SciLifeLab

Campus Solna Seminar Series: Greta Gudoityte & Stavros Azinas
2023-11-16 12:00 - 13:00 (Europe/Stockholm) | Gamma-6-Pascal, SciLifeLab, Tomtebodavägen 23, Solna, 17165, 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Greta Gudoityte

Brinton Seashore-Ludlow – alpha 4

Interplay between Cancer-Associated Fibroblasts and Ovarian Cancer.

Stavros Azinas

Marta Carroni – gamma3

Confirmational insights of bacterial dissagregase CLPG.

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

New Horizons for Swedish Sciences: World-unique (Bio)Solids Capabilities at the national UMU NMR facility
2023-11-16 09:30 - 17:00 | Carl Kempe-salen, KBC Building, Umeå University, Umeå, Sweden
Inauguration of world-unique combined solid-state NMR equipment (MAS CryoNMR Probe + Ultrafast MAS NMR Probe) for the next application level in sciences ranging from bio and medical sciences to novel material and environment. Equipment is installed at the Umeå University KBC NMR core facility, a national SciLifeLab and VR-RFI (SwedNMR) node.

Read more

Program

ProgramInaugurationNMR20231116finalDownload

DDLS Annual Conference 2023; The emerging role of AI in data-driven life science
2023-11-15 12:30 - 2023-11-16 12:30 | Jacob Berzelius salen, KI, Berzelius väg 3, Solna, 171 65, Sweden
Image generated with DALL-E 3

This 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.

Target group: All scientists interested in data-driven research are welcome to join the 2-day lunch-to-lunch Conference in Stockholm.

Registration

The 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.

Registration for zoom link

Poster session

Poster session, Flash Talk & Best Poster Award (click to open)
Poster list

Poster-List-DDLS-Annual-conference-2023Download

Poster booklet, including abstracts

Poster-Booklet-DDLS-Annual-conference-2023Download

The 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.

The Best Poster Award winner for 2022 was Adelina Rabenius, KTH, and we are proud to support her attendance at an EMBO conference this summer.

Organizer: SciLifeLab, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science, on behalf of the DDLS Steering group.

Pre-conference introductory lectures

In 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.

Post-conference activities

Note! The Post-conference workshop and different DDLS stakeholder meetings will be handled separately and require separate registrations.

Workshop

Building 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

Stakeholder meetings

DDLS Fellows meeting (DDLS Fellows only). November 16, at 13:30 – 15:30. Biomedicum, Solnavägen 9. Room B0317. Participant list here

DDLS 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

DDLS 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

DDLS Research area Cell and Molecular Biology Symposium, Nov 17

The 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.

More information here

Program

November 15

09:30Venue: 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

November 16

08:30CoffeeModerator: 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.

Abstracts

Pre-Conference Lectures

Anna Klemm – AI in bioimage analysis
In 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.

Example 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)

Magnus Sahlgren – Large Language Models
This 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.

Conference

Martin Eklund – Prediction models and artificial intelligence for improving prostate cancer diagnostics and treatment
Prostate 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).

Cemal Erdem – Multi-omics data integration with robust penalized regression identifies context-dependent signaling networks
Cells 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.

Juliette Griffié – From super resolution microscopy to modelling: how proteins spatial distribution regulates cellular processes
Single 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.

Rocío Mercado – Transforming Biomolecular Engineering Through AI
AI’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.

Wei Ouyang – AICell Lab: Laying the AI Foundation for Data-Driven Whole-Cell Modeling
As 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.

In 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.

Through 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.

Fabian J. Theis – Generative AI for modeling single-cell state and response
Advances 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.

After 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.

Wen Zhong – Blood proteome is a powerful tool to monitor human health and disease
The 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.

Workshop

Building and sharing machine learning demo applications within life sciences: a practical tutorial
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 within a couple of hours.

The 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.

Note that registration for the workshops is separate from the registration for the conference. Please see the workshop page for information on registration.

Scientific Committee

Chair: Ola Spjuth, Uppsala University

Johan Bengtsson-Palme, Chalmers

Laura Carroll, Umeå University

Fredrik Johansson, WASP, Chalmers

Project leader

Erika Erkstam, Operations office

Introduction to bioinformatics using NGS data
2023-11-13 09:00 - 2023-11-17 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
National workshop for PhD students, postdocs, researchers, and other employees within Swedish academia, introducing the analysis of next generation sequencing data.

The course is organized by: National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI)

Responsible teachers: Malin Larsson, Martin Dahlö, Roy Francis

Contact information: edu.intro-ngs@nbis.se

Apply here

Course website

Important dates

Application open: Jun 7, 2023

Application deadline: October 4, 2023

Confirmation to accepted participants: Week 41 (October 9-12)

Course fee

This on-site training event costs 3000 SEK for academic participants, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee.

Course description

This intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.

Course content

Briefly, the workshop covers the followings major topics:

Working on the UNIX/LINUX command line

Bioinformatic/NGS data formats and QC

DNA variant calling workflow essentials

RNA sequence analysis workflow essentials

Learning outcomes

After this workshop you should be able to:

Describe the basic principles of next generation sequencing.

Use the Linux command line interface to manage simple file processing operations, and organise directory structures.

Connect to and work on a remote high performance compute cluster.

Apply programs in Linux for analysis of NGS data.

Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.

Explain common NGS file formats.

Interpret quality control of NGS reads.

Explain the steps involved in variant calling using whole genome sequencing data.

Independently perform a basic variant calling workflow on example data.

Demonstrate hands-on experience with handling raw RNA sequencing data, QC and quantification of gene expression.

Explain the steps involved in differential gene expression using RNA seq data.

Entry requirements

To be able to follow the workshop you need to:

BYOL, bring your own laptop configured according to precourse instructions.

Have a background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable.

