SciLifeLab

Architecture of Active Human Enhancers and Molecular Features That Drive, Long-Range, Highly-regulated Transcription
2024-05-21 15:00 - 16:00 (Europe/Stockholm) | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Campus Solna Spotlight Seminar series welcomes Professor John Lis from Cornell university to Stockholm to present his outstanding work.

John Lis is a Professor in the Department of Molecular Biology and Genetics. He did his graduate research at Brandeis University and received his Ph.D. in Biochemistry in 1975. His postdoctoral work focused on Drosophila gene regulation and chromosome structure at Stanford University, during which time he was supported by a fellowship from the Helen Hay Whitney Foundation. Dr. Lis joined the faculty at Cornell in 1978. His research program has been supported by the National Institutes of Health, including a MERIT Award, March of Dimes, American Cancer Society, Cornell Biotechnology Institute, and a Proctor and Gamble University Exploratory Research Grant.

Abstract

Mechanisms of Transcriptional Regulation of Drosophila & Mammalian Genomes

Transcription by RNA Polymerase II (Pol II), the enzyme responsible for all mRNA synthesis, is highly regulated by protein factors at multiple steps in the transcription cycle. Two critical regulatory steps, whose regulatory integration is critical for the sophisticated gene regulation seen in multicellular eukaryotes, are 1) the recruitment of Pol II to promoters where it rapidly initiates transcription and can enter into a promoter-proximal, paused state 20-50 base pairs from the initiation site; and 2) the release of paused Pol II into productive elongation. Promoter-proximal pausing is dependent on protein complexes DSIF (DRB Sensitivity Inducing Factor) and NELF (Negative Elongation Factor) bind to Pol II early in transcription to stabilize pausing. Pause release occurs upon phosphorylation of Pol II, DSIF and NELF by the Cdk9, Cyclin T1 heterodimer P-TEFb (Positive Transcription Elongation Factor b). Several elongation factors, e.g., PAF1 and Spt6, engage with Pol II in its transition from its promoter-proximal pause to productive elongation. Although Pol II pausing is a key step in transcription regulation and has been extensively studied, the molecular mechanisms of pausing and pause release to productive elongation are far from being completely understood. Furthermore, recent studies have led to competing molecular mechanisms on the role of promoter-proximal pausing in the control of transcription. In this seminar, I will describe the evolution of our understanding of transcription regulation as well as describe our latest efforts to advance and resolve this understanding using a variety of state-of-the-art genomic and optical methods in Drosophila and mammals.

3D/4D X-ray Microtomography: Insight into materials critical for the green transition
2024-05-21 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 spring 2024. The seminars will be held in a hybrid format – IRL in Glasburen, KBC, Umeå, and online via Zoom.

Read more about the Seminar Series

On 21 May, at 12:00, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

3D/4D X-ray Microtomography: Insight into materials critical for the green transition

Presenter: Fredrik Forsberg, Senior Lecturer, Luleå University of Technology, Div. Fluid and Experimental Mechanics

Description: A seminar about high-resolution x-ray microtomography (XCT) and how it can be used for 3D/4D material and process characterisation to support the green transition. During the seminar selected applications will be presented from studies at the X-ray Microtomography Lab at LTU (using a Zeiss Xradia 620 Versa XRM) and using synchrotron tomography. For example, studies of modified wood for increased moisture resistance, studies on hydrogen and CO2 storage in porous bedrock, and studies of minerals critical for the green transition. The seminar ends with a look at future possibilities with Dynamic and Spectral XCT – a new XCT system that soon will be available at LTU.

Read more and Register

Uppsala University DDLS Fellows - public seminars with candidates - part II
2024-05-21 10:30 - 12:00
Welcome to the second data driven-rich morning of scientific presentations by 2 candidates for the DDLS program fellow position on Data-driven Precision Medicine and Diagnostics and Biträdande Universitets Lektor position at Uppsala University.

Schedule

Meeting details

Tuesday, May 21, 2024 10:30-12:00

Zoom link >>

Mötes-ID: 663 2681 5420

Schedule

10:30-11:05

Marcel Tarbier, Karolinska Institutet, Stockholm, Sweden

Into the Single-Verse: Inferring complex gene and cell features from gene expression – and an excursion through space and time

11:05-11:40

Muhammad Arif, National Institute on Alcohol Abuse and Alcoholism, Rockville, USA

Integrative Multi-Omics Frameworks for Understanding the Molecular Mechanism of Progressive Diseases

[The Svedberg seminar] - Multilevel drift and selection in the evolution of prokaryotic plasmids
2024-05-20 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Tal Dagan

ProfessorInstitute of general microbiology, Kiel University, Germany.

