SciLifeLab

Campus Solna Seminar Series: Styliani Papadaki & Moein Sorkhei
2024-11-14 12:00 - 13:00 (Europe/Stockholm) | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
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 20 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 Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Styliani Papadaki

Jiri Bartek – alpha 5

Translational studies on the role of hypusine in brain tumors. Two proteins, one post-translational modification

Moein Sorkhei

Kevin Smith – gamma 6

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

Glycomics of Human Immune Responses
2024-11-13 14:00 - 15:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Eurolife Distinguished Lecture

Professor Manfred Wuhrer, Leiden University Medical Center

SciLifeLab Solna venue Air & Fire and online here >>

Join Online

Welcome to this lecture by Prof Dr Manfred Wuhrer from Leiden University Medical Center, The Netherlands, as part of the Eurolife Distinguished Lecture Series (EDLS).

Glycosylation is a key factor in shaping multicellular life including immunological responses. Glycosylation modifies the activity and fate of both antibodies and immune cells involved in infections, inflammatory responses and cancer. Mass spectrometry approaches allow to unravel disease-associated glycosylation changes including specific glycans attached to the Fc portion of antibodies that dictate antibody effector functions in auto- and alloimmune conditions, inflammatory and infectious diseases, and cancer. Exploring the glycomic dimension of diseases has great promise in providing novel diagnostic and therapeutic leads.

More information about Prof Dr Manfred Wuhrer from Leiden University Medical Center

SciLifeLab Lund Seminar Series | BioMS
2024-11-12 15:00 - 16:00 | Belfragesalen, BMC D15, Klinikgatan 32, Lund, Sweden
Welcome to the SciLifeLab Lund seminar series!

These seminars are designed to highlight SciLifeLab Lund, our cutting-edge research infrastructure, and the diverse resources available to the scientific community.

In the 2nd seminar, we will have a in-depth look at the Swedish National Infrastructure for Biological Mass Spectrometry (BioMS). BioMS offers access to qualified projects in proteogenomics, targeted protein quantitation, glycoproteomics, hydrogen-deuterium exchange MS, glycomics, lipidomics, and chemical proteomics.

After an overview of BioMS and its advanced capabilities by Project Coordinator Anahita Bakochi, the session will continue with a user presentation showcasing a project carried out in collaboration with BioMS.

Please note that the seminars are site only but the recordings are available HERE.

Registration

Register for the next seminars!

18th December 2024 | Center Translational Genomics within Clinical Genomics Lund

Register Seminar December

29th January 2025 | CryoEM for Life Sciences at Lund University

Register Seminar January

26th February 2025 | Display and Selection Technologies

Register Seminar February

26th March 2025 | Lund University Bioimaging Centre (LBIC)

Register Seminar March

23rd April 2025 | Lund Protein Production Platform

Register Seminar April

28th May 2025 | National Bioinformatics Infrastructure (NBIS)

Register Seminar May

18th June | Structural Proteomics

Register Seminar June

Translational research as a boost for Swedish Life Science
2024-11-12 12:00 - 17:00 | Hotel Birger Jarl, Birger Jarlsgatan 61, Stockholm, Sweden
Learnings from the SciLifeLab model for drug discovery research, ten years perspective

This symposium is part of the 10 year anniversary of the Drug Development and Discovery Platform at SciLifeLab. Translational research as a boost for Swedish Life Science: Learnings from the SciLifeLab model for drug discovery research, ten years perspective

registration

Program

Program 10 års jubileum DDD_241107Download

Introduction to Python - with application to bioinformatics
2024-11-11 09:00 - 2024-11-15 17:00 | Uppsala University, Lund University or Umeå University
National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of fundamental Python skills. We also welcome applications from outside of Sweden and from the non-academic sector, for more info contact us!

Important dates and information

Application opens: 2024-06-11

Application closes: 2024-09-30

Confirmation to accepted students: 2024-10-02

Course Leader and teachers: Dimitris Bampalikis (CL), Jeanette Tångrot (CL), Nanjiang Shu, Nina Norgren

Contact: edu.intro-python@nbis.se

Course locations

SciLifeLab Uppsala, Entrance C11, BMC, Husargatan 3, Uppsala OR Umeå University, Naturvetarhuset, room NAT.D.370 OR Lund University, Biologihuset, rooms Cerebrum höger (D215b) and Cerebrum vänster (D215a)

Application

Course website

Course fee

A course fee* of 3000 SEK for academic participants and 15000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes lunches, coffee and snacks, and course dinner.

*Please note that NBIS cannot invoice individuals

Course content

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.

Format

This course runs in parallel on-site in Uppsala, Umeå and Lund. Lectures will be streamed online from our Uppsala site to the Umeå and Lund sites. Several teaching assistants will be present in all three classrooms all week to help with exercises and questions. When registering you will be asked to which site you apply.

The course consists of a mix of presentations, demonstrations, and practical exercises (either in the lab with assistants or on your own). Prior to the course, you can read a companion book “Programming Python”, or “Learning Python”. Such a book will also prove useful for your programming tasks, after the course is over. It is however not required, and material will be presented in class.

