BEGIN:VCALENDAR VERSION:2.0 PRODID:-//SciLifeLab - ECPv6.15.20//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:20231106T090000 DTEND;TZID=Europe/Stockholm:20231110T170000 DTSTAMP:20260511T021643 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:20231115T123000 DTEND;TZID=Europe/Stockholm:20231116T123000 DTSTAMP:20260511T021643 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:20231116T133000 DTEND;TZID=Europe/Stockholm:20231116T153000 DTSTAMP:20260511T021643 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:20260511T021643 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:20231121T150000 DTEND;TZID=Europe/Stockholm:20231121T160000 DTSTAMP:20260511T021643 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:20260511T021643 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:20231122T141500 DTEND;TZID=Europe/Stockholm:20231122T150000 DTSTAMP:20260511T021643 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:20231130T100000 DTEND;TZID=Europe/Stockholm:20231130T113000 DTSTAMP:20260511T021643 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 END:VCALENDAR