To get the maximum benefit from the workshop you should:

Have a research project where you are currently using or are planning to use next generation sequencing.

Selection criteria

Due to limited space the course can accommodate a maximum of 30 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Priority is given to PhD scholars followed by other researchers, and we will prioritise applications from Swedish academia.

Campus Solna Seminar Series: Adelina Rabenius
2023-11-09 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Adelina Rabenius

Anniina Vihervaara – alpha 3

Timers in genes: Introns define the order of heat-induced chaperone production

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

The Spatial Biology Tour 2023 - the Spatial Proteomics Unit and Lunaphore
2023-11-09 10:00 - 15:30 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
The Spatial Proteomics Unit at SciLifeLab hosts the Lunaphore Spatial Biology Tour at SciLifeLab Solna.

Take the opportunity to learn more about the COMET platform for automated sequential immunofluorescence and how you can work with the Spatial Proteomics Unit to generate highly multiplexed imaging data for your research project.

The Spatial Proteomics Unit was an early beta tester of the COMET platform in 2021 and since 2022 offer the COMET platform as a service in their unit. You will also get the chance to see the instrument live in the Spatial Proteomics unit.

Read more and register here

Multiplexed image of a colon FFPE sample generated on the COMET platform

Program

10:00Welcome and registration10.15Spatial cell profiling with hyperplex immunofluorescenceAngelo Da Rosa11.00COMET – opportunities in the Spatial Proteomics FacilityCharlotte Stadler11.45RNAscope™: Single-molecule RNA in situ hybridization. ANY Gene. ANY Species. ANY tissue.Joan Raouf12.15Lunch and networking13.00COMET™ on-site instrument demonstration14.15Refreshment and networking

Discovery of SARS-CoV-2 Main Protease inhibitors at the DDD platform
2023-11-07 13:00 - 14:00
Pandemic preparedness and the generation of SARS-CoV-2 inhibitors – A new exit from SciLifeLab Drug Discovery and Development platform

DDD Exit Event 2023-11-07, zoomcast 13.00

Presenters

Dr. Ulf Ribacke. Dept. of Microbiology, Tumor and Cell Biology, Karolinska InstitutetTel: +46 70 497 5196, Email: ulf.ribacke@ki.se

Prof. Jens Carlsson, Dept. of Cell and Molecular Biology, Uppsala UniversityTel: +46 72 227 7976, Email: jens.carlsson@icm.uu.se

Abstract

SciLifeLab has been commissioned by the government to build laboratory capacity to assist in future pandemics through research and competence and technology development. Hear more about the SciLifeLab Pandemic Laboratory Preparedness program from Ulf Ribacke, (SciLifeLab and Karolinska Institutet) and groundbreaking research performed by researchers at Uppsala University that led to discovery of potent main protease SARS-CoV-2 inhibitors.

Jens Carlsson, Helena Danielson, Anja Sandström and Lindon Moodie have recently signed an agreement for international partnering of a project focusing on development of drugs for treatment of COVID-19 (DP_JC_188).

The project was funded by the National COVID-19 Research Program initiated by the Knut and Alice Wallenberg Foundation. Hit compounds identified by virtual screening were published in 2022 by Luttens et al. (https://doi.org/10.1021/jacs.1c08402). Hit-to-lead generation was then performed together with the Drug Discovery and Development Platform in the DP_JC_188 project. Lead optimization and preclinical development of assets are now supported by an international pharmaceutical company.

Short speakers biography:

Ulf Ribacke: Ulf is scientific co-director of the SciLifeLab Pandemic Laboratory Preparedness program and heads two research labs located at Karolinska Institutet and Uppsala University, both dedicated to resolve how malaria parasites adapt to evade cellular stress with the ultimate goal to identify targets for new interventions.

Jens Carlsson: Jens is a Professor of Computational Biochemistry at Uppsala University, where his group uses computational models to understand protein function at the molecular level and develops strategies for drug discovery.For more information, visit http://www.carlssonlab.org/.

Ulf RibackeKarolinska InstitutetScientific Lead – Pandemic Laboratory Preparedness at SciLifeLabulf.ribacke@ki.se

Jens CarlssonUppsala Universityjens.carlsson@icm.uu.se

21st Swedish Bioinformatics Workshop 2023 in Stockholm
2023-11-06 10:00 - 2023-11-07 17:00 | Sune Bergström Aula, BioClinicum, New Karolinska University Hospital, Solnavägen 30, Stockholm, 17164, Sweden
We’re pleased to invite you to the 21st Swedish Bioinformatics Workshop (SBW) that will take place in Stockholm on November 6th – 7th (Mo-Tu). SBW is an annual event that is hosted by different universities across Sweden. This year, the event will take place at Karolinska Sjukhuset Solna at the Sune Bergström’s Aula.

As is tradition, SBW will be a chance for PhD students and postdocs as well as all researchers working with bioinformatics or computational biology to present their work, discuss the latest developments in the field, and improve their bioinformatic skills through different workshops. In addition, the program includes lectures from invited speakers, participant presentations, and poster sessions.

This year SBW is part of the Nordic Computational Biology Week. It features SBW (6th-7th of Nov., Mo-Tu), the Danish Bioinformatics Symposium (8th-9th of Nov., We-Th) and the Finish Symposium on Computational Biology (10th of Nov., Fr). More information can be found under: bit.ly/ncb-week-2023

More information regarding SBW will be updated on the website: sbw2023.eu. On-site registration is closed, but you can still sign up for free for virtual attendance. There you can also sign up for the other events that are part of the Nordic Computational Biology Week. If you have any questions, feel free to reach out to sbw2023@scilifelab.se.

Welcome to the Swedish Bioinformatics Workshop 2023!

DDLS Population genomics in practice
2023-11-06 09:00 - 2023-11-10 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
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.