Topics covered will include:

Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments

Different ways to control program flow using loops and conditional tests

Regular expressions and pattern matching

Writing functions and best-practice ways of making them usable

Reading from and writing to files

Code packaging and Python libraries

How to work with biological data using external libraries.

Learning Outcomes

Upon completion of this course, you will be able to:

Describe and apply basic concepts in Python, such as:LoopsIf/else statementsFunctions

Reading/writing to files

Being able to edit and run Python code

Write file-processing Python programs that produce output to the terminal and/or external files

Create stand-alone python programs to process biological data

Know how to develop your skills in Python after the course (including debugging)

Entry requirements

The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises.

Selection criteria

Due to limited space the course can accommodate a maximum of 25 participants in Uppsala and 15 in Umeå and Lund. 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.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to 1.5 hp credits, however the estimated credits are just recommendations. 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.

Swedish Reference Genome Portal Launch
2024-11-08 14:00 - 15:00 | Online event via Zoom
Join us for the official launch of the Swedish Reference Genome Portal. This free service is developed and maintained by the DDLS Data Science Node in Evolution and Biodiversity (DSN-EB) team as part of the SciLifeLab Data Platform, operated by the SciLifeLab Data Centre. At this event, we will demonstrate how the Genome Portal reduces barriers to the visualisation and interpretation of genome data studied in Sweden, while facilitating collaboration, showcasing researchers’ work, and promoting Open Science and FAIR data sharing.

The Swedish Reference Genome Portal is a web platform for showcasing, aggregating, and visualising non-human eukaryotic genome assemblies and genome annotations (co-)produced by researchers affiliated with Swedish institutions. The Genome Portal aims to:

Highlight and showcase genome research conducted in Sweden.

Lower barriers to accessing, visualising, and interpreting genome data.

Promote the publication of genomic annotations, which are rarely shared.

Ensure all data displayed on the Genome Portal aligns with FAIR principles and is available in public repositories.

The DSN-EB team comprises system developers, data stewards, and bioinformaticians affiliated with SciLifeLab Data Centre and the National Bioinformatics Infrastructure Sweden (NBIS), based at Uppsala University and the Swedish Museum of Natural History.

This service is supported by SciLifeLab and the Knut and Alice Wallenberg Foundation through the Data-Driven Life Science (DDLS) program, as well as by the Swedish Foundation for Strategic Research (SSF).

Registration

Agenda

2:00-2:10 pmWelcome and introduction, Henrik Lantz, NBIS2:10-2:45 pmOverview of the Swedish Reference Genome Portal Introduction and live demo, Daniel Brink, SciLifeLab Data CentreTechnical implementation, Rory Crean, SciLifeLab Data CentreFeatures that boost and facilitate researchers’ work, Angela P. Fuentes-Pardo, SciLifeLab Data Centre2:45-3:00 pmQ&A

Registration will be open until the day of the event (November 8th, 2024) at 12:00 CEST.

This event will be recorded and made available on the SciLifeLab Youtube channel.

For more information, please contact dsn-eb@scilifelab.se.

Pushing the boundaries of performance with the next generation of single cell solutions
2024-11-08 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Imagine seeing biology in new ways! Join this joint seminar between 10x Genomics and Clinical Genomics Gothenburg where Johanna Stergiadou, Science & Technology Advisor at10x Genomics, explains how the Chromium Single Cell solutions can help push the boundaries of your research.

The vast complexities of biology require approaches that build a complete picture from single cells to tissues and beyond. Single cell analysis is a powerful technique to characterize complex tissue types, identify rare cell populations, uncover regulatory relationships between genes, and track cell trajectories.

Join us for this seminar to learn how Chromium Single Cell solutions from 10x Genomics can help you push the boundaries of your research. Dissect cell-type differences, investigate the innate and adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. Uncover molecular insights from fresh or fixed samples, including FFPE, with robust, flexible workflows that simplify experimental logistics. Unravel highly complex biological systems, while bringing into focus the details that matter most.

registration

Lunch will be provided for onsite participation.Onsite registration deadline: November 5

Zoom link

Campus Solna Seminar Series: Mengxiao He & Pauline Granit
2024-11-07 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
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 20 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.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Mengxiao He

Joakim Lundeberg – alpha 3

Spatial analysis of metastatic prostate cancer: Tracing metastatic tumor subclones and unveiling microenvironment dynamics

Pauline Granit

Per-olof Syren – gamma 5

Developing visible light-driven biocatalytic cross-copulings

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

Advancing archaeology with multi-disciplinary analysis
2024-11-07 09:00 - 17:00 | Humanities Theater, Engelska parken, Uppsala, 75238, Sweden
Archaeology thrives on its intrinsic interdisciplinary nature, drawing from a diverse range of scientific disciplines. SciLifeLab, together with ArchLab, Sweden’s newly initiated national research infrastructure for archaeological laboratories, plays a key role in advancing these investigations by providing access to a wide array of analytical tools and methodologies.

