SciLifeLab

BioImage Analysis support – Call4Help
2022-08-23 09:00 - 12:00 (Europe/Stockholm) | Online event via Zoom
Every month (mainly on Tuesdays, but there might be exceptions) the BioImage Informatics Facility together with microscopy expert Sylvie Le Guyader (LCI, Karolinska Institutet) organizes a Call4Help session. The aim is to offer combined expertise towards microscopy and bioimage analysis. All researchers from Swedish institutes can participate.
The ideal timepoint to join the Call4Help session is when a researcher has performed pilot experiments and has tried out first analysis approaches – but before having recorded hundreds of images. Combining BIIF’s expertise in BioImage Analysis with microscopy expertise we can discuss ways to record the images that allow analysis afterwards. We will discuss different analysis approaches using mainly open-source software (Fiji, CellProfiler, QuPath, Ilastik, KNIME), but also commercial systems, if needed (Imaris).
The Call4Help session format has been introduced to the BioImage Analysis community by NEUBIAS and ScopeM.

How to participate?
Step1:
Prepare a short presentation (5-7 min) – use the following template for your presentation:
http://bit.ly/BIIF_C4H_slideTemplate
Slide template by NEUBIAS/ScopeM
Step2:

a) Upload your presentation

Upload your presentation to a drive of your choice. You can also use our Call4Help google drive. Note that files shared on our Call4Help drive will be available to everyone until the session is over.
http://bit.ly/BIIF_C4H_Drive

b) Upload example images for testing.

Upload example images for testing either to the drive of your choice or our Call4Help google drive above.
http://bit.ly/BIIF_C4H_Drive

c) Register by filling out the registration form:

http://bit.ly/BIIF_C4H_Registration
Step 3:
Join the zoom-session.
If your problem is selected for presentation, you will get a time-slot of 30 – 60 minutes within the session.

What are the Deadlines
Submission of a problem and upload of example data: Friday the week before the session.
Notification about participation: The day before the session.
Next Call4Help session: Tuesday, August 23, 2022, 9.00-12.00
Deadline for application: Friday, August 19, 2022

Queer in Science
2022-08-26 17:30 - 19:00 | Biomedicum, Solnavägen 9, Solna
Karolinska Institutet Post-Doc Association’s Diversity and Inclusion Office is organising our Queer in Science event. We are having guest speakers to share their personal and professional experiences being openly queer in science as well as their work on gender-related topics. We will also be discussing the gender (in)equality issues in STEM. Join us for this interactive and conversational session. It is a safe space for all. Sign up your interest here!

Contact: Elga Bandeira and Hazel Ang

Spatial omics data analysis
2022-08-29 08:00 - 2022-09-02 17:00 | Online event via Zoom
This workshop provides resources to advanced tools for analysis of spatial datasets via a series of online lectures and computer practicals. The total course duration is 40 hours, including the online lectures and practical coding workshop that will be held online.

Important dates

Application open: 2022-05-20

Application deadline: 2022-07-31

Course Leaders

Paulo CzarnewskiChristophe Avenel

Lecturers and content creators

Lars BormCarolina WählbyGiovanni PallaNaveed IshaqueAnna SchaarDavid FischerHanna SpitzerSergio SallasÅsa BjörklundSebastian TiesmeyerLudvig BergenstråleEduard Chelebian

Contact information and Application

Course website

Email

Application

Course fee

This workshop is free of charge.

Course content

Topics covered will include

Hands-on experience with ST (Visium), ISS, scRNAseq data analysisFluorescence-based image formats, standards and quality controlImage alignment, registration and ISS decodingNuclei-based and segmentation-free cell identificationData imputation using ISS and single cell datasetsAnalysis of Spatial Transcriptomics datasetCell-type deconvolution (ST and single cell)Cell-cell and ligand-receptor interaction analysisMapping of multiple spatial data to a common referenceHigh-resolution projection of gene expression to H&E imagesInteractive visualisation of spatial omics data

Who can apply?

This is an international course hosted by the National Bioinformatics Infrastructure Sweden (ELIXIR-SE) in collaboration with the Human Developmental Cell Atlas (HDCA), the Royal Institute of Technology, Stockholm University, Karolinska Institutet, Uppsala University, Charité Clinical University (ELIXIR-DE), Helmholtz Munich (Germany) and the European Molecular Biology Organisation. The course is open for PhD students, postdocs, group leaders and core facility staff working on spatial omics technologies.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Practical exercises will be performed in Python, so we only accept students that fulfill the entry requirements (see below).

Entry requirements

Required for being able to follow the course and complete the practical exercises:

Basic knowledge in PythonBe able to use your own computer with a web cameraHave miniconda3 installed in your computerDesirable: Previous experience with single cell RNA-seq analysis is an advantage.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.

Due to limited space the course can accommodate a maximum of 32 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.