Important dates and information

Application opens: 2023-08-17

Application closes: 2023-09-30

Confirmation to accepted students: 2023-10-10

Course Leader and teachers: Per Unneberg (CL), Nikolay Oskolkov, Jason Hill, André Soares

In case you miss information on any of the above dates, please contact: edu.population-genomics-in-practice@nbis.se

Course fee

A course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches, coffee and snacks.

*Please note that NBIS cannot invoice individuals

Application

Course Website

Course content

The 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.

Topics covered will include:

Foundations of population genetics

Introduction to simulation and the coalescent

Basics of variant calling

Variant filtering and sequence masks

Characterization and interpretation of DNA sequence variation

Calculation and interpretation of summary statistics from variation data

Investigating population structure with admixture modelling and principal component analyses

Demographic modelling using sequentially Markovian coalescent models and linkage disequilibrium

Selection scans

Learning Outcomes

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

describe the different forces of evolution and how they influence genetic variation

understand and interpret genealogical trees and how they relate to genetic variation data

describe the basics of the coalescent

perform simple coalescent simulations with msprime

run simple SLiM forward simulation models

describe and run the steps of a variant calling pipeline, including quality control of raw reads, read mapping, and variant calling

know how and when to filter raw variant calls using manual coverage filters

describe and calculate nucleotide diversity from variation data

analyse population structure with admixture modelling and dimensionality reduction methods

perform demographic modelling with sequential Markovian coalescent models

describe methods that identify regions undergoing adaptation and selection

run selection scans, score identified regions and interpret findings in the context of genome annotations

Entry Requirements

The following is a list of skills required for being able to follow the course and complete the exercises:

Basic knowledge in R or Python

Basic knowledge of variant calling, or the equivalent of NBIS course “Introduction to Bioinformatics using NGS data”

Basic knowledge of population genetics

Basic understanding of frequentist statistics

A computer

Desirable, but not essential, skills increasing the output of the course, include:

Experience with analysis of NGS and other omic data

Due 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.

Campus Solna Seminar Series: Emilie Flaberg & Kiana Hosseinpour Moghaddam
2023-11-02 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Emilie Flaberg

Päivi Östling – alpha 4

Kiana Hosseinpour Moghaddam

Ola Larsson – gamma 5

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
2023-10-31 13:00 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Välkommen till en fortbildning där du får uppleva delar av det nationella forskningscentret för molekylära biovetenskaper i Stockholm.

Denna eftermiddag får du möta fyra forskare som berättar om sin forskning och så gör vi en rundvandring på SciLifelab. Fortbildningen avslutas med mingel med tilltugg.

Program12:30-13:00 Kaffe13:00-14:30 Föreläsningar – fyra forskare från SciLifeLab14:30-15:00 Visning av labb15:00-16:00 Mingel med tilltugg

Plats: SciLifeLab, Tomtebodavägen 23, SolnaKarta: Google Maps

Välkommen med din anmälan!

Registrering

From Genes to Proteins: The Power of the Human Protein AtlasFredrik Edfors, SciLifeLab/KTHFramtidens målsökande läkemedelStefan Ståhl, SciLifeLab/KTHKlinisk GenomikAnna Lyander, SciLifeLab/Karolinska InstitutetMikrobernas samhällenAnders Andersson, SciLifeLab/KTH14:00-15:00 Rundvandring i lokalerna15:00-16:00 Mingel med tilltugg

From Genes to Proteins: The Power of the Human Protein AtlasFredrik Edfors, SciLifeLab/KTH

Human Protein Atlas (HPA) som finansieras av Knut och Alice Wallenbergs stiftelse är ett svenskt projekt som är baserat på SciLifeLab, en nationell samarbetsplattform för molekylär biologi som drivs av KTH, Karolinska Institutet, Stockholms universitet och Uppsala universitet. Människan har cirka 20 000 gener som kodar för proteiner, och HPA hjälper till att identifiera olika kombinationer av proteiner som är avgörande för mänsklig biologi. HPA strävar efter att systematiskt kartlägga det mänskliga genomet på proteinnivå och på www.proteinatlas.org presenteras dessa nivåer inom flera olika fokusområden. Dessa inkluderar bland annat inkluderar proteinuttryck i vävnader, hjärna, cell-linjer eller nivåer blod och hur dessa skiljer sig mellan olika sjukdomstillstånd. Förutom att stödja andra forskare är atlasen också en värdefull utbildningsresurs för ämnen som rör den mänskliga kroppen, cellbiologi och molekylärbiologi.

Framtidens målsökande läkemedelStefan Ståhl, SciLifeLab/KTH

Små bindarproteiner kan med hjälp av riktad evolution fås att binda till sjukdomsrelaterade proteiner, så kallade biomarkörer, som kan utnyttjas som måltavlor för nya typer av proteinläkemedel. Som exempel kan cancertumörceller målsökas på detta sätt. Dessa målsökande bindarproteinerna kan “beväpnas”, t.ex. med cellgifter eller lämpliga radioisotoper som dödar tumörcellerna, med minimal påverkan på frisk vävnad.

Klinisk GenomikAnna Lyander, SciLifeLab/Karolinska Institutet

Clinical Genomics är en infrastrukturplattform vid Scilifelab. Plattformen arbetar med avancerade genomikmetoder, olika typer av sekvenseringsteknologier och dataanalysverktyg, för att stötta forskning och sjukvård. Clinical Genomics erbjuder en helhetslösning inom next generation sequencing för translationella forskningsprojekt och kliniska studier, och bidrar till att optimera tekniker så att de kan användas inom precisionsmedicin. Plattformen arbetar också inom ramen för Genomic Medicine Sweden för att harmonisera precisionsmedicin i Sverige vilket banar väg för bättre diagnostik, vård och behandling i hela landet.