Bio

Prof. Tal Dagan graduated her PhD in 2005 and moved to Germany for her postdoctoral studies. Since 2013 she is a professor of microbiology at Kiel University. Her main research interest is microbial genome evolution via lateral gene transfer with a focus on the evolution of prokaryotic plasmids

Multilevel drift and selection in the evolution of prokaryotic plasmids

Plasmids are an extrachromosomal genetic elements that populate prokaryote cells. Due to their interaction with a hosting cell, drift and selection operate on plasmid alleles at two hierarchical levels: the collective of plasmids within the host and the collective of cells within the host population. The effect of these two levels on plasmid evolution remains understudied. Using experimental evolution approach integrated with phylogenomic reconstruction we found that: i) drift and selection at the level of the host population leads to contrasting effects on the plasmid fitness and ii) segregational drift of plasmid alleles during cell division constrains the rate of plasmid evolution. Our findings may apply for the evolution of other extrachromosomal genetic elements having a similar population structure. Focusing on plasmids, our research thus uncovers general principles in the evolution of autonomously replicating genetic elements.

Host: Maliheh Mehrshad maliheh.mehrshad@slu.se, SLU and Helen Wang helen.wang@imbim.uu.se UU

NBIS workshop in Neural Nets and Deep Learning
2024-05-20 09:00 - 2024-05-24 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 Neural networks and Deep Learning skills within all Swedish universities

Important dates

Application opens: 2024-01-25

Application closes: 2024-04-10

Confirmation to accepted students: 2024-04-25

Responsible teachers: Claudio Mirabello, Christophe Avenel

If you do not receive information according to the above dates please contact: edu.neural-nets-deep-learning@nbis.se

Application

Course website for updates

Course Fee

A course fee* of 3000 SEK will be invoiced to accepted academic participants. A higher fee applies to applicants from private companies. The fee includes lunches, coffee and snacks. *Please note that NBIS cannot invoice individuals

Course content

This course will give an introduction to the concept of Neural Networks (NN) and Deep Learning.

Topics covered will include:

NN building blocks, including concepts such as neurons, activation functions, loss functions, gradient descent and back-propagation

Convolutional Neural Networks

Recursive Neural Networks

Transformers and attention-based models

Autoencoders

Best practices when designing NNs

Learning Outcomes

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

Distinguish the concepts of “Artificial Intelligence”, “Machine Learning”, “Neural Networks”, “Deep Learning”

Distinguish between different types of learning (e.g. supervised, unsupervised, reinforcement) and recognise which applies to their own problem

Distinguish between linear and non-linear approaches and recognise which is best suited for application to their own problem

Describe what a feed-forward neural network (FFNN) is, along with its components (neurons, layers, weights, bias, activation functions, cost functions)

Explain how training of a FFNN works from a mathematical point of view (gradient descent, learning rate, backpropagation)

Execute with pen and paper a few steps of training of a very simple FFNN model

Tell the difference between a shallow and a deep network

Explain broadly how different NN architectures are wired and how they work

Implement and apply the most appropriate architecture to a given problem/dataset

Analyze training curves and prediction outputs to evaluate if the training has been successful

Debug possible issues with the training and suggest changes to fix them

Explain the difference between training, validation and testing

Define what overfitting is from a mathematical point of view, and what issues it causes

Identify what constitutes good practices of dataset design and how to avoid introducing information leakage or other biases when building their own datasets

Entry requirements

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

Familiarity with Unix/Linux

Ability to bring your own laptop with Python and Jupyter Notebooks installed for the practical exercises

Programming/scripting experience in Python (e.g. having attended the NBIS workshop in basic Python or equivalent)

Basic experience of statistics and mathematics (e.g. having attended the NBIS workshop Introduction to Biostatistics and Machine Learning or equivalent)

Desirable:

You have experience of working with Jupyter Notebooks

You have a necessity to work with large datasets (e.g. thousands of samples)

Due to limited space the course can accommodate a maximum of 25 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.

2nd CryoNET course on advanced single particle cryo-EM analysis
2024-05-20 08:00 - 2024-05-24 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
CryoNet is a Nordic network in cryogenic electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryogenic electron microscopy as a strong pillar of Nordic life science research.

The core of the network is constituted by the cryo-EM facilities at University of Copenhagen, Aarhus University, Stockholm University and Umeå University.

We are happy to announce the 2nd CryoNET course on advanced single particle cryo-EM analysis that will take place in Stockholm on 20-24 May 2024. Aim of the course is to provide training in cryo-EM image processing including latest developments of the field.

Participants will receive hands-on training in state-of-the-art techniques for single particle cryo-EM image processing, model building and validation from a range of international specialist guest lecturers. The course also includes theoretical talks and discussions on the use of cryo-EM to address difficult biological questions, which can help the participants address their own research problems. New for this year is to include Micro-ED and basic processing of Micro-ED data.

Participation in the entire course is mandatory and an attendance certificate will be given at the end of the course.

Course Objectives

To provide training in state-of-the-art techniques for high resolution structure determination by cryo-EM, including hands-on practical training in latest software suites for image processing

Discuss data collection strategies

Training in basic principles of structure determination using cryo-EM

Get an introduction to Micro-ED and softwares used for processing of Micro-ED data

Develop problem solving skills through discussions and practical sessions in the presence of international experts in the field

Networking with experts, software developers, and researchers in cryo-EM and learn of not only the latest but also upcoming developments

Course fee covers

Attendance in the course 20-24 May 2024

Lunches, coffee and refreshments on the course dates

Course materials

Certificate of attendance

Course dinner

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

Course fee payment: The course fee of 2,500 SEK should be paid either by bank transfer (latest 30th of April), or via invoice that has been sent out to those that have selected this option.