Snakemake BYOC (bring-your-own-code) workshop (ONLINE)
2022-08-31 09:00 - 2022-09-02 13:00 | Online event via Zoom
National workshop open for PhD students (prioritized), postdocs, researchers and others from all Swedish universities who have previously participated in the NBIS Tools for reproducible research course or with demonstrated experience in writing Snakemake workflows.

COURSE WEBSITE

REGISTRATION

Important dates

Application opens: May 15

Application closes: June 17

Confirmation to accepted students: June 28

Responsible teachers: Verena Kutschera, John Sundh, Per Unneberg, Marcel Martin

Contact information: edu.byoc-snakemake@nbis.se

Workshop fee

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 1,700 SEK.

*Please note that NBIS cannot invoice individuals

Workshop content

As data analysis projects grow and change over time, it gets increasingly difficult to keep track of how the different parts of the data analysis fit together. Workflow management systems such as Snakemake can be used to set up, perform and monitor defined sequences of computational tasks (“workflows”), thereby making data analyses reproducible and scalable. Snakemake was developed in the bioinformatics community and has some features that make it particularly well suited for bioinformatics workflows.

The NBIS Tools for reproducible research course is held twice a year and provides an introduction into Snakemake and a tutorial to learn how to use Snakemake.This Snakemake BYOC (bring-your-own-code) workshop provides a follow-up to that introduction. Here, participants will get support from experienced bioinformaticians to A) convert their data analysis from a programming language such as bash, R or python into a Snakemake workflow, or B) apply more advanced techniques to their existing Snakemake workflows.

Learning outcomes

After participation in the BYOC workshop, participants will:

Be able to create Snakemake workflows for bioinformatics data analysisDemonstrate knowledge of the structure and syntax of different types of Snakemake workflowsDemonstrate knowledge of advanced features of the Snakemake workflow language

Entry requirements

Previous participation in the NBIS Tools for reproducible research workshop. The workshop is also open for participants who can demonstrate experience in writing Snakemake workflowsYour own bioinformatics analysis scripts in any programming language that you would like to convert into Snakemake OR your own Snakemake workflow that you would like to improveA computer with a webcam running Linux or Mac OS (if you run Windows and are accepted as a participant, additional setup will be required). You will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the workshop.

The workshop can accommodate a maximum of 16 participants. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.

InfraLife integrative structural biology - Open Day
2022-09-01 09:00 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Save the date for a super Thursday!

Join in on the InfraLife integrative structural biology course, open lectures Thursday sept 1st 2022. Lessons on modelling/computational methods and scientific key note: Feel free to join the course participants in lecture hall Air&Fire Campus Solna.

9.00-10.30

Different approaches to the study of cotranslational protein foldingProfessor Gunnar von Heijne, Stockholm University,

10:45-12:00

The protein structure prediction problem: from Anfinsen to AlphaFold.Principal Research Engineer Claudio Mirabello,NBIS, Linköping University,

13:00-14:00

Coupling lipid nanoparticle structure and compositionResearch Specialist Hanna Barriga, Karolinska Institutet

14:00-15:00

Integrative structural biology: Combining cryo-EM, simulations and electrophysiology to understand membrane protein functionsProfessor Erik Lindahl, Stockholm University

15:15-16:00

Integrating physics-based and evolutionary modelling to investigate the conformational dynamics of membrane proteinsAssociate professor Lucie Delemotte, KTH,

Followed by SciLifeLab pub and InfraLife course poster sessions

Campus Solna Seminar Series: Ioannis Siavelis and Sarah McComas
2022-09-01 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 5-10 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.

Ioannis Siavelis

Janne Lehtiö – alpha1

Detecting proteoforms from mass-spectrometry-based bottom-up proteomics

Sarah McComas

Lucie Delmotte – gamma3

Sugar recognition and turnover for the mammalian fructose transporter GLUT5

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

Computer simulations of complex biological systems
2022-09-02 11:00 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to a lecture by Professor Carmen Domene, University of Bath, UK.11.00-12.00 Friday September 2nd 2022 in Air&Fire lecture hall

SciLifeLab Campus Solna, Tomtebodavägen 23.

Prof Domene’s research uses computational techniques to study the structure and dynamics of biological systems aiming to understand biochemical and biophysical processes from a microscopic perspective and thereby aid in interpreting and devising experiments.

A keynote lecture part if the InfraLife integrative structural biology course 2022

Instruments and methods at Umeå Centre for Electron Microscopy (UCEM)
2022-09-06 12:00 - 13:00
In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during autumn 2022, in turn with IceLab Lunch Pitches. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Take the chance to get information on facilities, possibilities and services that infrastructure, both SciLifeLab-associated and local, can offer! Learn more about the seminar series and the schedule for autumn 2022 here.

On September 6th, 12:00-13:00, you are welcome to participate in the seminar

Instruments and methods at Umeå Centre for Electron Microscopy (UCEM)

by Linda Sandblad, Centre Coordinator / Director

Read more

A guided tour to the UCEM facility could be organised for on-site participants after the seminar.