Mikrobernas samhällenAnders Andersson, SciLifeLab/KTH

Campus Solna Seminar Series: Stavros Azinas & Marco Grillo
2023-10-26 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Stavros Azinas

Marta Carroni – gamma 3

Conformational insights of bacterial dissagregase CLPG

Marco Grillo

Mats Nilsson – gamma 4

Open source tools for high-throughput spatially resolved transcriptomics

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

Subtomogram averaging workshop for cryo electron tomography
2023-10-25 08:00 - 2023-10-27 13:00 | Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16C, Stockholm
Cryoelectron tomography is anemerging field in structural biology. We are happy to announce that we are hosting a Subtomogram averaging workshop for cryo electron tomography, taking place on 25-27 October 2023 at Stockholm University.

The aim of the course is to provide training in Subtomogram averagingusing e.g. Dynamo and Relion4 including the latest developments of the field.

Registration is now closed

The workshop provides hands-on training in all practical aspects of tomography and sub-tomogram averaging using the Dynamo software, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this two-day course.

Participants will be selected on the basis of applications that describe their current research projects and plans. Priority will be given to participants that are currently processing their own cryo-ET data and are users of the SciLifeLab cryo-EM facilities.

Deadline for application: 15 September 2023

Notification: Applicants will be notified of the outcome of their application by 20 September 2023

Course fee payment deadline: 30 September 2023

The registration fee: 1000 SEK and includes

Attendance in the course 25-27 October 2023

Lunches, coffee and refreshments on the course dates

Course materials

Certificate of attendance

Course dinner on first night of the course

Please note, the registration fee does not cover hotel, travel expenses, breakfasts, and dinners (expect the course dinner second night)

Course Content

The course content can be found here

Read more

As a general guideline, we will cover:

Alignment and reconstruction of tilt series.

Manual and automated particle picking in different geometries (filaments, membranes, isolated particles…).

Archiving and cataloguing of tilt series, tomograms and annotations.

Creation of subtomogram averaging projects.

Advanced tools in subtomogram averaging.

Classification methods.

Creation of 3d scenes.

Scripting in Dynamo: gentle introduction to programming.

Computing facilities

Computer room at KÖL, Stockholm University

Venues

25-26/10-23

Department of Biochemistry and BiophysicsComputer room at KÖL, K343Stockholm University, Svante Arrhenius väg 16CStockholm

27/10-23

SciLifeLab Seminar room in building gamma 2, Air&Fire Tomtebodavägen 23ASolna

Program

Program_231018_1Download

SciLifeLab Campus Solna Science Talks
2023-10-24 09:00 - 19:00 | Jacob Berzelius salen, KI, Berzelius väg 3, Solna, 171 65, Sweden
We would hereby like to warmly welcome you to take part in this year’s Campus Solna Science Talks symposium on October 24th – a meeting for everyone in the community to learn more about ongoing research and activities at SciLifeLab’s Campus Solna, which aims to bring the community together, inspire exchange and new collaborations.

Research presentations will be given by group leaders and junior researchers (selected with consideration for balance in topics, presenters’ career stages, and affiliations) as part of a plenary session between 9:00 and 16:00 (including lunch), and the event will conclude with a poster session, mingle and food in Campus Solna’s meeting place Delta.

We invite all Campus Solna research groups to be represented with at least 1 poster (and maximum 3). Furthermore, we want to encourage all infrastructure units and committees (The Diversity, Equity and Inclusion-committee, the Public Engagement-committee, the CSI and the PhD- & Postdoc-council) to partake with posters!

List of Posters (titles & numbering)

Program
08:30Arrival, registration and coffeeJacob Berzelius hall, Karolinska Institutet09:00Welcome and opening of symposiumScientific Committee & Per LjungdahlSession I. Moderator Yerma Pareja09:15Mapping B and T cell receptors using spatial transcriptomicsCamilla Engblom09:30Use the Flow, Leukocyte: ion and water fluxes are required for T cell migrationLeon de Boer09:45B cell repertoire analysis of SARS-CoV-2-infected individualsGunilla Karlsson Hedestam10:15Coffee BreakSession II. Moderator Marcel Tarbier10:45agoTRIBE detects microRNA-target interactions transcriptome-wide in single cellsVaishnovi Sekar11:00Single cell-resolution in situ sequencing elucidates spatial dynamics of multiple sclerosis lesion and disease evolutionChristoffer Mattsson Langseth11:15Beyond the host’s spatial transcriptomeStefania Giacomello11.30Machine learning of immune escape dynamics from single cell and spatial tumor transcriptomicsJakob Rosenbauer11.45LunchSession III. Moderator Ute Hoffmann13:00Female sex hormones and the human microbiomeLuisa Hugherth13:15Environmental genomics for broadscale studies on aquatic microbial diversity and evolutionKrzysztof Jurdzinski13:30Interaction proteomics to explore protein regulation in photosynthetic organismsAnna Karlsson13:45Developmental Gene TranscriptionMattias Mannervik14:15Coffee BreakSession IV. Moderator Erdinc Sezgin14:45Modelling Glut1 Deficiency Syndrome (Glut1DS) for therapeutics and drug discoveryRekha Tripathi15:00Multiplexed high-content screening of drug and immune sensitivity in microwellsValentina Carannante15:15Dynamics at the molecular scale from cells to STARSSIlaria Testa15:45Concluding RemarksPer Ljungdahl16:00Poster SessionSciLifeLab DeltaMingle, pub and light food

Poster Session
Each group/unit is welcome to bring up to 3 posters to the grand Poster Session that will follow the talks. Submit the poster titles in the registration form. Please coordinate within your research group/unit beforehand who should bring a poster. Poster session will take place in the Delta building in SciLifeLab Solna.

Poster dimensions: 70×100

Scientific Committee
This event has been made possible through the hard work of the Scientific committee.