Program

Program_2nd-CryoNET-course-20-24-may-2024_240515Download

Supported by

Knut & Alice Wallenberg Foundation

Novo Nordisk Foundation

Thermo Fisher Scientific

MiTeGen

Organising committee

Karin Walldén, Stockholm University

Marta Carroni, Stockholm University

Thomas Boesen, Aarhus University

Jesper Lykkegaard Karlsen, Aarhus University

Andreas Bøggild, Aarhus University

Tillmann Pape, University of Copenhagen

Digital twins and integrative systems biology
2024-05-17 10:00 - 11:00 | Online event via Zoom
NBIS, Scilifelab’s Bioinformatics platform, arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms, typically between 10 and 11 am, with ca. 45 min long presentation and 15 min discussion.

For further info, please see this website.

Digital twins and integrative systems biology

Gunnar Cedersund, Linköping University

Click here to join zoom conference

Training Hub Fika
2024-05-16 15:00 - 16:00, 2024-05-02 15:00 - 16:00 | Online event via Zoom
We are thrilled to invite you to the first series of Training Hub Fika – grab your Thursday afternoon coffee and join us online for short talks and discussion on topics from digitalizing courses to using the Training Portal to career-spanning learning!

Everyone is welcome to attend and chat about supporting knowledge transfer and personnel development across Sweden. As one of SciLifeLab’s newest entities, we look forward to meeting people from Lund to Umeå and sharing our support and expertise!

Uppsala University DDLS Fellows - public seminars with candidates
2024-05-16 14:15 - 16:35
Welcome to a data driven-rich afternoon of scientific presentations by 4 candidates for the DDLS program fellow position on Data-driven Precision Medicine and Diagnostics and Biträdande Universitets Lektor position at Uppsala University.

Meeting details

Monday, May 6, 2024 14:15-16:35

Zoom link >>

Mötes-ID: 640 7985 9903

Schedule

14:15-14:50

Sergi Sayols Baixeras, Uppsala University, Dep. of Medical Sciences, Sweden

Novel Insights fromZMetagenomics and Metabolomics on Atherosclerotic Disease

14:50-15:25

Qiaoli Wang, Harvard University Medical School, Cambridge, USA

Anticipatory Detection of Upper-Gastrointestinal Cancers: Staying One Step Ahead with a Dash of Wit

15:25-16:00

Muhammad Arif, National Institute on Alcohol Abuse and Alcoholism, Rockville, USA

Integrative Multi-Omics Frameworks for Understanding the Molecular Mechanism of Progressive Diseases

16:00-16:35

Filipe Barata, Centre for Digital Health Interventions, ETH Zurich, Switzerland & Stanford University, Palo Alto, USA.

Advancing Personalized Healthcare Through Digital Biomarkers

Campus Solna Seminar Series: Wenjing Kang & Maximilian Senftleben
2024-05-16 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:

Wenjing Kang

Magda Bienko – alpha 4

A new group of long intronic RNAs may shape genome architecture of neurons

Maximilian Senftleben

Hjalmar Brismar – gamma 3

Open source light sheet microscopy: descspim advanced

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

Catalyzing Confidence: A Novel Strategy for Enhancing DEL Hit Validation in Drug Discovery
2024-05-15 15:00 - 15:45 | https://uu-se.zoom.us/j/65812174262
Drug Discovery Seminars: Catalyzing Confidence: A Novel Strategy for Enhancing DEL Hit Validation in Drug Discovery

Presenter: Dr Stefan Geschwindner, PhD, Director Biophysics, AstraZeneca, Mölndal, Sweden

Host: Pauliina Turunen, Unit Target Protein Engineering (TPE), SciLifeLab DDD

Abstract

In the realm of drug discovery, validating hits derived from DNA-encoded library (DEL) screening is an indispensable step. This process necessitates the resynthesis and retesting of compounds to ascertain the consistency of observed activity while mitigating experimental artifacts. However, the complexity arises from the fact that DNA barcodes in DEL libraries encode synthetic routes rather than chemical structures. This intricacy often leads to challenges in identifying genuine actives, primarily due to incomplete chemical transformations during encoding, resulting in low validation rates.

In response, we will present a novel strategy for DEL hit validation. We will elucidate our approach, which prominently features on-DNA compound resynthesis, mirroring the methods employed during initial library synthesis. This seamlessly integrates with subsequent hit validation endeavors by using highly sensitivity surface-based biosensing in combination with a novel assay format. We will illustrate affinity correlations between on-DNA and off-DNA compounds, offer insights into assay development, and emphasize the utilization of enhanced sensitivity to allow us to detect low-abundancy on-DNA compounds. We will describe a systematic framework for DEL hit validation, enhancing the identification of genuine binders with unwavering confidence and heightened sensitivity for drug discovery.