Registration:

Sign up (latest by September 5th, 10 a.m.) for on-site attendance to reserve your free lunch sandwich:

or follow online via Zoom: https://umu.zoom.us/j/63138997026 (registration is not required).

Organisers: SciLifeLab Site Umeå and Chemical Biological Centre (KBC)

Workshop on Data Visualization in R - Lund - CANCELLED
2022-09-07 08:00 - 2022-09-09 17:00 | Biologihuset, Sölvegatan 35, Lund, 223 62, Sweden
National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R – CANCELLED

The course is organized by NBIS (ELIXIR-SE).

Responsible teachers: Lokeshwaran Manoharan, Louella Vasquez, Markus Ringner

Contact information: edu.plotting.r@nbis.se

Important dates

Application open: Jul 28, 2022

Application deadline: Aug 21, 2022

Confirmation to accepted participants: Aug 25, 2022

Application

Course website (previous version)

Course fee

This training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced * 2000 SEK.

A course fee* of 1300 SEK will be invoiced to accepted participants. This includes 3 lunches, 1 dinner, coffee and cakes.

*Please note that NBIS cannot invoice individuals

Course description

This course aims to help researchers to visualize their data in different ways using R. This course will also aim to show researchers how they can make publication grade figures using R. A part of this course is also about making interactive plots that the researchers can view and share in a web-server to make interactive visualizations of the data.

Course content

In this course you will learn how to visualize your data in R.

In particular, you will learn:

· how to format the data necessary for ggplot

· how to make bar-charts, box-plots and others using ggplot

· how to make PCA plots in ggplot

· how to use R packages for heatmaps

· how to plot data on maps using R (optional)

· how to plot and handle phylogenetic trees in R (optional)

· how to make interactive plots in R using Rshiny

· how to host a Rshiny app in one of the available servers

Learning outcomes

By the end of the course the participant will be able to:

· handle data in R for visualizations

· apply the grammar efficiently in ggplot to get the desired plot

· combine different data and/or different plots that are of publication-grade

· write your own simple Rshiny app

· deploy Rshiny apps in public servers.

Entry requirements

Required for being able to follow the course and to complete computer exercises:

familiarity with using R and Rstudioa computer with R and Rstudioyou will be asked to install different R packages necessary for the course prior to the course.

Selection criteria

The course can accommodate 25 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

SciLifeLab Campus Solna Science Talks
2022-09-07 09:00 - 17:00 | Samuelssonsalen, Tomtebodavägen 6, Solna, Sweden
We would hereby like to warmly welcome you to take part in this year’s, and the first IRL version, of the Campus Solna Science Talks symposium on September 7th – 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 15:45 (including lunch), and the event will conclude with a poster session and mingle 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, and the PhD- & Postdoc-council) to partake with posters!

register here

Program
08:30Arrival, registration and coffeeSamuelssonsalen, Karolinska Institutet09:00Welcome and opening of symposiumScientific Committee & Per Ljungdahl09:15Metabolic and spatio-temporal determinants of fungal virulencePer Ljungdahl09:30The role of co-translational mRNA decay in mRNA metabolism and gene regulationMengjun Wu09:45Metabolite interactions in the bacterial Calvin cycle and implications for flux regulationEmil Sporre10:00In vitro neurovascular modelsAnna Herland10:15Coffee Break11:00Unexpected CRISPR/Cas9 editing consequences when targeting non-coding genomic regionsKeyi Geng11:15From in situ to in vivo sequencingDaniel Fürth11:30Functional and transcriptomic mapping of serotoninergic projectionsJakub Mlost11:45Spatial inference through reconstruction of molecular networksIan Hoffecker12:00LunchLight lunch served for all registered participants13:00High-throughput screening to identify microproteins required for cell survivalDörte Schlesinger13:15Targeted peptide delivery using the Adaptable-Drug Affinity Conjugate (ADAC) technologySara Mangsbo13:30Characterizing dynamic cellular processes from static microscopy imagesJuliette Griffié13:45Adaptive three-dimensional super-resolution imaging deep through thick tissuesRuizhe Lin14:00Coffee Break14:45A mass-spectrometry draft of the COVID-19 plasma proteome: in-depth profiling and meta-analysisHaris Babačić15:00Structural analysis of proteolysis by MecA/ClpC/CLpP in S. aureusKarin Walldén15:15The wonders of small molecule transportDavid Drew15:30Tracking Molecular Modifications of Engaged Pol II Complexes at Nucleotide Resolution Genome-WideAnniina Vihervaara15:45Concluding Remarks16:00Poster SessionSciLifeLab Delta18:00Mingle, 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: A1, portrait orientation.

Poster List is available here.