Scientific Committee

Erdinc Sezgin

Marcel Tarbier

Ute Hoffman

Stefania Giacomello

Kristoffer Sahlin

Per Ljungdahl

Operations Office representatives

Isolde Palombo

Disa Larsson Hammarlöf

[The Svedberg seminar] - Peptide nucleic acid (PNA)-mediated pretargeting for radionuclide therapy
2023-10-23 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Amelie Karlström

Professor of Molecular BiotechnologyDepartment of Protein Science, KTH

Bio

Amelie Eriksson Karlström is Professor of Molecular Biotechnology at the Department of Protein Science, KTH, where her research group is focused on protein engineering, affinity technologies and bioconjugation chemistry for diagnostic and therapeutic applications. Amelie Eriksson Karlström has a background in solid phase peptide synthesis methodology from PhD studies at the Department of Neurochemistry and Neurotoxicology at Stockholm University. She did postdoctoral studies at the Scripps Research Institute, La Jolla, CA, working on catalytic antibodies and display technologies with Profs. Richard A. Lerner and Carlos Barbas, III, before starting her independent research at KTH

Peptide nucleic acid (PNA)-mediated pretargeting for radionuclide therapy

Targeted radionuclide therapy utilizes tumor-specific radiolabeled molecules to deliver cytotoxic radiation to tumor cells. To avoid unwanted exposure of non-tumor organs, a pretargeting strategy can be used, where the tumor-targeting step is uncoupled from the delivery of the toxic radionuclide. The primary agent is administered first and the secondary, radiolabeled agent is administered after the primary agent has accumulated in the tumor and cleared from non-tumor tissue. We have developed and evaluated a system for pretargeting based on the high selectivity and high affinity of peptide nucleic acid (PNA) hybridization. We have demonstrated that the PNA-based pretargeting system gives high tumor-to-normal tissue contrast in vivo both using affibody molecules and monoclonal antibodies as the tumor-targeting agents.

In this seminar, the molecular design and technological aspects of the PNA-based pretargeting system will be discussed. Results from preclinical evaluation of the PNA-based pretargeting strategy will be presented.

Host: Abhimanyu Thakur,UU

R Foundations for Life Scientists
2023-10-23 09:00 - 2023-10-27 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of programming in R.

Important dates & Information

Application opens: 2023-08-20

Application closes: 2023-09-20

Confirmation to accepted students: 2023-09-27

Course Leader and teachers: Nima Rafati (CL), Prasoon Argawal (CL), Marcin Kierczak (CT), Sebastian DiLorenzo (CT)

In case you miss information on any of the above dates, please contact us via edu.r@nbis.se

Application

Course website

Course fee

A course fee* of 2000 SEK will be invoiced to accepted participants. The fee includes lunches, coffee and snacks.

*Please note that NBIS cannot invoice individuals

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 emphasizing the parts useful for life scientists. After introductory lectures on good programming practices, basic software design theory and a brief overview of R, we will delve into programming.

Topics covered will include:

Variables and Operators

Matrices, lists, and dataframes

Data manipulation

Visualization

R packages

Bioconductor

Learning Outcomes

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.

Explain about R packages and steps to create them.

Install R packages from Bioconductor.

Entry requirements

The following is a list of skills required for being able to follow the course and complete the exercises:

Good general computer literacy

Basic knowledge in mathematics and statistics

Due to limited space the course can accommodate a maximum of 20 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

Campus Solna Seminar Series: María Bueno Alvez & Diana Mahdessian
2023-10-19 12:00 - 13:00 | Gamma-6-Pascal, SciLifeLab, Tomtebodavägen 23, Solna, 17165, 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

María Bueno Alvez

Linn Fagerberg – alpha 6

Next generation blood profiling of pancreatic cancer

Diana Mahdessian

Emma Lundberg – alpha 2

Identification and Validation of Critical Mediators Driving Human Hepatic Stellate Cell (hHSC) activation via human Scar-Associated Macrophages (SAM) Using Spatial Proteomics

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

Using containers to simplify ML training on Berzelius and other supercomputers: beginner-friendly introduction
2023-10-19 10:00 - 11:00 | Online event via Zoom
This webinar is part of the Tools for AI/ML research in life sciences event series arranged by the SciLifeLab Data Centre.

Title: Using containers to simplify ML training on Berzelius and other supercomputers: beginner-friendly introduction

Speakers: AI engineers from the SciLifeLab Data Centre and application experts from Berzelius (NSC, LiU).

Where and when: October 19, 2023 at 10:00-11:00 Stockholm time, online. Registration is open till Oct 18 at 24.00.

Abstract: A common approach to train machine learning models is to first create a prototype using a small dataset on a local machine to verify that it works and thereafter use a large scale compute infrastructure such as Berzelius for the full-scale training. One of the challenges with this approach however is incompatible systems in terms of differences in available software packages, versions, etc. An effective way to solve this issue is to use a container solution. Using a container environment allows a highly portable workflow and reproducible results between systems as diverse as a laptop, Berzelius or EuroHPC resources such as LUMI for instance. During this beginner-friendly event, we will introduce and demonstrate how to work with containers on Berzelius (Apptainer and Enroot) using an example from life sciences, starting from raw data and finishing with a trained model. During the Q&A session, the Berzelius life science support team will answer your questions.

