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DTSTART;TZID=Europe/Stockholm:20261027T100000
DTEND;TZID=Europe/Stockholm:20261027T110000
DTSTAMP:20260923T161235Z
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UID:10001899-1793095200-1793098800@www.scilifelab.se
SUMMARY:Webinar: Reinventing Bioinformatics: AI-mediated refactoring at scale
DESCRIPTION:Welcome to join us for the Tools for AI/ML research in life sciences event series for our next webinar. We welcome Johan Henriksson (Umeå university and SciLifeLab) to present “Reinventing Bioinformatics: AI-mediated refactoring at scale”. \n\n\n\nDate and time: October 27 at 10:00-11:00 Stockholm time (CEST)Speaker: Johan Henriksson\, Umeå university and SciLifeLab \n\n\n\nRegistration: Please register before October 26\, at 18.00 CEST. \n\n\n\n\nRegister\n\n\n\n\nAbstract \n\n\n\nBioinformatics and academic Open Source software have always been at mercy of available resources\, limiting software quality and what we realistically can produce. However\, agentic AI has now drastically reduced the cost of producing sophisticated software. \n\n\n\nThis talk will be a “call to arms”\, showing what can now be done using AI\, and aimed to inspire a major refactoring of the academic software ecosystem. I will give examples of (1) How lab software can be written to fit your needs rather than the other way around. (2) How proprietary file formats can be cracked open and how we can push for file format standardization. (3) How to completely remove the need for Conda and containers\, and never have a version conflict again. (4) How to make bioinformatics code faster\, safer and more ecofriendly. (5) How major commercial software legally can be replaced. (6) How all of this enables the SciLifeLab AI strategy. \n\n\n\nExamples will especially be provided in the context of microscopy and image analysis; but also examples beyond imaging\, to avoid domain-specific data management solutions. \n\n\n\n\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 data science and machine learning methods in their work. The goal of the events in this seminar 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. We organise in-person workshops and webinars as part of the event series. The events are open to all researchers in Sweden and beyond\, regardless of SciLifeLab affiliation. \n\n\n\nContact: SciLifeLab Data Centre  serve@scilifelab.se
URL:https://www.scilifelab.se/event/reinventing-bioinformatics/
LOCATION:Online event via Zoom
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261102T100000
DTEND;TZID=Europe/Stockholm:20261102T153000
DTSTAMP:20261006T200937Z
CREATED:20260916T073033Z
LAST-MODIFIED:20261006T200937Z
UID:10001894-1793613600-1793633400@www.scilifelab.se
SUMMARY:Hands-on Workshop: Developing AI Agents in Life Sciences (Lund)
DESCRIPTION:We are delighted to invite you to join our upcoming workshop on “Developing AI Agents in Life Sciences”\, organized by SciLifeLab Data Centre and SciLifeLab Lund site in collaboration with the eScience Hub at Lund University. AI agents are emerging as autonomous systems that orchestrate scientific workflows by interacting with digital tools and data sources. These have various implications for life science research. They can\, for example\, simplify complex analyses by automating data integration\, run computational models\, and coordinate experimental steps\, making research pipelines more efficient and reproducible. In this on-site hands-on workshop held at Belfragesalen\, BMC D15 (Klinikgatan 32) in Lund\, we will introduce and discuss AI Agents in life science\, and engage in collaborative practical sessions. Welcome! \n\n\n\nDate: 2026-11-02Time: 10.00-15.30 (coffee will be served from 9.30). Fika and lunch provided free of charge. Location: room Belfragesalen\, BMC D15\, Klinikgatan 32\, Lund. No remote participation. \n\n\n\nTarget audience: Researchers\, PhD students\, research infrastructure interested in learning more about and trying hands-on exercises with AI Agents. Participants with any university affiliation and industry researchers are welcome. Basic Python programming skills are required; previous experience working with Jupyter notebooks would be helpful. Participants must bring their own laptop. \n\n\n\nRegistration: We expect many to be interested in attending this event. After we reach max capacity\, we will open a waitlist. If you cannot join\, please cancel your registration as soon as possible to make your spot available for someone else. Please add dietary restrictions to your registration. \n\n\n\n\nRegister for the workshop\n\n\n\n\nSpeakers and Facilitators:  Chris Long Huynh (PhD candidate\, Uppsala University)\, and Mahbub Ul Alam and Johan Alfredéen (Data Engineers (AI) at SciLifeLab