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

Scientific Committee

Erdinc SezginMarcel TarbierRyan HullVaishnovi SekarVicent PelechanoYerma Pareja SanchezPer Ljungdahl

Operations Office representatives

Disa Larsson HammarlöfDavid GottholdErika Erkstam

Single-cell and spatial atlases of the adult and developing human brain
2022-09-07 14:00 - 15:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Recently, we have generated single-cell atlases of the adult and developing human brain using a combination of single-cell RNA sequencing and spatial transcriptomics. In the adult, we found an unexpectedly high diversity of neuronal types especially in the midbrain and hindbrain, with conservatively more than 3000 distinct types. In the developing human brain, we revealed highly refined trajectories of differentiation of cortical neurons. We further found that astrocytes and oligodendrocytes were regionally patterned, and that these region-specific types persisted in the adult. These findings may provide a basis for the brain region-specific occurrence of pediatric brain tumors.

–

Speaker

Sten LinnarssonResearch Division of Molecular Neurobiology, Karolinska Institutet, Stockholm, Sweden

Human Developmental Dell Atlas (HDCA) is the Swedish effort within the human cell atlas (HCA), one of the largest international scientific projects. The project aim is to create a comprehensive molecular atlas of human prenatal development at the molecular resolution using state-of-the-art multi-omic technologies such as single-cell RNA-seq, Spatial Transcriptomics, in situ sequencing in order to provide deeper insight into how variations and deviations contribute to health and disease.

The HDCA Seminar Series 2022 invites you to join us on a journey of early human organogenesis of several organs at the single-cell and spatial resolution. Seminars will be held at SciLifeLab Gamma building on Wednesdays at 14:00 or 15:00 and also via Zoom. After each seminar, we will have up to 30 min round up discussions with the speaker on how you can contribute to the atlas!

access zoom meeting

SciLifeLab Symposium in Microscale Acoustofluidics for Life Sciences
2022-09-08 08:00 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
SciLifeLab Symposium in Microscale Acoustofluidics for Life Sciences, Sept. 8th 2022Organizers: Martin Wiklund (KTH) and Thomas Laurell (Lund University)

Location: Scilifelab, Air/Fire, Gamma-2, Tomtebodavägen 23, Solna

Program

Session 1 (Air/Fire)

08:20-08:30 Opening by Martin Wiklund, KTH-Biophysics

08.30-08.45 Cecilia Magnusson, Lund, ”Acoustic label-free isolation of circulating tumor cells in metastatic prostate cancer”

08.45-09.00 Megan Havers, Lund, ”Silica seed particles improves performance in acoustic nanoparticle trapping”

09.00-09.15 Axel Broman, Lund, ”Acoustic trapping for isolation of extracellular vesicles”

09.15-09.30 Björn Hammarström, KTH, ”Acoustic focusing of protein crystals for improved sample delivery in serial crystallography”

09.30-09.45 Thierry Baasch, Lund, ”High-throughput acoustic particle separation”

09.45-10.00 Wei Qiu, Lund, ”High-performance bulk-wave-acoustophoresis devices using side actuation”

10.00-10.30 coffee break (lobby outside Air/Fire)

Session 2 (Air/Fire)

10.30-10.45 Po-yin Chen, Lund, ”Microfluidic droplet shooter as a sample injection interface for MS”

10.45-11.00 Niklas Sandström, KTH, ”Microwells for live cell assays”

11.00-11.15 Valentina Carannante, KTH-KI, ”Multiplexed high-content screening of drug and immune sensitivity in microwells”

11.15-11.30 Karl Olofsson, KTH, ”Multicellular tumor diskoids: A solid tumor model optimized for imaging”

11.30-11.45 Giovanni Marinaro, Lund, “Design of acoustically-controlled ultrasmall droplet ejection in a microfluidic chip”

Structural insights on the E-site specificity of the C. albicans ribosome
2022-09-08 10:00 - 11:00 | Becquerel, SciLifeLab, Tomtebodavägen 23, Solna
Yury ZgadzayInstitute of Genetics and Molecular and Cellular Biology, Strasbourg, France

Date: Thursday 08 September 2022Time: 10.00 – 11.00Location: Becquerel“Structural insights on the E-site specificity of the C. albicans ribosome”Host: Alexey Amunts

Campus Solna Seminar Series: Ludvig Larsson and Alisa Alekseenko
2022-09-08 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:

Ludvig Larsson

Joakim Lundeberg – alpha 3

Spatially resolved transcriptomics on degraded samples

Alisa Alekseenko

Vicent Pelechano – gamma 5

Spatially resolved transcriptomics on degraded samples

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

Data-Driven Evolution and Biodiversity Research
2022-09-08 12:00 - 2022-09-09 12:00 | Europasalen, Konferenscentrum Wallenberg, Gothenburg, Medicinaregatan 20, Göteborg, 413 90, Sweden
Mini-symposium

Welcome to the first mini-symposium in data-driven evolution and biodiversity research sponsored by the Data-Driven Life Science (DDLS) program! At the mini-symposium, the first group of DDLS Fellows in evolution and biodiversity will present themselves and their research plans. There will be several inspiring keynote talks, presentations of the Swedish infrastructure for data-driven research in evolution and biodiversity, and discussions of the future of the DDLS program.