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

CSI Seminar: ‘Burnout and Stress’
2023-10-17 14:00 - 14:30 | Hybrid event in Gamma 2 lunchroom and zoom, Tomtebodavägen 23 B, Solna, 17165, Sweden
We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled: ‘Burnout and Stress’
The number of people with a burnout diagnosis has sky-rocketed during the last decade and it is now considered to be one of our major national diseases. Stress is a natural and important reaction but when the response is kept active for too long it can have negative effects. In this seminar, we will cover some basic aspects of stress and burnout, and share personal experiences of going through a burnout process. Together we’ll discuss where we currently experience negative stress and what measures we can take to find and keep a sustainable balance in life.
Date: 17/10/2023
Time: 14:00 – 14:30
Zoom link: https://kth-se.zoom.us/j/68847309081
On-site location: Gamma 2 lunch room
We will begin with a ca 20 min talk, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI.
To help facilitate discussion and reflection, consider the follow starter questions:
Awareness: where do we experience high risk for negative stress in our lives?
Analysis: how well do I currently handle negative stress?
Alternative: how can we relate to burnout/stress, in ourselves and others?
Action: how will knowledge of burnout/stress change my decisions going forward?

Introduction to Data Management Practices - Cancelled
2023-10-17 08:00 - 2023-10-19 17:00 | Uppsala University, Uppsala and Chalmers University, Gothenburg
This national workshop in Data Management is a co-arranged event between Uppsala University and Chalmers University, and provides an introduction for PhD students, postdocs, researchers, and other employees within all Swedish universities. The workshop will introduce important aspects of research data management through a series of lectures, demonstrations, and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. CANCELLED – next time (preliminary) in Stockholm, April 2024

Topics covered will include:

Open Science and FAIR in practice

Organising data, files and folders in research projects

Describing data with metadata

Publishing data to public data repositories

Cleaning tabular data and metadata with OpenRefine

Writing basic recipes for data analysis and visualisation with R

Versioning data, documents and scripts

Writing Data Management Plans

Important dates

Application opens: now

Application closes: 2023-09-27

Information to accepted students will be sent: 2023-09-29

Contact

edu.intro-dm@nbis.se

Application

Course website

Format

This workshop runs in parallel on-site in Uppsala, and Göteborg. Lectures will be streamed online from our Uppsala site (mainly) to the Gothenburg classrooms, and vice versa. Teachers and teaching assistants will be present at both locations all week to help with exercises and questions. When registering you will be asked to select a preferred site.

Venues

Uppsala

Trippelrummet (E10:1307-1309), SciLifeLab Navet, Entrance C11, Biomedical Centre (BMC)

Husargatan 3, 752 37 Uppsala

Gothenburg

CLS Room Scrum 1, University library, 2nd floor

Hörsalsvägen 2 (entrance), 412 96 Gothenburg

Course fee

This on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals.

Entry requirements

No previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. Installation instructions will be provided before the course starts, and the course organisers arrange a pre-course event approximately one week prior to first course day.

Credits & Certificate

Please note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop.

Due to limitations in space and capacity the course can accommodate a maximum of 25 participants per site. If we receive more applications, participants will be selected based on several criteria, including correct entry information, motivation to attend the course, as well as gender and geographical balance.

For more detailed information about the workshop, please visit the workshop website.

Cryo-EM sample preparation and data collection
2023-10-17 08:00 - 2023-10-19 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
The purpose of the course is to prepare and train Cryo-EM facility users in sample preparation methods, introduce users to the image data acquisition workflow, expand knowledge about cryo-EM methods among researchers and show that everyone can learn how to use cryo-EM for structure and cell biology.

The course is open for facility users or potential facility users, such as PhD students, postdocs, and researchers within the life sciences who are curious and will profit from cryo-EM skills. Swedish and international course participants are welcome. To attend, the course participants must have experience in basic electron microscopy and be familiar with structure or cell biology.

This course is supported by SciLifeLab, CryoNET and Umeå University and organized by the SciLifeLab Cryo-EM facility, both UmU and SU nodes together.

Read more

Application deadline

Application should be submitted before September 29, 2023

Course organizers

Michael Hall

Location

UCEM and Chemical Biological Centre (KBC) BuildingUmeå University, Linnaeus väg 6

Teachers and course instructors

Linda Sandblad

Michael Hall

Lars-Anders Carlson

Additional teachers t.b.a

Social program

A social program depending on the current corona restriction will be communicated to the participants after acceptance.

Course content

This course will cover practical aspects of cryo-EM sample preparation and data acquisition.

Topics covered

Basic theory of vitreous water, how to handle a cryo sample and consequences

Plunge freezing methods, tools and cryo-transfer

Sample and instrument requirements for single particle and tomography methods

Image data acquisition, concept of low dose and the cryo-specific workflow

Introduction to automatic data acquisition software, EPU, Tomography

Introduction to cryo-EM image processing methods

The course consists of lectures, cryo lab work, demonstrations and practical exercises for all participants, hands-on experiences of microscopy operation and discussions. A detailed schedule will be provided to accepted participant.

Course literature

Handouts and material online.

Entry requirements

Priority will be given to researchers involved in project where the use of cryo-EM is needed, which are to be briefly described upon application.

The course will be held at an advanced level, assuming that participants have a master’s degree or equivalent in a technical life science discipline. It aims to be relevant for a broad research community, also to participants not working in research environments using cryo-EM today.

A maximum of 15 participants will be admitted. Selection criteria include correct entry requirements, motivation to attend the course as well as gender balance.

Examination

Participation in all parts of the course, lectures, lab, microscopy demonstrations and evaluation are mandatory. SciLifeLab and Umeå University will provide successful participants with a course certificate and a recommendation for 1 ECTS

Campus Solna Seminar Series: Annika Bendes & Alexander Petri
2023-10-12 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Annika Bendes

Jochen Schwenk – alpha 2

Proteome profiling of self-sampled dried blood spots to enhance population-based studies and precision medicine

Alexander Petri

Kristoffer Sahlin – gamma 6

isONform: reference-free transcriptome reconstruction from Oxford Nanopore data

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

Metabolomics at speed – can direct analysis fingerprinting metabolomics be used for rapid sample screening?
2023-10-11 12:00 - 13:00 | Online event via Zoom
On-line seminar by Alastair Ross, Senior researcher/Metabolomics team lead at AgResearch, New Zealand.