Speakers biography

Dr. Stefan Geschwindner is currently a Director at AstraZeneca R&D Gothenburg in Sweden where he is heading the Biophysics department within Discovery Sciences. He obtained his Ph.D. at the University of Frankfurt/Germany working predominantly with NMR to elucidate protein structures. After his Ph.D. he joined the Astra Structural Chemistry Laboratory with focus on protein engineering and characterization and helped to implement a variety of different biophysical methods and technologies in the early drug discovery process. Before moving into his current role, he had different roles as Team leader in Protein Engineering and as Principal Scientist in Biophysics. His over 50 peer-reviewed publications are frequently cited leading to an h-index of 26.

New insights into the lateral organization of biological membranes: Investigating the role of membrane dipole potential and the midplane interface
2024-05-13 11:00 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Seminar by Frederick A. Heberle, Department of Chemistry, University of Tennessee, Knoxville, TN, USA

Abstract

Cells can dynamically alter the spatial organization of lipids and proteins in the plasma membrane to regulate processes including cell signaling. The size and morphology of membrane domains, and how these depend on lipid composition, have drawn attention as potentially key variables in these processes. Model membrane studies have proven invaluable for elucidating the influence of phospholipid chains and headgroups, as well as cholesterol concentration, on membrane properties and phase behavior. Using this kind of bottom-up approach, my group employs a diverse set of biophysical techniques including fluorescence microscopy and spectroscopy, small-angle neutron scattering, and cryogenic electron microscopy to characterize the phase behavior of lipid bilayer mixtures. In this talk, I will show how two important yet poorly understood features of lipid membranes—namely, the membrane dipole potential and the midplane interface of a compositionally asymmetric bilayer—can profoundly affect lateral lipid organization.

Zoom link

Harnessing AI Transforms Research: Smart Strategies for Advanced Productivity
2024-05-13 09:00 - 2024-05-14 16:00 | Conference Centre Wallenberg, Medicinaregatan 20A, Gothenburg, 413 90, Sweden
SciLifeLab Gothenburg invites you to a hands-on workshop during two days led by PD Dr. Daniel Mertens, who is a biochemist and group leader at the German Cancer Research Center (DKFZ) and at the University of Ulm. He is both a successfull scientist, with more than 100 publications within life science that have been cited more than 5000 times (Daniel Mertens – Web of Science Core Collection) and an experienced lecturer, who has been training scientists, physicians, administrators and other staff in different transferable skills (www.scientistsneedmore.de). So far, more than 4000 participants have taken part in his international workshops around the world. Take the chance to learn more about how to use AI to increase your scientific productivity and quality in this instructive hands-on workshop lead by Dr. Mertens!

The workshop will cover these topics:

Why use AI? Productivity and quality increase.

How do LLMs work?

Prompting like a Pro

Using AI for structuring text, and telling a story

Using AI for brainstorming of experiments and projects

Using AI for decision making, introspection, career development and for training of interpersonal interactions

Good Scientific Practice using AI Assistants: plagiarism, copyright, usage for brainstorming, publishing and for grant writing

more information and registration

SciLifeLab Research Data Management Roadshow 2024
2024-05-13 08:00 - 2024-05-14 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
SciLifeLab Data Centre and NBIS, in collaboration with SciLifeLab Umeå, welcome you to join a 2-day event with presentations, workshops, & networking.

SciLifeLab Data Management is a collaborative activity between SciLifeLab Data Centre and NBIS Data Management team. Together we support and collaborate with the Swedish life sciences research community and infrastructure. Our aims are to: maximize the value of life science data, highlight and disseminate information about Open Science, FAIR, and good RDM practices, offer services, tools, and support, and offer courses and training.

SciLifeLab Research Data Management Roadshow will visit all SciLifeLab sites during 2024 and 2025.

During the Roadshow Umeå, the following activities are offered:

(1) Lunch seminar “Overview of Research Data Management services and support available locally and from SciLifeLab”, 13 May 12:00-13:00, Stora Fokusrummet (KB.G3.01), KBC

The seminar will be organised in the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”

Target group: PhD students, postdocs, researchers and infrastructure staff

(2) FAIR Frukost, 14 May, 9:00-10:00, Glasburen, KBC

Target group: PhD students and postdocs

(3) Workshop, 14 May, Stora Fokus rummet (KB.F3.01)

Part I: Data Management Plans, 14 May, 10:00-12:00

Part II: Data submission to public repositories, 14 May, 13:00-15:00

Target group: PhD students, postdocs, researchers and infrastructure staff

Find more information and register: https://www.umu.se/en/chemical-biological-centre/kbc_events/rdm-roadshow-2024/

Registration deadline: 6 May

Aiming for the clinics
2024-05-08 09:00 - 16:30 | University Main Building, Biskopsgatan 3, Uppsala, 75310
– Strengthened interactions in translational medicine

Welcome to this symposium in translational medicine jointly organized by the Drug Discovery and Development Platform at SciLifeLab and Uppsala Clinical Research Center.