Join us for an inspiring lunch-to-lunch meeting, and help shape the future of data-driven evolution and biodiversity research in Sweden!

Hybrid event

Participate on site: New venue! Europasalen, Konferenscentrum Wallenberg, Medicinaregatan 20A, Gothenburg, Sweden.

Participate online: Online participation info, e.g, zoom link will be sent out upon registration

Download the Program here (PDF)

Registration

Short program

Thursday, September 8

12:00Lunch13:00Symposium starts (first day)17:00End of first day19:00SYMPOSIUM DINNER at Koks, Vasagatan 9, GothenburgAttendance is optional and the cost is the participant’s responsibility.

Friday, September 9

08:30Symposium starts (second day)12:00Lunch, end of the symposium

Practical information

IT support and adaptors will be available for presentersDeadline for onsite registration is August 29 (due to catering). Zoom registrations can be done until the event starts day 2.Lodging for September 8th is the attendee’s responsibility, and there are many different kinds of options nearby the site. The speakers are booked at Hotel Poseidon.

Exploring the Human Proteome with Antibodies, Transcriptomics and Mass Spectrometry
2022-09-11 08:00 - 2022-09-16 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
The summer school is aimed at graduate students, post-docs, and young independent investigators who want to learn about new techniques to explore the proteins encoded by the human genome. The course will teach state-of-the-art analysis of the human proteins with a focus on antibody-based methods, transcriptomics and mass spectrometry. The course will have several daily lectures by experts in the field and this will be complemented with workshops in which the participants will annotate genes/proteins. Each participant will take part in an annotation effort with the aim to go through all experimental evidence of the respective protein and to evaluate the quality of the underlying data to score the evidence for protein profiles and functionality.

Read more

The course will be held at the Science for Life Laboratory located at the campus of Karolinska Institutet in proximity of the city center of Stockholm, hosting researchers in the field of molecular bioscience affiliated with Karolinska Institutet, Royal Institute of Technology and Stockholm University. The center has infrastructures for life science, such as next generation sequencing, proteomics, single cell genomics, bioimaging, cryo-EM, protein expression, antibody engineering, bioinformatics and systems biology. Accommodation and meals will be provided by the organizers. Social evenings and joined meals will provide ample opportunities for informal exchange with lecturers.

Mathias UhlenChair, Organization Committee

Introduction to biostatistics and machine learning
2022-09-12 08:00 - 2022-09-16 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 need of biostatistical skills within all Swedish universities. The course is geared towards life scientists wanting to be able to understand and use basic statistical methods. It would also suit those already applying biostatistical methods but have never got a chance to reflect on and truly grasp the basic statistical concepts, such as the commonly misinterpreted p-value.

Important dates

Application open: now

Application closes: 2022-08-14

Confirmation to accepted students: 2022-08-19

Responsible teachers: Olga Dethlefsen, Eva Freyhult

If you do not receive information according to the above dates please contact

edu.ml-biostats@nbis.se, olga.dethlefsen@nbis.se, eva.freyhult@nbis.se

COURSE WEBSITE

APPLICATION

Course content

Probability theoryHypothesis testing and confidence intervalsResamplingLinear regression methodsIntroduction to generalized linear modelsModel evaluationUnsupervised learning incl. clustering and dimension reduction methodsSupervised learning incl. classification

Education

In this course we focus on an active learning approach. The course participants are expected to do some pre-course reading and exercises, corresponding up to 40h studying. The education consists of teaching blocks alternating between mini-lectures, group discussions, live coding sessions etc.

Entry requirements

Basic R programming skillsBYOL (bring your own laptop) with R and RStudio installedNo prior biostatistical knowledge is assumed

The course can accommodate a maximum of 24 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.

Course fee

2000 SEK (includes lunches and coffee)

*Please note that NBIS cannot invoice individuals

Clinical (phospho)-proteomics for precision medicine
2022-09-12 16:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Clinical (phospho)proteomics for precision medicine

Welcome to a lecture by Professor Connie R Jimenez, Amsterdam University Medical Center, Netherlands

16.00-17.00 Monday September 12Air & Fire (Gamma 2) or via zoom https://kth-se.zoom.us/s/69393882589

Connie Jimenez is Professor of Translational OncoProteomics at the Amsterdam University Medical Center in The Netherlands, where she is heading the OncoProteomics Laboratory as well as the Proteomics Core Facility.

She is a molecular/cellular biologist with focus on the global analysis of the functional building blocks of life, i.e., the proteins which activity and functions are highly deranged in disease. Her lab’s mission is to apply innovative mass spectrometry-based proteomics and data analysis to obtain systems biology insights into disease and to improve early diagnostics and treatment, most notably of cancer and neurodegenerative disease.