Arranged by Otto Savolainen, Head of Unit, Chalmers Mass Spectrometry Infrastructure (CMSI), Metabolomics Platform.

Registration

SciLifeLab Day Linköping
2023-10-10 08:00 - 17:00 | Campus US, Linköping University, Lasarettsgatan 20, Linköping, Sweden
This event is a kick-off for the national SciLifeLab site in Linköping.

Learn more about the services and capabilities that are offered from SciLifeLab, both nationally and locally, and how you can participate in the activities.

Welcome to the SciLifeLab Day in Linköping. Here, life-science researchers will have a unique opportunity to meet experts in research infrastructure, participate in discussions on societal challenges and learn about what SciLifeLab have to offer both locally and nationally.

Exhibition, poster session, and mingle

Show your research in a poster and take the opportunity to discuss how you can implement SciLifeLab’s advanced technologies with the infrastructure experts and visit the exhibitions or posters from the infrastructure units to learn what services they can offer you.

Read more and find the program

SciLifeLab etablerar nytt forskningssäte i Linköping

Program

Detailed-program-SciLifeLab-Day-LinkopingDownload

Contact

linkoping@scilifelab.se

Josefine SandströmLinköping UniversitySite Coordinator SciLifeLab Linköpingjosefine.sandstrom@liu.se

SciLifeLab Days on the national sites

Gothenburg, April 17

Umeå, September 11

Lund, September 28

Linköping, October 10

Python programming with applications to bioinformatics
2023-10-09 09:00 - 2023-10-13 17:00
National course open for PhD students, postdocs, researchers and other employees in need of fundamental Python skills within all Swedish universities

Responsible teachers: Nina Norgren, Dimitris Bampalikis, Jeanette Tångrot

Contact information: edu.intro-python@nbis.se

Venues: SciLifeLab Uppsala, Trippelrummet, BMC & Umeå University, Naturvetarhuset, room NAT.D.370

Application

Course Website

Important dates

Application open: June 15

Application deadline: September 8

Confirmation to accepted participants: September 15

Course fee

A course fee* of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner

*Please note that NBIS cannot invoice individuals

Course description

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 both on-site in Uppsala and in Umeå. Lectures will be streamed online from our Uppsala site to the Umeå site. Several teaching assistants will be present both in the Umeå and Uppsala classroom 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.

Course content

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

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. 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.

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.

Seminar "Stereo-Seq to study the brain gene expression across species" - Prof. Wei-Wu
2023-10-06 15:30 - 16:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Speaker: Prof. Wei-Wu

Title of Talk: Stereo-Seq to study the brain gene expression across species

The whole-brain single-cell spatial transcriptome atlas and cross-species comparisonThe brain is the most complex organ of humans with the highest heterogeneity of cell types. The composition and spatial location of different neuron subtypes, as well as their precise connections, are the basis for brain functions. Rapid advances in spatial transcriptomic technologies allow spatial mapping of gene expression as well as cellular subtypes at single-cell resolution of brain sections. We applied Stereo-Seq technology developed by BGI, to construct the whole-brain cell atlas for macaques, marmoset, and mice, with hundreds of coronal slices of spatial transcriptome across the whole brain per animal. Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex and cross-species comparative analysis identified primate-specific cell types enriched in cortical layer 4, whose marker genes are expressed in a region-dependent manner (Chen et al., Cell 2023). Whole-brain cell atlas provides the cellular and molecular basis for understanding the function, evolution, development, aging, and pathogenesis of the brain.

Host: Vicent Pelechano & Claudia Kutter

From sequences to structures, from structures to biology - On homo-oligomers and co-translational assembly
2023-10-06 11:00 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Emmanuel Levy, Weizmann

Host: Arne Elofsson

In this talk, I will provide an overview of our research, emphasizing two recent pieces of work. The first goes from sequences to structures, with the development of an atlas of homo-oligomerization spanning proteomes and lineages (https://www.biorxiv.org/content/10.1101/2023.06.09.544317v1). The second goes from structures to biology, leveraging protein complexes’ structures to crack the code of co-translational assembly.

Campus Solna Seminar Series: Daniela Almeida & May Britt Rian
2023-10-05 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 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

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

This week:

Daniela Almeida

Marc Friedländer – gamma 5

Exploring bioactive peptides from Octopus vulgaris proteome after bacterial challenge

May Britt Rian

Jonathan Martin – alpha 1

Nontarget Analysis of Organic Micropollutants in Swedish Waters

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

6th CryoNET Symposium in Stockholm
2023-10-04 09:00 - 2023-10-05 17:00 | Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16C, Stockholm
We are very much looking forward to seeing you all in Stockholm on Wednesday. We’ll have a full house of around 200 participants, some 50 posters and a bunch of exciting speakers. It will be two intense and, we hope, enjoyable days!

CryoNet is a Nordic network in Cryo-electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryo-electron microscopy as a strong pillar of Nordic life science research.

The core of the network is formed by the Cryo-EM facilities at the University of Copenhagen, Aarhus University, Stockholm University and Umeå University. The network also reaches out to Cryo-EM sites in Norway and Finland.

The 6th CryoNET Symposium will take place October 4-5 2023 at Stockholm University. Take the opportunity to hear from world leaders in the field and network with students and researchers!

Participation in the symposium is free of charge and includes two days of lectures and a symposium dinner on October 4. We will start at 9:00 on Wednesday 4 October and finish 16:30 on Thursday 5 October.

We strongly encourage students and postdocs to submit an abstract about their research project. A number of abstracts will be selected for short talks and there will be a poster session for everyone during the symposium.