The aim of this symposium is to demonstrate and discuss the powerful combination of techniques such as DNA analysis, isotope analysis, dating methodologies, palaeobotany, osteological analysis, spatial analysis, and environmental archaeology, to address key research questions concerning the past.

SciLIfeLab
Ancient DNA
Foto. Mikael Wallerstedt

Attendance is free of charge and on-site participation includes lunch and coffee but registration is required.

Register here

Program
09:00Welcome and introduction to multidisciplinary archaeologyPhil Buckland, Department of Historical, Philosophical and Religious Studies, Umeå University, Sweden09:30Keynote presentation: Building bridges: practices of interdisciplinary researchMari Tõrv, Department of Archaeology, University of Tartu, Estonia10:10Coffee break10:40Bringing together life history studies from isotope analysis with ancient DNA. Hannah Moots, Dept. of Zoology, Stockholm University, Sweden11:00A Migration period Lady from Viken, Uppland – methodological issues & cultural historical frameworkTorun Zachrisson, Upplandsmuseet, Sweden11:20DNA analyses of archaeological cereal finds: challenges and possibilities Matti Leino, Dept. of Archaeology and Classical Studies, Stockholm University, Sweden11:40Multi-disciplinary analyses of intra-site variation at Neolithic AjvideHelena Malmström, Dept. of Organismal Biology, Uppsala University, Sweden12:00Mingle lunch with possibility for consultation with archaeological analysis service providers.13:30Crisis, Conflict & Climate – an archaeological research program advancing multi-disciplinary analysisSven Isaksson, Dept. of Archaeology and Classical Studies, Stockholm University, Sweden13:50From Bison to Aurochs: Exploring the Prey Preferences of Mesolithic South Scandinavians through Ancient DNA AnalysisErika Rosengren, Dept. of Archaeology and Ancient History, Lund University, Sweden14:10Odontology in archaeology- multidisciplinary examinations of teeth and jawsCarolina Bertilsson, Institute of Odontology, University of Gothenburg, Sweden14:30The socio-cultural dynamics of (some of) the last hunter-gatherer communities in Western Europe: a multidisciplinary approachLuciana Simoes, Dept. of Organismal Biology, Uppsala University, Sweden14:50Coffee break15:30Panel discussion on multi-disciplinary analysis in archaeologyRita Peyroteo Stjerna, Dept. of Organismal Biology, Uppsala University, SwedenPhil Buckland, Department of Historical, Philosophical and Religious Studies, Umeå University, SwedenCarina Schebusch, Dept. of Organismal Biology, Uppsala University, SwedenMatthew Collins, Section for Geobiology, University of Copenhagen, DenmarkMari Tõrv, Department of Archaeology, University of Tartu, Estonia16:20Keynote presentation: Strained and fragmented: how manuscript studies could be a focus for interdisciplinary research across ScandinaviaMatthew Collins, Section for Geobiology, University of Copenhagen, Denmark17:00 End of symposium

Organizers

SciLifeLab Ancient DNA unit

Archlab national research infrastructure

Swedigarch national research infrastructure

Uppsala University Human Evolution research program

Centre for Palaeogenetics

Contact: Magnus Lundgren, magnus.lundgren@scilifelab.uu.se.

Imaging the molecular processes of cell division across scales
2024-11-06 16:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Program

15:40Coffee and cake served16:00Imaging the molecular processes of cell division across scalesJan Ellenberg, Director SciLifeLab16:45QuestionsModerator: Per Ljungdahl, SciLifeLab Campus Solna Director17:00Meet the speakers fika Room Earth, arranged separately by the Postdoc & PhD-council

Speaker: Jan Ellenberg, SciLifeLab Director

Jan Ellenberg is distinguished for many contributions to the cell biology and imaging field. The majority of these were made at the European Molecular Biology Laboratory (EMBL) where he is Senior Scientist and Head of the Cell Biology and Biophysics Unit. His major research contributions cover several aspects of the cell division cycle and nuclear organization, including systematic analysis of mitosis, nuclear pore complex structure and assembly, as well as chromatin organization and formation and segregation of mitotic and meiotic chromosomes. Since July 2024, Professor Ellenberg is appointed Director of SciLifeLab.

His goal has been to obtain structural and functional measures of the required molecular machinery inside cells using quantitative 4D imaging, single molecule spectroscopy, as well as light sheet and super-resolution microscopy, which his group is constantly developing and automating to address all molecular components comprehensively.

Register HERE

Host: Per Ljungdahl, Campus Solna Director

Precisionsmedicin vid autoimmuna sjukdomar
2024-11-06 12:15 - 13:00 | Hedstrandsalen | Ingång 70, Akademiska sjukhuset, Uppsala
Välkommen till ett lunchseminarium om spännande framsteg inom Sjögrens sjukdom och MS som pågår här i Uppsala.