During her graduate studies at the Vrije Universiteit in Amsterdam (1993-1997), she pioneered single cell peptide profiling by mass spectrometry. During her post-doc in the Burlingame lab at UCSF, San Francisco ((1997-1999), she applied proteomics to study neuron differentiation. In 2006, she founded the OncoProteomics Laboratory (www.oncoproteomics.nl) with a start-up grant of the Cancer Center Amsterdam.

To date, Dr. Jimenez (co)authored > 200 scientific peer reviewed articles. Underscoring her (inter)national esteem, she founded the Netherlands Proteomics Platform in 2000 and is member of its steering board; she is general council member of the European Proteomics Association since 2005 and elected Vice-President since 2021; she is member of the steering committee of the Cancer HPP project of the Human Proteome Organisation. Finally, she is editorial board member of several leading proteomics journals.

This keynote lecture is part of the FEBS Advanced Course – Exploring the Human Proteome

Spatial and Single Cell Biology Webinar
2022-09-13 13:00 - 15:00 | Online event via Zoom
The Spatial and Single Cell Biology Platform at SciLifeLab invites you to a virtual event where you can learn about the service we provide within the field of spatial and single cell omics. Take the opportunity to learn about cutting edge methods including spatial transcriptomics with Visium, in situ sequencing, spatial proteomics using highly multiplexed imaging, spatial metabolomics with MALDI imaging and advanced FISH technologies. The presentations will be given by our experts in there respective methods, working within the platform.

The event is open for anyone to attend, who are interested in including spatial omics in their research projects or with a general interest to learn about the methods.

register here

Program

13:00 Short introduction to the Spatial and Single Cell Biology platform13:10 Single cell sequencing Anja Mezger13:25Spatial Transcriptomics Xesus Abalo13:40In situ sequencing Chika Yokota13:55Spatial Proteomics (multiplexed IF) Charlotte Stadler14:10Advanced FISH Technologies Quentin Verron14:25Spatial Mass Spectrometry Anna Nilsson14:40Additional Q&A and end of webinar

SciLifeLab Navet Open House
2022-09-13 15:00 - 16:45 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Welcome to SciLifeLab Navet Open House on September 13 from 15:00 to learn more about SciLifeLab and the possibility to book meetings in Navet. Take the chance to network and talk science!

Some of the activities:• General presentation of SciLifeLab 15:30, E10:1309, Jenny Alfredsson, Acting Head of Operations• A Quiz tour as a walk around Navet’s meeting rooms 15:00 – 16:00. Price ceremony at 16:15• SciLifeLab poster exhibition• Mingle photographer on site• Relaxed networking with the opportunity to meet several SciLifeLab representatives on site

If SciLifeLab representatives want to participate in the poster exhibition, please contact lokalbokning@SciLifeLab.uu.se.

For catering reasons, please Register here

Mass spectrometry-based proteomics: technological advances and their application to plasma and single cell type resolved tissue proteo
2022-09-13 16:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Mass spectrometry-based proteomics: technological advances and their application to plasma and single cell type resolved tissue proteomics

Welcome to a lecture by Professor Matthias Mann, Max Planck Institute, Germany.

16.00-17.00 Tuesday September 13Air & Fire (Gamma 2) or via zoom https://kth-se.zoom.us/s/69393882589

Matthias Mann obtained his PhD in chemical engineering at Yale, contributing to the Nobel Prize for his supervisor John Fenn for electrospray ionization. He is a director at the Max Planck Institute of Biochemistry, Munich and also director of the Department of Proteomics, Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen. He has obtained numerous prizes and is one of the most cited scientists with an h-factor of 250 and 300,000 total citations (Google Scholar). He has pioneered advances in sample preparation, chromatography, mass spectrometry and computer algorithms, making mass spectrometry applicable to molecular biology. Apart from proteomics technology development, the team works on biological questions in systems biology. Today, the main focus is on clinically relevant topics, especially the analysis of the blood plasma proteome and cancer tissues at the single-cell level.

This keynote lecture is part of the FEBS Advanced Course – Exploring the Human Proteome

Mapping the development and regeneration of reproductive tissues
2022-09-14 13:00 - 14:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Mapping the development and regeneration of reproductive tissues

Welcome to a lecture by Roser Vento-Tormo, Wellcome Sanger Institute, UK.

13.00-14.00 Wednesday September 14Air & Fire (Gamma 2) or via zoom https://kth-se.zoom.us/s/69393882589

Vento-Tormo’s research interest is to understand the influence of cellular microenvironments on individual cellular identities and responses, in the context of development and immunity. Her team employs single-cell and spatial transcriptomics methods to deconstruct the cell signals in human organs and tissues, and utilise this information to inform the reconstruction of novel in vitro models. Essential for this work, is the novel computational tools her team develops to build cell–cell interactions networks from transcriptomics data. In her predoctoral research, she studied the interplay between cell signalling and epigenetic machinery key to regulating cellular fate decisions in myeloid cells. She pursued her postdoctoral studies in the Teichmann laboratory as an EMBO / HFSP fellow, where she developed CellPhoneDB.org, a computational tool to study cell-cell communication from single-cell transcriptomics data. She used CellPhoneDB to disentangle the complex communication between maternal and fetal cells in the uterine-placental interface during early human pregnancy. Vento-Tormo work has been funded by many recognised international agencies (H2020, MRC, CZI, Wellcome-LEAP), and she has recently obtained the Early Career Research Award from the Biochemistry Society (2021).