OrganizersGunnar von Heijne, Marta Carroni, Arne Elofsson och Xiaodong ZouContact: Gunnar von Heine

Program & Abstracts

Cryonet_program_abstracts_finalDownload

Keynote Speakers

Tamir Gonen, UCLA, USA

Ellen Zhong, Princeton University, USA

Confirmed Speakers

Henriette Autzen, Univ. Copenhagen, Denmark

Tristan Croll, Altos Labs, Cambridge, UK

Friedrich Förster, Utrecht Bioinformatic Center, The Netherlands

Emil Kristoffersen, Aarhus University

Karin Lindkvist, Lund University, Sweden

Misha Kudryashev, Max Delbrück Center, Berlin, Germany

Shintaro Aibara, AstraZeneca, UK

Ville Paavilainen, University of Helsinki, Finland

Anastassis Perrakis, NKI, Amsterdam, The Netherlands

Suparna Sanyal, Uppsala University, Sweden

Ludovic Sauguet, Institut Pasteur, Paris, France

Suyang Zhang, LMB-MRC, Cambridge UK

Exhibition in Navet at BMC
2023-10-03 09:00 - 2023-10-05 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
On October 3-5, 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 09:00-10:00 and 13:00-14:00 for external visitors.

Tuesday, Oct 3

AH DiagnosticsWe help laboratories within life science and diagnostics to reach optimal performance by providing innovative quality products and full workflow solutions.

Bio-TechneBio-Techne´s family of brands includes R&D Systems, Novus Biologicals, Tocris, Protein Simple, ACD and Exosome Dx, creating a unique portfolio of products & services to empower researchers in Life Science & Clinical Diagnostics.

BioNordika

EppendorfEppendorf in the house, Navet October 3rd!

Move-it pipettes, first centrifuge with “green cooling”, lab consumables made from recycled cooking oils, new PCR and competitions.

Kem-En-Tec Nordic

SENSE Multilabel Plate Reader, Mirus Transfection reagents Efficient, Low Toxic, Instant Coomasie Stain 15 min w/o washes, Antibodies and ELISA kits, Metabolomic kits, DNA/RNA extraction kits

MercodiaFocuses on the development and manufacturing of immunoassays for research and clinical diagnostics, as well as offering bioanalytical services to pharma- and biotech companies.

MicromedicMicromedic provides a range of products for microscopy. The portfolio includes brands like Leica Microsystems (microscopes), Ibidi (consumable for live cell imaging) and SunJinLab (clearing reagents).

Nordic BioLabsDistributor representing e.g. Promega (enzymes, reagents), Active Motif (epigenetics), Lexogen (RNA-seq), Invitek (kits), Biosearch Technologies (enzymes, competent cells), Cytiva and Capricorn (cell culture)

PeproTech

RAMCON ABKombinerar globala produkter och expertis med lokal kunskap för att garantera att våra kunder uppnår bättre resultat på kortare tid. Vi riktar oss till forskare och tillverkare inom industrin, läkemedel, kemi och bioteknik.

Thermo Fisher Scientific

Wednesday, Oct 4

Akoya BiosciencesAkoya Biosciences offers comprehensive single-cell imaging solutions that allow researchers to phenotype cells with spatial context and visualize how they organize and interact to influence disease progression and response to therapy.

Beckman Coulter

Dedicated to developing and providing advanced technologies and equipment for research and discovery to explore new treatment methods.

Becton DickinsonBD Biosciences provides high-quality single cell multiomics (scM) instruments, reagents, and bioinformatics tools for reliable, reproducible scM data

Hyperfine studiosHyperfine Studios, an animation, video and illustration production studio. We produce visuals that are scientifically correct and visually appealing. The studio possesses expertise in both science and visual communication.

Meso Scale

Mettler Toledo

Nordic BioSiteNordic BioSite is a supplier of products for research & diagnostics throughout the Nordics. Let’s talk about your workflow for Genomics and Transcriptomics, antibodies available in BULK, and services.

QiagenQIAGEN delivers Sample to Insight solutions for molecular testing and offers products and services that enable our customers to gain valuable insights from any biological sample – from basic research to clinical healthcare.

Science ImagingDistributes selected Life Science Products mainly in Scandinavia and Finland. Our goal is to offer comprehensive solutions to the image related problems faced by today’s research communities

Tecan NordicTecan is a Swiss company founded in 1980, a world-leading provider of automated solutions for laboratories. We develop, manufacture and distribute our own products worldwide, with production in Switzerland, Austria and the USA.

Thursday, Oct 5

Bio-WorksWe supply the biopharmaceutical and biotech industry with WorkBeadsTM chromatography resins and GoBio™ prepacked columns for the purification of a wide range of biomolecules, e.g. proteins and peptides.

GenScriptGenscript biotech is global CRO provider of genes, protein, peptides and antibodies as a products and services for research and clinical use

Hamilton Nordic

Integrated DNA Technologies

LabLife NordicExciting news for cell- and molecular biosciences, Label-free cell characterization and sorting, NGS & single cell sample prep and target enrichment panels,Oligo synthesis, Cell assay sample prep, Cleanup and extraction, Western blot

NavinciNavinci is a Swedish biotech company that specializes in developing innovative solutions for the study of protein interactions based on our proprietary proximity ligation technology – Bringing Precision to Spatial Proteomics.

Pacific BiosciencesPacBio is a life science technology company that is providing advanced sequencing solutions that enable scientists to improve their understanding of the genome and ultimately, resolve genetically complex problems.

ShimadzuShimadzu Sweden provides a broad range of analytical instruments indispensable for research, development, and quality control in a variety of fields.

Takara Bio

Committed to helping scientists break new ground with innovative technologies. Our extensive portfolio offers solutions to support advancements across many areas of research, diagnostics, & clinical applications

Techtum LabA distributor of cutting-edge laboratory equipment and solutions for molecular biology research will exhibit at BMC Navet October 5. Live demos of a selection of our instruments!