Date: May 8, 2024Time: 09:00-16:30Venue: Lecture hall IX, University Main Building, Uppsala (Universitetshuset)

There is a large gap between basic scientific research and translation to novel therapeutics, and to bridge this gap, translational research and knowledge need to be strengthened. In this seminar, we aim to bring preclinical and clinical expertise together by highlighting and discussing some of the hurdles to overcome in order to progress from preclinical to clinical studies and make novel drugs available to the patients. We will show some of the resources available within SciLifeLab and the broader community, and there will be ample time for inspirational case studies that have succeeded in bringing academic as well as small biotech discoveries into clinical phase. These cases include different modalities and the differences in ways to move forward depending on drug modality will be shown. Concrete expert and scientific advice will be given in different areas of preclinical and clinical trials including biostatistics and national regulatory guidelines. There will also be time for networking and interaction between academic researchers, scientists from the SciLifeLab infrastructure as well as the broader community.

Meet the experts from:

RISE (Research Institutes of Sweden), Testa Center, SciLifeLab Drug Discovery & Development, Uppsala University Innovation, The Swedish Drug Delivery Center (SweDeliver), CCRM Nordic, Uppsala Clinical Research Center (UCR), ATMP-Center Uppsala, UU samverkan and Uppsala Preclinical Cancer Treatment Center, Precisionsmedicinskt centrum Uppsala (PMCU), NorthX Biologics and The Swedish Medical Products Agency (Läkemedelsverket).

Register for the Conference

Registration closed May 1. If you want to register, please contact erika.erkstam@scilifelab.uu.se. We may have seats available in case of late cancellations.

For late cancellations, please follow the cancellation link in your personal confirmation letter so we can let someone else take your place.

Read more about the DDD Platform

Program

updated 2024-04-29

Conference_UCR_SciLifeLab-DDD_agenda_240429Download

Flyer

Aiming-for-the-clinics_2024_extended-final-1Download

Advanced Technologies for Spatial Omics
2024-05-07 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

Advanced Technologies for Spatial Omics

Presenter:

Katarina Tiklova, PhD, Head of the in situ sequencing unit, Science for Life Laboratory

Description: The seminar will present In situ sequencing technology, which is part of SciLifeLab’s spatial platform.

The advancements of single cell spatial imaging analysis provided by In Situ Sequencing gives scientists the capability to view their samples with subcellular resolution, by profiling up to 1,000s of targets, each in the context of their spatial localization patterns. This type of analysis enables studies to not only locate and type cells within their biological context, but also address questions about cell–cell communication, profile cellular microenvironments, and identify rare cell infiltration.

More about In Situ Sequencing Infrastructure Unit: https://www.scilifelab.se/units/in-situ-sequencing/

Registration: Sign up for the IRL seminar and reserve your free lunch (sandwich, drink, and little sweet snack) by Monday, 6 May, 10:00 a.m.:https://www.umu.se/en/chemical-biological-centre/kbc_events/registration-form-infrastructure-seminar2/

or follow online (registration is not required):Meeting URL: https://umu.zoom.us/j/67909354528Meeting ID: 679 0935 4528

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

In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during spring 2024. The seminars will be held in a hybrid format – IRL in Glasburen, KBC, Umeå, and online via Zoom. Learn more about the seminar series and Schedule for Spring 2024 here.

[The Svedberg seminar] Genetics of Type 2 Diabetes: Advances, Prospects, and Challenges
2024-05-06 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Benjamin F. Voight

Associate Professor, Pharmacology and GeneticsUniversity of Pennsylvania – Perelman School of Medicine, USA

Bio

Ben Voight received his PhD from the University of Chicago, with postdoctoral training at Massachusetts General Hospital, staying on at the Broad Institute as a research scientist. He is currently an Associate Professor at the University of Pennsylvania in the Department of Systems Pharmacology and Translational Therapeutics, and the Department of Genetics. As a human geneticist, research from his group focuses on understanding the genetic, biological, and evolutionary basis of metabolic phenotypes in human populations, particularly diabetes, cardiovascular, and liver disease. Recent data scientific efforts focus on new association studies for discovery using biobank-scale data (e.g., the Million Veteran Program), post-association study analyses to understand the genetic architecture of disease and ultimately the underlying causal variants, and quantitative trait locus mapping for expression and chromatic accessibility using primary pancreas and liver data sets.

Genetics of Type 2 Diabetes: Advances, Prospects, and Challenges

Type 2 diabetes is a heterogeneous disease that develops through diverse pathophysiological processes and molecular mechanisms. Elucidating the processes and mechanisms by identifying new loci associated with disease, the underlying causal variants and genes, and the cell types of action are areas of current focus by the research community. I will describe recent contributions by the Type 2 Diabetes Global Genomic Initiative, our newly minted consortium focused on expanding locus discovery across diverse ancestries, understanding physiological mechanism and prediction of susceptibility to complications through genetic subtyping, and nomination of putative causal genes and mechanism through statistical colocalization. I will also briefly discuss prospects for exciting potential advances in the near term from new data types and improved computational methods, as well as my perceptions of open challenges and potential thoughts on how to take those on – ultimately to understand disease etiology and to generate prospects for therapeutic intervention.