This keynote lecture is part of the FEBS Advanced Course – Exploring the Human Proteome

Systems Analysis of Human Metabolism for Identification of Drug Targets and Biomarkers
2022-09-14 14:00 - 15:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Systems Analysis of Human Metabolism for Identification of Drug Targets and Biomarkers

Welcome to a lecture by Professor Jens Nielsen,

Bioinnovation Institute, Copenhagen, Denmark.

Jens Nielsen is MSc in Chemical Engineering and PhD (1989) in Biochemical Engineering from the Danish Technical University (DTU). Fulbright visiting professor at MIT in 1995-1996. Professor at DTU in 1998. In 2008 he was recruited as Professor to Chalmers University of Technology, Sweden. In 2015 he was founding Head of the Department of Biology and Biological Engineering, which now encompass more than 200 people. Jens Nielsen was also a co-founder of the Novo Nordisk Foundation Center for Biosustainability that now have more than 300 people affiliated, for which he served as CSO 2013-2018. From 2019 CEO of the BioInnovation Institute in Denmark, which is a new institute financed by USD0.5B that fosters translational research and support new spin-out companies in life sciences. He has trained more than 280 scientists in his research group and published >850 publications that have been cited more than 98,000 times (current H-factor 142). Inventor of >50 patents and founder of seven biotech companies. Has received numerous awards, including the ENI Award, the Eric and Sheila Samson Prime Minister Prize for Transportation Fuels, the Novozymes Prize, and the Gold Medal from the Royal Swedish Academy of Engineering Sciences. Member of 12 academies, including NAS, NAE, Chinese Academy of Engineering, EMBO and Royal Swedish Academy of Science. He will discuss the challenges of using systems medicine for advancing the development of personalized and precision medicine, and it will be illustrated how the concept of genome-scale metabolic models can be used for integrative analysis of big data with the objective of identifying novel biomarkers that are foundational for personalized and precision medicine.

This keynote lecture is part of the FEBS Advanced Course – Exploring the Human Proteome

SciLifeLab Genomics platform retreat
2022-09-15 10:30 - 2022-09-16 13:30 | Haga slott, Haga slott, Enköping, 745 93, Sweden
Very welcome to this event for the Genomics platform. We look forward to fun days with time to interact with new and old colleagues, discuss science and our operation, and get the latest information on the development of SciLifeLab and our platform. The meeting will take place at beautiful Haga Slott, just outside of Enköping.

There will be buses that leave from BMC, Uppsala and SciLifeLab Campus Solna at 09:00 on Sept. 15, and return from Haga Slott at 13:30 on Sept. 16.

Registration has closed.

For questions about the program and participation, contact magnus.lundgren@scilifelab.uu.se

For information about the venue, see https://hagaslott.se/en/haga-castle/

Program

September 1509:00 Buses depart from SciLifeLab Solna and BMC (Uppsala)10:00 Arrival Haga Slott and coffee10:30 The SciLifeLab Genomics platform: status, plans and visions11:15 Scientific keynote “DeepTime genomics”, Love Dalén, Professor at Department of Zoology, Stockholm University12:00 Lunch13:00 SciLifeLab national nodes: opportunities for synergies14:00 Check-in14:30 Coffee15:00 Social activity, bring clothes and shoes suitable for being outside16:30 Free time for spa, gym, sauna swimming, etc.18:00 Drinks reception19:00 DinnerSeptember 1609:00 Introduction to group discussion09:15 Group discussions, including coffee break11:00 Summary of group discussions and meeting wrap-up12:00 Lunch13:30 Buses depart for SciLifeLab Solna and BMC (Uppsala)

Campus Solna Seminar Series: Christoffer Mattsson Langseth
2022-09-15 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:

TBD

TBD

Christoffer Mattsson Langseth

Mats Nilsson – gamma 4

Spatial mapping of oligodendroglial, neuronal and immune cell-type heterogeneity in a model of multiple sclerosis

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

Molecular analysis of human diversity and its impact on drug discovery using iPS cells
2022-09-15 18:00 - 19:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Molecular analysis of human diversity and its impact on drug discovery using iPS cells

Welcome to a lecture by Professor Angus I. Lamond,

University of Dundee, UK.