För att kunna ge patienter med autoimmuna sjukdomar precisionsmedicin är det viktigt att identifiera undergrupper av patienter som löper risk att drabbas av svårare sjukdom och som kan ha bäst nytta av specifik behandling, samt att genomföra nya behandlingar i kliniska studier. Vi lyfter framgångsrika exempel på detta inom Sjögrens sjukdom och MS i detta seminarium.

Program

Sjögrens sjukdom – ett steg mot precisionsmedicinGunnel Nordmark, överläkare och professor i reumatologi, Akademiska Sjukhuset, Uppsala universitet

Autolog blodstamcellstransplantation som behandling för MSJoachim Burman, överläkare och docent i neurologi, Akademiska Sjukhuset, Uppsala universitet

Alla registrerade bjuds på enklare lunchmacka och dryck.

Seminariet är ett samarrangemang mellan Uppsala universitet, Akademiska sjukhuset, Region Uppsala och SciLifeLab.

Precision Medicine Centre Uppsala

Precisionsmedicin Akademiska

SciLifeLab Capability Precision medicine

https://www.scilifelab.se/capabilities/precision-medicine/

Maximising exclusivity for Academic Startups, Pharma and Biotech Companies in the Life Sciences
2024-11-06 11:00 - 12:00 | Online event via Zoom
Welcome to this Drug Discovery Webinar, organized by OligoNova and SciLifeLab Drug Discovery and Development, to learn more about how academic and biotech interventions can be protected with the goal to benefit patients.

Join us for an insightful seminar focusing on strategies to maximize the exclusivity of medicinal products in the marketplace. This session will delve into the intricacies of regulatory intellectual property (IP), including patenting strategies, patent term extensions such as Supplementary Protection Certificates (SPCs), and regulatory exclusivities like data and market exclusivity. Additionally, we will explore further exclusivities available for orphan and paediatric medicines.

The seminar will emphasise the critical role of exclusivity in attracting and securing investor interest. Gain valuable knowledge on how to navigate and leverage these mechanisms to extend the market life of your medicinal products effectively, thereby enhancing their appeal to potential investors.

registration

Agenda

Introduction – Fredrik Wångsell, OligoNova

Maximizing exclusivity in the Life Sciences – Fiona Hey, Tony Proctor and Michel Pears, Potter Clarkson

Q&A and discussion

One follow-up webinar will take place later this year <ADD LINK>

Welcome

SciLifeLab DDD and OligoNova

Other Seminars

OligaNova organizes three seminars during the fall 2024

Trade secrets in the Life Sciences, October 15

Maximizing exclusivity in the Life Sciences, November 6

IP Strategies in the Life Sciences, December 18

Postponed! New hybrid approaches to Precision Medicine: machine learning, generative AI, and digital twins
2024-11-05 10:30 - 17:00
Workshop postponed to the spring – date to be decided!

If you have questions or suggestions regarding symposia program, please feel free to contact the chair of the program committee at gunnar.cedersund@liu.se.

We look forward to welcoming you to Linköping in the spring 2025!

Members of The Data-driven Precision Medicine & Diagnostics expert group:Gunnar Cedersund, Linköping UniversitySven Nelander, Uppsala UniversityLars Klareskog, Karolinska InstitutetJohan Trygg, Umeå UniversityPatrik Georgii-Hemming, Karolinska InstitutetPäivi Östling, KI (adj. SciLifeLab Precision Medicine Capability lead)Francis Lee (adj. WASP-HS representative in DDLS)David Gisselsson Nord (adjunct as GMS representant)Janne Lehtiö, chair (DDLS SG member)

Make your data count: Process, publish and reuse your metabarcoding output in SBDI
2024-11-05 10:00 - 11:00 | Online event via Zoom
Join this seminar by the Swedish Biodiversity Data Infrastructure (SBDI) to discover tools for converting amplicon sequence reads into species occurrence data that contribute to global biodiversity knowledge. We will introduce SBDI and GBIF platforms, and demonstrate SBDI resources for metabarcoding data, including a guide for ENA submission, a pipeline for denoising reads into Amplicon Sequence Variants (ASVs), a web interface for submitting and accessing ASV data in SBDI, and an R package for processing downloaded data into ASV table format.

When: Tuesday November 5, 10-11 CET (Zoom)

Speakers: Anders Andersson, SciLifeLab, KTH Royal Institute of TechnologyMaria Prager, SciLifeLab, Stockholm University / Karolinska InstitutetJeanette Tångrot, NBIS, SciLifeLab, Umeå University

SciLifeLab 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, including 15 minutes for discussions and Q & A. The videos will be published openly after the seminars at the SciLifeLab YouTube channel.More information about SciLifeLab Data Centre and NBIS joint Data Management team: https://data-guidelines.scilifelab.se/

Welcome!Organisers: SciLifeLab Data Centre and NBIS National Bioinformatics Infrastructure SwedenFor more information or inquiries please contact: data-management@scilifelab.se

[The Svedberg seminar] - Talking to cells: biomolecular ultrasound to image and control cells deep inside the body
2024-11-04 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Mikhail G. ShapiroProfessorCalifornia Institute of Technology, USA

Bio

Mikhail Shapiro is the Max Delbrück Professor of Chemical Engineering and Medical Engineering, an HHMI Investigator, and Director of the Center for Molecular and Cellular Medicine at Caltech. The Shapiro laboratory develops biomolecular technologies allowing cells to be imaged and controlled inside the body using noninvasive methods such as ultrasound. Mikhail received his PhD in Biological Engineering from MIT and his BSc in Neuroscience from Brown. He conducted post-doctoral research at the University of Chicago and UC Berkeley. During the 2024-5 academic year, Mikhail is conducting research at the Physics for Medicine Institute in Paris and ESPCI as a Fulbright-Tocqueville Distinguished Chair.