Host: Marcel den Hoed marcel.den_hoed@igp.uu.se UU

Biology is predictable!
2024-05-02 16:15 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Seminar by Professor Lucas Pelkmans from the University of Zurich.

Read more

Campus Solna Seminar Series: Christopher Dirks & Lisa Engelhardt
2024-05-02 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:

Christopher Dirks

Sean Rudd – alpha 5

Deoxyguanosine analogues allosterically modulate the dNTPase activity of chemoresistance factor SAMHD1

Lisa Engelhardt

Marta Carroni – gamma 6

Freeze. Predict. Link. Exploring integrative structural biology

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

Protistology Nordics Meeting 2024
2024-05-02 09:00 - 2024-05-03 17:00 | Evolutionsbiologiskt centrum (EBC), Norbyvägen 18, Uppsala, Sweden
The Protistology Nordics 2024 will be held in Uppsala, providing an opportunity for scientists in Nordic countries to come together and showcase their research on the genetics, cell biology, ecology, and evolution of protists.The meeting is designed to facilitate vibrant discussions about the latest research in protistology, social interaction, and networking with fellow participants.

This meeting is sponsored by the Planetary Biology Capability. Apart from assisting the organizers, the Capability is coordinating an interactive session to discuss opportunities and challenges to use SciLifeLab platforms.

Brief Program

2 May 2024Workshop for Early Career Researchers, and Pub NightA workshop for Masters students, PhD students, and postdocs!3 May 2024Symposium on Protist Cell Biology, Ecology, and Evolution

Important dates

Registration and Abstract Submission Deadline: 25 March 2024Selected abstracts/Participants Will Be Notified By: 2 April 2024

Register here!

Conference website

Cancelled: The role of diagnostics in precision cancer medicine
2024-05-02 09:00 - 09:30 | Online event via Zoom
This event has been cancelled. We apologize for the inconvenience.

Clinical Talks

Clinical Talks is an educational seminar series open to everyone. It is organized by the SciLifeLab Precision Medicine Capability, and invites a mixture of speakers that are experts with a clinical perspective on topics concerning rare diseases, cancer, microbiology and bioinformatics.

Health is individual and patients can benefit greatly from personalized treatments, tailored for their specific molecular disposition. This rapidly emerging field, known as Precision Medicine, relies on technology development and requires close collaboration between scientists and healthcare professionals. SciLifeLab aims to bring cutting-edge technologies, first-class expertise and data infrastructure to build the foundation of tomorrow’s Precision Medicine.

Campus Solna Seminar Series: Szabolcz Hetey & Morteza Aslanzadeh
2024-04-25 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:

Szabolcz Hetey

Simon Elsässer – alpha 4

Dissecting the regulatory hierarchies of the PRC2 shielding mechanism in human pluripotent stem cells

Morteza Aslanzadeh

Marc Friedländer – gamma 5

Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells

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

Cell and Molecular Biology - DDLS symposium
2024-04-25 11:30 - 2024-04-26 17:00 | Birgit Thilander Lecture Hall, Academicum, Medicinaregatan 3, Gothenburg
Welcome to the Cell and Molecular Biology Symposium, starting with lunch at Restaurant Lyktan from 11:30. The conference then takes place in the Birgit Thilander Lecture Hall in Academicum. The program includes presentations from local and national experts within data driven life science research – and a keynote lecture by Prof. Edda Klipp from the Humboldt University in Berlin.

Day two, on April 26, takes place in the AstraZeneca facilities in Mölndal. Here we will meet with the exciting BioVenture Hub and learn about how AstraZeneca works with data driven life science in a clinical setting. Bus transfer from Clarion Hotel Post leaves at 07:30 directly to Astra Zeneca.

Practical information

Public Transport to Medicinareberget

Thursday, April 27

Please note that due to construction work, there are disturbances in the tram operations at nearby stops Medicinaregatan and Sahlgrenska Huvudentrén.

Find your best route through the Västtrafik website or app.

Coach to Astra Zeneca

Friday, April 26

A chartered bus will depart from Clarion Post Hotel at 07:30, directly to the Astra Zeneca Conference Center (PGN Entrance).

Guidelines for Self-Transport Arrivals to Astra Zeneca

Friday, April 26

Whether you’re arriving by public transport, bike, or car, kindly make your way to the KC-entrance at Pepparedsleden 1.

Please be punctual at 08:00, as you’ll be guided from the entrance to the conference area.

