrastructure Sweden":MAILTO:education@nbis.se END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Stockholm:20231206T090000 DTEND;TZID=Europe/Stockholm:20231206T160000 DTSTAMP:20260403T205612 CREATED:20231025T125024Z LAST-MODIFIED:20231124T132106Z UID:10001008-1701853200-1701878400@www.scilifelab.se SUMMARY:Integrated Structural Biology users meeting DESCRIPTION:We invite Structural Biologists in Sweden to participate in 2023 Integrated Structural Biology Users meeting\, held in Solna on Dec 6\, 9-16\, see program below.  \n\n\n\nPlease register before November 30 \n\n\n\nregistration\n\n\n\nAll PhD students and post docs within areas such as Cryo-EM\, Structural Proteomics\, NMR\, protein production and other relevant areas are welcome and encouraged to send an abstract and be provided a time slot for a flash talk. If traveling to Solna is needed\, we will pay for travel and one hotel night (December 5). If more applicants than time slots\, we will distribute nationally and from different areas. \n\n\n\nProgram\n\n\n\nISB-User-MeetingDownload URL:https://www.scilifelab.se/event/isb-users-meeting/ LOCATION:Wangari\, Widerströmska building\,\, Tomtebodavägen 18\, Solna\, Sweden CATEGORIES:Event ORGANIZER;CN="Integrated Structural Biology Platform at SciLifeLab":MAILTO:cecilia.persson@nmr.gu.se END:VEVENT END:VCALENDAR