Mikhail’s awards include the NIH Pioneer Award, the Vilcek Prize for Creative Promise, the Camille Dreyfus Teacher-Scholar Award and the Carl Hellmuth Hertz Ultrasonics Award. Mikhail is an inducted Fellow of the World Molecular Imaging Society. Alongside academic research, Mikhail has been involved as a founder and adviser to several biotechnology and medical device startups.

Talking to cells: biomolecular ultrasound to image and control cells deep inside the body

Studying biological function in intact organisms and developing targeted cellular therapies requires methods to image and control the function of specific cells deep inside the body. Fluorescent proteins and optogenetics serve this purpose in small, translucent specimens, but are limited by the poor penetration of light into deeper tissues. In contrast, most non-invasive techniques such as ultrasound and magnetic resonance – while based on energy forms that penetrate tissue – are not effectively coupled to cellular function. In this talk, I will describe our work to bridge this gap by developing biomolecular reporters and actuators for ultrasound based on gas vesicles – a unique class of air-filled protein nanostructures derived from buoyant photosynthetic microbes. By scattering sound waves, gas vesicles enable noninvasive imaging of tumors, immune cells, gut microbes and cell-based diagnostics and therapies. In addition, they serve as receivers of acoustic radiation force or seeds of localized bubble cavitation, enabling acoustic remote control.

More information about the Shapiro Lab can be found online at shapirolab.caltech.edu.

Host: Maria Tenje, UU maria.tenje@angstrom.uu.se

Design Principles of Living Membranes
2024-11-04 15:00 - 16:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Ilya Levental, PhD
Professor of Molecular Physiology and Biological PhysicsUniversity of Virginia School of Medicine, Charlottesville, VA, USACampus Solna ɣ2 Lunchroom

The Swedish Bioinformatics Workshop 2024
2024-11-04 08:00 - 2024-11-05 17:00 | Swedish University of Agricultural Sciences, Auditorium, Undervisningshuset, Almas Allé 10,, Uppsala, 756 51, Sweden
We are thrilled to invite you to the 22nd Swedish Bioinformatics Workshop (SBW), which will take place in Uppsala on November 4th-5th. SBW is an annual event organized by various universities throughout Sweden since 2000. This year, we are happy to announce that the event will be hosted in the Aula at the Swedish University of Agricultural Sciences.

Join us for an exciting lineup of lectures from invited speakers, participant presentations, poster sessions, and workshops designed to enhance your bioinformatics skills. SBW also offers an excellent opportunity to network and discuss the latest developments in the field with fellow researchers in bioinformatics or computational biology.

SBW 2024 is a hybrid event offering free on-site participation for PhD students and postdocs, as well as free virtual attendance for all participants. As part of the Nordic Computational Biology Week, SBW is open to participants across the Nordic countries.

If you have any questions, please contact info@sbw2024.org

Registration

Event Website

Program

Campus Solna Seminar Series: Josefin Kenrick & Carlos Santolaria
2024-10-31 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
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 20 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.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Josefin Kenrick

Fredrik Edfors – gamma 6

Profiling the Blood Proteome in Autoimmune Disease Using Proximity Extension Assay

Carlos Santolaria

Vicent Pelechano – gamma 5

Mapping the Allosteric Regulation sites in Metabolism and Gene Expression

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

I Forskningens Framkant – Fortbildning för Gymnasielärare
2024-10-29 13:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Eventet är inställt

Microbes are a girl’s best friend: en introduktion till människans mikrobiota och hur den kan påverka vår reproduktiv hälsa

Luisa Hughert

Alla ytor i och på människokroppen är täckta i mikrober. Deras gemensamma arvsmassa är mer än hundra gånger större än människans och de har därför tillgång till betydligt flera metabola vägar. I den här föreläsningen undersöker vi hur våra könshormoner samspelar med våra mikrober, och vilket nytta eller skada de kan göra.

Framtidens målsökande läkemedel

Stefan Ståhl

Intensiv forskning pågår för att utveckla läkemedel som kan målsöka sjuk vävnad, t.ex. cancertumörer. Detta möjliggör att man kan koppla “tumördödande” substanser till målsökaren, för att minska risk för biverkningar. Utmaningen är dock att måltavlan, den s.k. biomarkören, för målsökaren inte bara finns på tumören, utan även i frisk vävnad. Därför eftersträvar man idag att utveckla målsökare som aktiverar sin “tumördödande” substans enbart i närhet av cancertumören.