Program

Click to expand and see the program

Thursday, April 25
April 2510:30Expert Group meeting11:30LunchRestaurant Lyktan13:00Welcome WordsMargit Mahlapuu, University of GothenburgSverker Holmgren, ChalmersOla Engkvist, AstraZeneca13:10Precision Glycomics: How AI and advanced mass spectrometry are changing the gameDaniel Bojar, University of Gothenburg13:40Towards a universal molecular framework for structure prediction and designPatrick Bryant, SciLifeLab/Stockholm University (DDLS Fellow)Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly, given a multiple sequence alignment representation of the protein, protein pocket information, and a SMILES string representing the ligand.14:10Integrating single-cell transcriptomics with cellular phenotypesJoan Camuñas, University of Gothenburg14:40Thermodynamics-informed modeling of biochemical reaction and regulation networksEdda Klipp, Humboldt-Universität zu Berlin15:20Coffee Break15:50Tumor biology using multiomicsAnders Ståhlberg, University of Gothenburg16:10Multiomics – state of art data generation and analysis at NGIMattias Ormestad and Franziska Bonath, National Genomics InfrastructureMultiomics projects can span over long time frames, sometimes years, until all data is created. Often sequencing is an integral part and is outsourced to a core facility like NGI. For projects in which data generation is performed by different groups, it is crucial that important information about library preparation, sequencing and analysis is recorded and available to all other participants. Therefore, NGI applies quality control measures and reports important metadata to ensure that our users can use our data with confidence even years after data generation.16:30Data-Driven Microscopy: the automation of end-to-end imaging workflowsElisabet Carlsohn and Rafael Camacho, SciLifeLab/University of GothenburgBiological complexity mandates comprehensive imaging for statistically significant results. Manual operation impedes large dataset acquisition, affecting reproducibility. Smart microscopy, integrating image analysis and computer-controlled microscopes, streamlines workflows. At GU’s Centre for Cellular Imaging, we offer open-access “smart microscopy” services optimizing data management with next-gen file formats, ome-zarr, community-driven visualization tools, napari, and collaborative platforms, webknossos. This ensures efficient resource utilization in the era of data-driven life sciences.17:00Tour to SciLifeLab units in Gothenburg Optional, sign up in registration form18:00Dinner for CMB fellows and experts, and speakers

Friday, April 26
April 2607:30Bus transport to Astra Zeneca Conference Centre in Mölndal08:00Visitor registration Astra Zeneca Conference Centre in Mölndal08:25IntroductionOla Engkvist, AstraZeneca & Margit Mahlapuu, University of Gothenburg08:30Empowering data-driven innovations in Life Sciences: A journey with GU VenturesKlementina Österberg, GU Ventures & Carl-Peter Mattsson, GU VenturesKlementina Österberg CEO & Carl-Peter Mattsson Investment director at GU Ventures will present their experiences and the journeys to create successful new business in collaborations with investors, industry and the eco system. They will also show some examples of these journeys with their companies.09:15BioVentureHub – an antidote to the incubent’s curseMagnus Björsne, AstraZeneca BioVentureHub10:00Coffee Break10:30Precision Medicine from the start – using omic data to deliver actionable insight to drug discovery and developmentDaniel Muthas, AstraZeneca11:15Data driven life sciences in a clinical settingJesper Havsol, AstraZeneca12:00Networking lunch12:40Tour – “The Amazing Journey the story about Astra Zeneca in Mölndal”Optional, sign up in registration form

Symposium Program for Download and PrintDownload

Data-driven Life Science

The future of life science is data-driven, providing major new opportunities to explore and understand biology, human health and changing ecosystems. The SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS) is set up to make use of these opportunities.

Building capacity to upskill the community: How the SciLifeLab Training Hub can help
2024-04-23 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during spring 2024. The seminars will be held in a hybrid format – IRL in Glasburen, KBC, Umeå, and online via Zoom. Learn more about the seminar series and Schedule for Spring 2024 here.

On 23 April, at 12:00, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

Building capacity to upskill the community: How the SciLifeLab Training Hub can help

Presenter:

Nina Norgren, Training Manager, Umeå University.

Description: Come join us for a session that is all about boosting skills and training the community with the Scilifelab Training Hub. We will be presenting how the Training Hub can support your platform/unit in designing and delivering training to your users. Whether you are just starting out or looking to level up your skills, we have resources and support to help you along the way. Everyone interested in training is welcome!

More about SciLifeLab Training Hub: https://www.scilifelab.se/training/

Visit the new Training Portal to see all our courses and materials: https://training.scilifelab.se/

Registration: Sign up for the IRL seminar and reserve your free lunch (sandwich, drink, and little sweet snack) by Monday, 22 April, 10:00 a.m.:

https://www.umu.se/en/chemical-biological-centre/kbc_events/registration-form-infrastructure-seminar

or follow online (registration is not required):

Meeting URL: https://umu.zoom.us/j/67909354528Meeting ID: 679 0935 4528

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

Organizer:KBC

Event type:Seminar

Introduction to Data Management Practices
2024-04-23 08:00 - 2024-04-25 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
National Bioinformatics Infrastructure Sweden (NBIS) gives a course in research data management practices. This workshop in Data Management is a unique event to provide an introduction to practices for better management of data 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 who want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.

Important dates

Application closes: 2024-03-22

Information to accepted students will be sent: 2024-04-02

Contact: edu.intro-dm@nbis.se

Application

Workshop Website

Format & Content

This workshop runs on-site in Solna, Stockholm. Teachers and teaching assistants will be present all week to help with exercises and questions.