Data Centre). \n\n\n\nThe workshop will feature a series of engaging presentations\, interactive discussions\, and collaborative sessions focusing on: \n\n\n\n\nIntroduction to AI agent technologies\n\n\n\nApplications\, opportunities and challenges of AI Agents in life science\n\n\n\nHands-on tutorials with reasoning models\, LangChain and MCP servers\n\n\n\nDiscussions on the role of AI agents in shaping the future of life science\n\n\n\n\nAgenda \n\n\n\n09:30-10:00 Light breakfast and networking \n\n\n\n10.00-10.15 Presentation session 1: Introduction: Exploring how AI agents can transform life sciences. Speaker: Johan Alfredéen. \n\n\n\n10.15-10.30 Demonstration Session: AI agents in action. Facilitators: Mahbub Ul Alam. \n\n\n\n10:30-12:00 Hands-on Session 1: Developing AI agents with LangChain & ReAct. Session Facilitators: Dinh Long Huynh\, Mahbub Ul Alam.  \n\n\n\n12:00-13:00 Lunch and networking \n\n\n\n13:00-13:30 Continuation of Hands-on Session 1: Developing AI agents with LangChain & ReAct. \n\n\n\n13:30-15:00 Hands-on Session 2: AI agent collaboration with the Model Context Protocol (MCP). Session Facilitators: Mahbub Ul Alam\, Johan Alfredéen\, Dinh Long Huynh. \n\n\n\n15:00-15:15 Presentation Session 2: Deploying AI Agents: Legal\, Technical\, and Practical Considerations. Speaker: Johan Alfredéen. \n\n\n\n15:15-15:30 Concluding Session: Open Q&A  \n\n\n\n15:30 Fika and networking \n\n\n\nRegistration: Please add dietary restrictions to your registration. If you cannot join\, please cancel your registration. \n\n\n\nThis event is a organised by SciLifeLab Data Centre and SciLifeLab Lund in collaboration with the eScience Hub at Lund University. For questions please contact  open-llm@scilifelab.se .
URL:https://www.scilifelab.se/event/ai-agents-in-life-science-lund/
LOCATION:Belfragesalen\, BMC D15\, Klinikgatan 32\, Lund\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Stockholm:20261110T133000
DTEND;TZID=Europe/Stockholm:20261110T153000
DTSTAMP:20261022T072219Z
CREATED:20260825T091248Z
LAST-MODIFIED:20261022T072219Z
UID:10001880-1794317400-1794324600@www.scilifelab.se
SUMMARY:DDLS Annual Conference 2026 workshops
DESCRIPTION:During the second day of the DDLS Annual Conference 2026 held at Aula Magna at Stockholm University participants will have an opportunity to attend one of the workshops. The workshops are directed at researchers in data-driven life science in all career stages. \n\n\n\nPlease note that each workshop has a limited number of seats\, on the first come first served basis. Those registered after the limit is reached will be placed on a waiting list (and get invited to register if a spot becomes available). The workshops will take place in various rooms of the main venue of the conference – Aula Magna at Stockholm University. The workshops start at 13:30 and last for up to 2 hours. Coffee/tea and fika will be served during the workshops. \n\n\n\nFeel free to email datacentre@scilifelab.se with any questions about the workshops. \n\n\n\nWorkshops\n\n\n\nWorkshop 1. How to use LLMs to present results from your research project as a web application\n\n\n\nHeld by: team members at SciLifeLab Data Centre\, TBA \n\n\n\nWhere and when: November 10\, 2026 at 13:30-15:30\, room Spelbomskan (Frescativägen 6 Stockholm) \n\n\n\nParticipants: max 30 \n\n\n\n\nRegistration\n\n\n\n\nDescription: In case of many research projects\, there is a need to present results not only as a traditional conference or journal paper but also as an interactive web-based tool that can be used by the readers or collaborators to e.g.\, explore the project data as interactive dashboards\, test out performance of a machine learning model\, input own arbitrary parameters in a simulation tool\, etc. Building such web applications for research projects has become rather easy with the help of large language model based tools such as ChatGPT\, Mistral\, Claude\, etc. This means that researchers can build and share web applications for their research projects without learning Python for web in depth (i.e. only using scientific Python knowledge). In this workshop\, we will demonstrate a few examples of where a web-based application can be built to present the results. Subsequently\, we will show how to package the resulting application and make it available to collaborators or general public through a URL using a SciLifeLab hosting service. Participants can follow along on their own laptops and either use our examples or build web-based applications for their own research projects during the workshop. We will be using a SciLifeLab hosted LLM tool during this workshop so that no data is shared with commercial companies. \n\n\n\nParticipants will need to bring a laptop to this workshop to be able to