En nål i en höstack- att kartlägga immunceller i tumörer

Camilla Engblom

Genteknisk modifiering av alger och växter för att förbättra fotosyntes

Paul Hudson

Plats: SciLifeLab, Tomtebodavägen 23, SolnaKarta: Google Maps

Välkommen med din anmälan!

Anmälan

Organiseras av SciLifeLab tillsammans med Vetenskapens Hus.

R Programming Foundations for Data Analysis
2024-10-28 09:00 - 2024-11-01 17:00 | Uppsala University, Lund University
The course is addressed to individuals with little or no experience in programming but who are enthusiastic about learning how to use R for data analysis and streamline their work. It is a national course open for PhD students, postdocs, researchers and other employees in all Swedish. We also welcome applications from outside of Sweden (EU-zone) and from the non-academic sector, for more info contact us. NOTE: In October 2024, the course will be a 5-day-course on-site both in Uppsala and Lund.

Venue – onsite

Uppsala University: Experimental room, Campus Blåsenhus, von Kraemers allé 1A, 2nd floor

Lund University: Retina D227, Biologihuset

Important dates

Application open: August 08, 2024

Application deadline: September 30, 2024

Confirmation to accepted students: October 4, 2024

Responsible teachers: Nima Rafati, Guilherme Dias, Miguel Angel Redondo, Marcin Kierczak, Lokeshwaran Manoharan, Louella Vasquez

Contact for questions: edu.r@nbis.se

Course fee

A course fee* of 3000 SEK for non-profit organizations or 15000 SEK for private companies will be invoiced to accepted participants. This includes lunches, coffee, snacks, and one course dinner.

*Please note that NBIS cannot invoice individuals

Application

Course website

Course content

The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting. After introductory lectures on good programming practices, basic software design theory and a brief overview of R, we will delve into programming. We start by learning how to use R as a basic calculator, what are variable types, how to use data structures, how to implement repeating actions with and without loops, and how to take actions based on certain conditions. We gradually proceed to loading data, importing data from common file formats, some basic matrix algebra and learning how to perform basic statistical tests and visualize results. You will learn how to document your work and how to generate automatic reports using real-life datasets. During the course you will also be working on a small dataset to apply knowledge you learnt in the course and will present that in a report format towards the end of the workshop.

Topics covered will include:

Variables and Operators

Matrices, lists, and dataframes

Data manipulation

Visualization

R packages

Bioconductor

Upon completion of this course, you will be able to:

Describe different data structures commonly used in R.

Work with different data types.

Import and export data from and to R environment.

Manipulate data.

Work with dataframes and lists.

Visualize the data.

Use R Markdown to create reports containing text, code, tables and/or figures.

Entry requirements

Good general computer literacy is expected, but no previous experience in programming or R is required. You are expected to know basic concepts in mathematics and statistics, but the emphasis of the course is to learn how to use R.

Participants are expected to use their own computers with pre-installed R and R Studio (detailed instructions will be given upon acceptance).

Due to our best practice to have a high teacher to student ratio, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Precision Omics Initiative Sweden (PROMISE) Symposium
2024-10-28 08:30 - 2024-10-29 13:00 | Lecture Hall X, Uppsala University Main Building, Biskopsgatan 3, Uppsala, Sweden
Sweden is uniquely positioned to advance medical research and implement precision medicine on a national scale, benefiting its entire population. Integration of cutting-edge biomedical research technologies with Sweden’s uniform healthcare system has the potential to position our country as a global frontrunner, leading the development of precision medicine in this new technological era. However, data fragmentation and data isolation currently hinder the Swedish ability to fully capitalize on its potential and maximize the use of already available infrastructure and prior investments.

Precision Omics Initiative Sweden (PROMISE) is a new transformative initiative that will be centered around SciLifeLab and Genomic Medicine Sweden (GMS) to completely integrate medical research with the healthcare system in Sweden.

PROMISE will have three major focus areas: 1) Generate extensive multi-omics data from both patients and the general population in Sweden, 2) Develop a strong and effective infrastructure to integrate healthcare generated multi-omics data for research applications, improve data sharing and data accessibility across Sweden, 3) Develop legal and regulatory frameworks for better alignment with modern capabilities, for maximum utilization of Sweden’s great potential.