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 (e.g. by using Git & GitHub)

Writing Data Management Plans

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.

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 the topics covered and the duration of the workshop.

Due to limitations in space and capacity, the course can accommodate a maximum of 25 participants. 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

Entry requirements

No previous programming experience is required, but you are required to bring your own laptop with the required software pre-installed. The course organisers arrange a pre-course event approximately one week prior to the first-course day.

NBIS/ELIXIR-SE Tools for Reproducible Research
2024-04-22 08:00 - 2024-04-26 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
NBIS / ELIXIR-SE course open for PhD students, postdocs, group leaders and core facility staff at all Swedish universities interested in making their computational analysis more reproducible.

Course Website

Important dates and information

Application opens: 2024-02-19

Application closes: 2024-03-18

Confirmation to accepted students: 2024-03-22

Course Leader and teachers:

John Sundh (CL)

Erik Fasterius (CL)

Estelle Proux-Wéra

Lokeshwaran Manoharan

Tomas Larsson

Cormac Kinsella

Mahesh Binzer-Panchal

In case you miss information on any of the above dates, please contact: edu.trr@nbis.se

Course fee

A course fee* of 3000 SEK will be invoiced to accepted participants. The fee includes lunches, coffee/tea and snacks as well as a course dinner.

*Please note that NBIS cannot invoice individuals

Course content

This course will introduce best practices in making research reproducible – from code tracking to software packaging and documentation – via short lectures and hands-on tutorials.

Topics covered will include:

Good practices for data analysis

Version control and collaborative code development

Package and environment management

Workflow management

Documentation and reporting

Containerized computational environments

Learning Outcomes

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

Organize and structure computational projects

Track changes and collaborate on code using Git

Install packages and manage software environments using Conda

Structure computational steps into workflows with Snakemake and Nextflow

Create automated reports and document their analyses with Quarto and Jupyter

Package and distribute computational environments using Docker and Singularity

Entry requirements

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

Familiarity with using the terminal (e.g. be familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.)

Some knowledge in R and/or python is beneficial but not strictly required

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.

Contact information: edu.trr@nbis.se

Introduction to Biostatistics and Machine Learning
2024-04-22 08:00 - 2024-04-26 17:00 | BMC Trippelrummet, Husargatan 3, entrance C11, Uppsala, Sweden
National course open for PhD students, postdocs, researchers and other employees in need of biostatistical and machine learning 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: 2024-03-24

Confirmation to accepted students: 2024-03-28

Responsible teachers: Olga Dethlefsen, Eva Freyhult

If you do not receive information according to the above dates, please contact edu.ml-biostats@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

Course content

Probability theory

Hypothesis testing and confidence intervals

Resampling

Linear regression methods

Introduction to generalized linear models

Model evaluation

Unsupervised learning incl. clustering and dimension reduction methods

Supervised 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 lectures, group discussions, live coding sessions etc.

Entry requirements

Basic R programming skills (check your R skills by taking our self-assessment test)

BYOL (bring your own laptop) with R and RStudio installed

No prior biostatistical knowledge is assumed, only basic math skills (pre-course studying materials will be available upon course acceptance)

The course can accommodate a maximum of 25 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.

Registration

TEM sample preparation practical course
2024-04-22 08:00 - 2024-04-26 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
This is a practical course on sample preparation for TEM and includes:

Ultra-microtome sectioning

Chemical fixation

Plastic embedding

TEM imaging

High-pressure freezing & freeze substitution

Immunolabeling techniques (Immunogold, CLEM)

Volume EM (FIB-SEM & Tomography)

Participants will practice TEM sample preparation and TEM imaging with a sample from their own project. Lab space limits the number of participants to 8, chosen by motivation and project aim. Write a short project description, motivation for participating and what sample you would like to bring for the course. Fixation and plastic embedding take time, therefore one test-sample should be brought to be prepared before the course, and a new test-sample is brought for the first day.

In addition, a small presentation about an EM-project idea of your own should be prepared and presented on the last day.

Participants should attend all theoretical and practical parts of the course to receive a certificate of 1,5 hp.

Pre-requisite criterion: Basic EM course at UCEM or previous equal experiences with EM methods.

Teachers: Sara Henriksson, Agnieszka Ziolkowska, Narin Mohamad and Linda Sandblad

Contact: linda.sandblad@umu.se

Application deadline: 27 March 2024.

More Information and registration

Model-guided ML approaches to integrative omics analyses
2024-04-19 10:00 - 11:00 | Online event via Zoom
NBIS, Scilifelab’s Bioinformatics platform, arranges an open AI and IO Seminar Series aimed at knowledge-sharing about Artificial Intelligence and Integrative Omics (AI & IO) analysis and applications in the Life Science community. The seminar series is open to everyone. The seminar is run over Zoom on the third Friday of the month during academic terms, typically between 10 and 11 am, with ca. 45 min long presentation and 15 min discussion.

For further info, please see this website.

Model-guided ML approaches to integrative omics analyses

Cemal Erdem, DDLS fellow, Umeå University

Click here to join zoom conference