16.00-17.00 Thursday September 15

Air & Fire (Gamma 2) or via zoom https://kth-se.zoom.us/s/69393882589

Professor Lamond has over thirty years of experience as a Principal Investigator, studying molecular mechanisms regulating gene expression and pre-mRNA splicing. This includes major contributions to the biochemical analysis of the human splicing machinery and to the study of functional compartments and subnuclear bodies in mammalian cells. The AIL group have developed new methods and technical approaches in these fields that have advanced mechanistic studies at the molecular and cellular levels, spanning biochemical, microscopy and MS-based proteomics technologies. During the past fifteen years, the AIL laboratory has developed and applied state of the art mass spectrometry-based proteomic approaches in research projects studying molecular mechanisms regulating gene expression in both human cells and model organisms. This includes, specifically, integrated poly-omics analyses of human induced pluripotent stem cells (hiPSCs), derived from both healthy donors and patient cohorts with inherited disorders. Other studies have focused on proteome dynamics in the context of biological response mechanisms and ongoing studies identifying and characterizing small molecule modulators of alternative splicing and analysis of how splicing mechanisms affect cell proteomes, protein isoform expression and resulting cell phenotypes. He will describe the progress in using both quantitative, MS-based proteomics and high throughput imaging technologies to characterize libraries of human induced pluripotent stem cell (iPSC) lines, derived from hundreds of different donors, and show how comparisons of such iPSC lines can provide a novel approach for assessing mechanisms of variable drug response and help to deliver more safe new drugs that cater for the needs of diverse human populations.

This keynote lecture is part of the FEBS Advanced Course – Exploring the Human Proteome

Ribosome heterogeneity and specialization during temperature acclimation in plants
2022-09-19 10:00 - 11:00 | Becquerel, SciLifeLab, Tomtebodavägen 23, Solna
Seidel, Max Planck Institute of Molecular Plant Physiology, Potsdam, GermanyDate: Monday 19 September 2022Time: 10.00 – 11.00Location: Gamma“Ribosome heterogeneity and specialization during temperature acclimation in plants”Host: Alexey Amunts

AIDA-SciLifeLab days
2022-09-21 11:00 - 2022-09-22 12:00
Welcome to AIDA-SciLifeLab days in Uppsala, September 21-22

Analytic Imaging Diagnostics Arena, AIDA, is a national arena for research and innovation around artificial intelligence, AI, for medical image analysis. Here, academia, healthcare and industry meet to translate technological advances in AI technology into patient benefits in the form of clinically useful tools. AIDA is an initiative within the Strategic Innovation Program Medtech4Health, a joint venture of VINNOVA, Formas and the Energy Agency. AIDA offers funding, technical infrastructure and a broad expert community. The community meets in regular intervals at AIDA-days; seminar days with current medical imaging themes.

The AIDA days are on tour, our first stop was Stockholm KTH, and this time we are happy to visit Uppsala. SciLifeLab and Carolina Wählby are kindly hosting the event. We will now have the great opportunity to get an insight into the work on AI in medical imaging in Uppsala – focus areas and ongoing projects. We can look forward to presentations in quantitative microscopy, image classification, image registration and the European Big Picture project (a central repository for digital pathology slides). In addition, we will listen to two final AIDA project presentations by the research groups of Robin Strand – MRI guided real-time adaptive radiotherapy and Joel Kullberg – Advanced Body Composition Analysis in SCAPIS. Each AIDAday will end with a study visit: at the radiology department (MR-Linac) and the pathology department, respectively.

Registration

Program September 21

Program September 22

Short Program

SEPT. 21:Venue: Nya Ångström, lecture hall 101136 B (floor1)11:00Internal meeting for AIDA members only 12:00Lunch (recommendation “Rullan”, Nya Ångström)13:00Official program17:00End of program19:00After Work at Stationen (optional)SEPT. 22:Venue: SciLifeLab Navet, Trippelrummet, BMC, entrance C1109:00Official program12:00End of program

Lunch and AW at your own expense.

For those who are not able to attend the AIDAdays physically, a Zoom link will be distributed to registered participants prior to the meeting. Please register here!

Most Welcome!

Campus Solna Seminar Series: Yuying Cheng and Osheen Sharma
2022-09-22 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:

Yuying Cheng

Simon Elsässer – alpha 4

Defining histone variant H3.3 dynamics using pulse-chase experiment and computational modeling

Osheen Sharma

Brinton Seashore-Ludlow – alpha 4

Image based Drug Mechanism of Action Clustering using Deep Neural Networks

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

Introduction to bioinformatics using NGS data
2022-09-26 08:00 - 2022-09-30 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
This is a national workshop open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. The workshop is organised by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI).

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.

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. For more detailed information about workshop syllabus, learning outcomes and entry requirements, please visit the workshop website.

Important dates

Workshop: 26-Sep-2022 – 30-Sep-2022

Application opens: 23-May-2022

Application closes: 19-Aug-2022

Confirmation to accepted students: 26-Aug-2022

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.

Contact

nbis.se

Malin Larsson, Martin Dahlö, Roy Francis

Workshop Website

Application