Register for the PROMISE symposium, October 28-29 2024, to contribute to further developing the scientific foundation and design of this transformative initiative.

registration

Program

PROMISE Symposium Uppsala October 28-29_FINALDownload

Organizing committee

Anna Clareborn

Sanna Gudmundsson

Bo Jacobsson

Åsa Johansson

Anders Kämpe

Tuuli Lappalainen

Kerstin Lindblad-Toh

Anna Lindstrand

Bengt Persson

Richard Rosenquist Brandell

Tobias Sjöblom

Colum Walsh

Campus Solna Seminar Series: Alberto Arenas Molina & Kiana Hosseinpour Moghaddam
2024-10-24 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
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 20 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.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Alberto Arenas Molina

Simon Elsässer – alpha 4

Translating the untranslated: Microproteins encoded by “non-coding” regions and their role in tumorigenesis

Kiana Hosseinpour Moghaddam

Ola Larsson – gamma 5

Di-codon organization orchestrates the malignant proteome

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

Lund: Building and sharing machine learning demo applications within life sciences
2024-10-24 10:00 - 13:00 | BMC Hus E, room Rådslaget, Sölvegatan 19, Lund, 223 62, Sweden
This event is open to everyone at Lund University. It consists of a workshop followed by a free lunch for participants. During the lunch the participants will have an opportunity to informally chat with AI data engineers from the SciLifeLab Data Centre to discuss the needs for services and research infrastructure in life science research using machine learning methods.

Title: Building and sharing machine learning demo applications within life sciences: a practical tutorial.

Organizer: AI Data Engineers from the SciLifeLab Serve team.

Where and when: October 24, 2024 at 10:00-13:00 at room Rådslaget, BMC Hus E (Sölvegatan 19, 223 62 Lund)

Agenda:10:00-12:00: Workshop12:00-13:00: Lunch

Abstract: 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.

The workshop will last for 2 hours with a break in the middle. We have room to accept 35 participants, on the first come first served basis. Those registered after that will be placed on the waiting list.

After the workshop all participants are invited for lunch.

Since there is a limited number of spots in this workshop please sign up only if you intend to attend.

Register to join the event

More about the event series:

Tools 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.

For questions about the events please contact the organizing team by emailing serve@scilifelab.se

Scientific lead: Prof. Ola Spjuth, SciLifeLab Data Centre and Uppsala University

Contact information: serve@scilifelab.se

Discover services for data-driven life science
2024-10-24 10:00 - 12:30 | https://uu-se.zoom.us/j/63809262140
Welcome to join SciLifeLab Data Centre and SciLifeLab Data Management for “Discover services for data-driven life science“- an overview of data-driven services, tools, and support aimed at the fellows community. The event will also include a feedback session to help SciLifeLab Data Centre best support your specific research needs. Share your views about your current and future research needs, e.g. state-of-the-art services that would further your research or the general research of your field, currently not available on the SciLifeLab Data Platform.

When: Oct 24, 10-12.30 CET (Zoom)Target group: Scilifelab Fellows, DDLS Fellows, and interested participants

Agenda

10.00-10.10 Welcome Johan Rung, Head of SciLifeLab Data Centre

10.10-10.35 Open Science 101 Chris Erdmann, Head of Open Science

10.35-11.00 SciLifeLab Data Management services and support Angela Fuertes-Pardo, Data Steward, SciLifeLab Data Centre

11.00-11.05 Coffee break

11.05-11.30 How to get access to Compute, Storage, and Hosting to support your research, speaker TBA

11.30-12.30 Feedback session: Share your needs for data-driven life science services and tools. Moderators: Johan Rung, Head of SciLifeLab Data Centre, and Niclas Jareborg, NBIS

For additional information please contact SciLifeLab Data Centre at datacentre@scilifelab.se

Drips and SliPS and Retirees, Oh My!
2024-10-22 15:15 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Jonathan Wilson Yewdell

Chief, Cellular Biology Section Laboratory of Viral DiseasesNational Institute of Allergy and Infectious Diseases (NIAID)National Institute of Health (NIH)Bethesda, MD, USA

Biography:

Jon Yewdell graduated from Princeton University in 1975 with an AB in biochemistry and received MD and immunology PhD degrees from the University of Pennsylvania in 1981. After a post-doctoral fellowship at Imperial College in London with David Lane, he spent 4 years as an Assistant Professor at the Wistar Institute in Philadelphia. In 1987 he joined NIAID. His lab uses influenza A, SARS-CoV2, vaccinia and other viruses to explore basic elements of cell biology, virology, and immunology, and has contributed to understanding how peptides are generated for CD8+ T cell immunosurveillance.

Title: Drips and SliPS and Retirees, Oh My!

Abstract for the talk:

MHC class I molecules present short peptides derived from biosynthesized proteins, enabling CD8+ T cell immunosurveillance of tumors, viruses and intracellular microbes. Many cellular peptides, and likely nearly all viral peptides, derive from rapidly degraded proteins, which consist of defective ribosomal products (DRiPs) and short-lived proteins (SLiPs). I will describe the nature of a number of influenza virus DRiPs and how ribosome profiling facilitates the identification of peptides derived from non-canonically translated cellular DRiPs. I will also discuss how cells with ribosomes lacking individual protein subunits demonstrate either enhanced or decreased peptide generation in a subunit-specific manner and how this can be exploited by cancer cells to escape immunosurveillance. I will present a model to explain how peptide generation avoids the law of mass action to generate a highly diverse peptide repertoire (immunopeptidome) that enables pathogen and tumor recognition. This talk will illustrate how, in over 4 decades of research, cell biology, virology, and immunology can be combined to dissect a medically important immune effector mechanism.