fully participate. \n\n\n\nWorkshop 2. Public hosting of Shiny apps: hands-on workshop\n\n\n\nHeld by: Staff at SciLifeLab Data Centre \n\n\n\nWhere and when: November 10\, 2026 at 13:30-15:30\, room Polstjärnan (Frescativägen 6 Stockholm) \n\n\n\nParticipants: max 30 \n\n\n\n\nRegistration\n\n\n\n\nDescription: Researchers often create R Shiny applications as part of their projects and want to publish them as research output – as analysis tools with a graphical interface\, as supplementary materials for publications\, in order to make annotation easier\, etc. In order to make Shiny apps available to the collaborators or general public\, they need to be hosted somewhere and have a URL. We will start this workshop by giving an overview of what it means to create and publish Shiny apps as researcher in terms of institutional and funder requirements. We will then take a look at different hosting options for Shiny apps. During the hands-on part\, we will focus on packaging Shiny apps for hosting as Docker images. Together with the participants\, we will step-by-step package and publish an example Shiny app or the participants’ own Shiny app. If you are a researcher with an existing Shiny app you’d like to host\, or if you plan to build a Shiny app in the future\, this workshop is for you. If you already have a Shiny app you would like to host\, bring it\, and we will help you with it. \n\n\n\nExpected outcomes: After this workshop\, the participants will both have an understanding of working with Shiny apps within research projects in a Swedish university context and have practical knowledge about public hosting of Shiny apps. \n\n\n\nParticipants will need to bring a laptop to this workshop to be able to fully participate. \n\n\n\nThe second workshop has been cancelled due to workshop leaders’ schedule conflict. This workshop will instead be offered to the DDLS community in some format in 2027.
URL:https://www.scilifelab.se/event/ddls-annual-conference-2026-workshops/
LOCATION:Aula Magna\, Frescativägen 6\, Stockholm\, 114 18 Stockholm\, Sweden
CATEGORIES:Event
ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
END:VEVENT
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DTSTART;TZID=Europe/Stockholm:20261118T100000
DTEND;TZID=Europe/Stockholm:20261118T110000
DTSTAMP:20261016T062905Z
CREATED:20261016T062904Z
LAST-MODIFIED:20261016T062905Z
UID:10001922-1794996000-1794999600@www.scilifelab.se
SUMMARY:Webinar: By the Community\, For the Crisis: the updated Swedish Pathogens Portal
DESCRIPTION:Join us for a webinar exploring how the Swedish Pathogens Portal supports infectious disease research\, data sharing and pandemic preparedness in Sweden. \n\n\n\nFollowing the portal’s biggest update since its launch in 2020\, this webinar will introduce new and improved features developed in response to feedback from the research community.  \n\n\n\nThese features include: \n\n\n\n– An updated interface to make the portal easier to navigate and use.– Clearer guidance on FAIR (Findable\, Accessible\, Interoperable and Reusable) data management to support researchers in sharing and managing their data.– The ability to dynamically gather and collate data on a greater diversity of pathogens and topics.– Expanded dashboard capabilities\, enabling researchers to explore and present more complex datasets through interactive visualisations.– The ability for research groups to update data directly within the portal. \n\n\n\nLiane Hughes\, Project Leader of the Swedish Pathogens Portal\, will introduce these latest developments and explain how researchers can use the portal in practice. Jaclyn Quin and Anna Székely will share how the portal supports their research. The webinar will also include speakers from the Pandemic Laboratory Preparedness (PLP) Program\, to share the importance of the portal to the program. \n\n\n\nRegistration\n\n\n\n\nRegister here\n\n\n\n\nPlease register before November 17 (18.00 CEST). \n\n\n\nSwedish Pathogens Portal\n\n\n\nThe Swedish Pathogens Portal is a national resource supporting infectious disease research and pandemic preparedness in Sweden. It brings together research data\, resources and information\, making them easier to find\, access\, share and reuse\, while promoting Open and FAIR data practices. \n\n\n\n\nView the Swedish Pathogens Portal\n\n\n\n\nIf you have any questions\, contact the Swedish Pathogens Portal team: pathogens@scilifelab.se.
URL:https://www.scilifelab.se/event/webinar-by-the-community-for-the-crisis-the-updated-swedish-pathogens-portal/
LOCATION:Online event via Zoom
CATEGORIES:Event
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ORGANIZER;CN="SciLifeLab Data Centre":MAILTO:datacentre@scilifelab.se
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