Host: Adnane Achour, adnane.achour@scilifelab.se

Exhibition in Navet at BMC
2024-10-22 09:00 - 2024-10-24 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
On October 22-24, between 09.00-15.00, you have a new opportunity to visit our exhibition in Navet at BMC. This is a chance to receive information and updates from 30 of the leading life science companies in Sweden. The entrance to Navet will be open between 09:00-15:00 for external visitors.

Long-Read Sequencing Uppsala Meeting 2024
2024-10-21 09:00 - 2024-10-23 17:00 | Universitetsaulan, Biskopsgatan 3, Uppsala, Sweden
In recent years, long-read DNA sequencing has replaced short-read technologies as the gold standard solution for a wide range of genomics applications. In addition to producing high-quality de novo genome assembly, long-read technologies can be used to study complex structural variation, full-length RNA isoforms, detection of epigenetic signals, and much more. The adaptation of long-read sequencing is sweeping through several areas of the life sciences, including agricultural, environmental, and medical research.

Join us in Uppsala for a three-day international event to catch up with the latest developments in long-read sequencing technologies and their applications, get inspired by peers presenting their research, and enjoy discussions with leading experts and company representatives.

Read more

Registration

Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis
2024-10-18 10:00 - 11:00 | Online event via Zoom
Accurate assessment of progression and disease course in multiple sclerosis (MS) is vital for timely and appropriate clinical intervention. The transition from relapsing-remitting MS (RRMS) to secondary progressive MS (SPMS) is gradual and diagnosed retrospectively with a typical delay of three years. To address this diagnostic delay, we developed a predictive model that is able to distinguish between RRMS and SPMS with high accuracy, trained on data from electronic health records collected at routine hospital visits obtained from the Swedish MS Registry containing 22,748 patients with 197,227 hospital visits. To be useful within a clinical setting, we applied conformal prediction to deliver valid measures of uncertainty in predictions at the level of the individual patient. We showed that the model was theoretically and empirically valid, having the highest efficiency at a 92% confidence level, and demonstrated on an external test set that it enables effective prediction of the clinical course of a patient with individual confidence measures. We applied the model to a set of patients who transitioned from RRMS to SPMS during the cohort timeframe and showed that we can accurately predict when patients transition from RRMS to SPMS. We also identified new patients who, with high probability, are in the transition phase from RRMS to SPMS but have not yet received a clinical diagnosis. We conclude that our methodology can assist in monitoring MS disease progression and proactively identify patients undergoing transition to SPMS. An anonymized, publically accessible version of the model is available at https://msp-tracker.serve.scilifelab.se/.

A preprint is available here: https://www.medrxiv.org/content/10.1101/2024.03.01.24303566v1

Kim Kultima, Uppsala University

NBIS arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms, typically between 10 and 11 am, with approx. 45 min long presentation and 15 min discussion.

Generation of context-specific genome-scale metabolic models using single-cell RNA-Seq data
2024-10-17 13:00 - 14:15 | Online event via Zoom
Johan Gustafsson, Postdoc researcher, Broad Institute, USA

Abstract

The metabolic networks in cells vary across tissues and cell types, and to accurately model the metabolism of cells, the full generic metabolic network defined in the genome needs to be reduced to a context-specific network representing the network expressed specifically in the cells of interest. Single-cell RNA-Seq promises to provide the information needed for such a reduction, but noise in the form of data sparsity is a challenge. Here, we present methods to handle data sparsity and estimate the uncertainty of modeling results.

Biography

Johan is an expert in modeling cancer metabolism and analyzing single-cell RNA/DNA sequencing data, aiming to uncover vulnerabilities in cancer. With a background in both computer science and biochemistry, Johan has completed a PhD in metabolic modeling at Chalmers University of Technology and now works as a postdoc in the Getz lab at the Broad Institute, focusing on CLL/Richter’s syndrome and hypoxia in solid tumors.

Host: Rasool Saghaleyni, NBIS Chalmers University, Gothenburg (rasool.saghaleyni@scilifelab.se)

Date: October 17, 13:00 – 14:15 CET online on zoom

Broadcast link (live event): link, pass:spd996The talk will also be available afterwards on the SciLifeLab YouTube channel.More information about the Oimcs Integration and Systems Biology Workshop here.

Campus Solna Seminar Series: Quentin Verron & Annika Bendes
2024-10-17 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
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 20 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.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

PhD students that are attending the Campus Solna Seminar lectures will have the opportunity to gain credits. For the syllabus and instructions on how to obtain these credits, read this document. Please contact your own department at your host University to confirm.See here the full schedule for this semester.

This week:

Quentin Verron

Magda Bienko – alpha 4

Exploring the Role of Trans-Interacting Intronic RNAs in Neuronal Genome Organization

Annika Bendes

Jochen Schwenk – alpha 2

Insights from highly frequent microsampling of the circulating proteome — A study of virus induced diabetes in mice

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.
