SciLifeLab

NBIS workshop in Neural Nets and Deep Learning
2022-01-17 08:00 - 2022-01-21 17:00 (Europe/Stockholm) | 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: 2021-11-01

Application closes: 2021-12-05

Confirmation to accepted students: 2021-12-19

Responsible teachers: Claudio Mirabello, Bengt Sennblad

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

Course fee

A course fee* of 2200 SEK will be invoiced to accepted participants. This 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-propagationConvolutional Neural NetworksRecursive Neural NetworksAutoencodersBest 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 problemDistinguish between linear and non-linear approaches and recognise which is best suited for application to their own problemDescribe 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 modelTell the difference between a shallow and a deep networkExplain broadly how different NN architectures are wired and how they workImplement and apply the most appropriate architecture to a given problem/datasetAnalyze training curves and prediction outputs to evaluate if the training has been successfulDebug possible issues with the training and suggest changes to fix themExplain the difference between training, validation and testingDefine what overfitting is from a mathematical point of view, and what issues it causesIdentify what constitutes good practices of dataset design and how to avoid introducing information leakage or other biases when building their own datasets

COURSE INFORMATION

APPLICATION

Entry requirements

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

Familiarity with Unix/LinuxAbility to bring your own laptop with Python and Jupyter Notebooks installed for the practical exercisesProgramming/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)

Desired

You have experience of working with Jupyter NotebooksYou 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.

Data Driven Life Science Seminars at Gothenburg University - Epidemiology and infection biology
2022-01-13 10:00 - 12:15
Welcome to attend the second open, digital seminar as part of the recruitment process given by the top candidates for the two group leader positions in data-driven life science (DDLS) at University of Gothenburg.

The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative funded with a total of 3.1 billion SEK from the KAW.

Read more about the Seminar

Data Driven Life Science Seminars at Gothenburg University - Precision medicine and diagnostics
2022-01-10 09:15 - 12:00
Welcome to attend the first open, digital seminar as part of the recruitment process given by the top candidates for the two group leader positions in data driven life science (DDLS) at University of Gothenburg.

The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative funded with a total of 3.1 billion SEK from the KAW.

Read more about the Seminar

Campus Solna Seminar Series: Halva Ozlem Altay and Erik Samuelsson
2021-12-16 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Profound Effects of Combined Metabolic Activators on Metabolic Diseases.Halva Ozlem Altay (Adil Mardinoglu, alpha 6)

Using Spatial Transcriptomics to Profile Tissue Architecture in Glioblastoma and Diffuse Midline GliomaErik Samuelsson (Mats Nilsson, gamma 4)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

Symposium on the ABC study: Biomarkers of Clinical Relevance – The ABC Risk Scores in Cardiovascular Diseases (CANCELLED)
2021-12-15 13:00 - 17:00 | Fåhræussalen, Rudbecklaboratoriet, Dag Hammarskjölds väg 20, Uppsala, -, Sweden
NOTE! Due to the current situation with the pandemic, in combination with several of the invited speakers being ill, this symposia has unfortunately been cancelled. The symposia will take place during the spring of 2022 and more details will come regarding a date and venue

In the ABC Risk Score project new tools for precision medicine in cardiovascular diseases have been developed. At this half-day symposium achievements obtained within the project will be presented and discussed. The ABC Risk Score project has been financed for 5 years by the Swedish Foundation for Strategic Research.

The symposium is free of charge, including coffee and some light refreshments. For attending the coffee break and evening mingle, please register by December 8.

Organizers

Agneta Siegbahn: SciLifeLab, Uppsala University, department of Medical Sciences and Uppsala Clinical Research Center (UCR) Lars Lind, Jonas Oldgren and Lars Wallentin: Uppsala University, department of Medical Sciences and Uppsala Clinical Research Center (UCR)

REGISTRATION

PROGRAM

RNA Medicine, the Next Frontier: Therapeutic Targeting of Non-Coding RNAs
2021-12-13 15:00 - 16:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Anders NäärDepartment of Nutritional Sciences & Toxicology, University of California, Berkeley

Biography/Talk content

Anders M. Näär is a Professor of Metabolic Biology in the Department of Nutritional Sciences & Toxicology at the University of California, Berkeley. He was a postdoctoral research fellow with Robert Tjian at UC Berkeley/HHMI, where he discovered the human Mediator transcriptional co-activator complex. Dr. Näär was a Professor in the Department of Cell Biology, Harvard Medical School and the Massachusetts General Hospital Cancer Center. A major focus of his lab is to understand transcriptional and microRNA regulatory mechanisms controlling metabolic homeostasis to guide novel therapeutic strategies for the treatment of cardiovascular disease, obesity, Type 2 diabetes, non-alcoholic fatty liver diseases (NAFLD/NASH), age-related macular degeneration (AMD), Duchenne muscular dystrophy (DMD), multi-drug resistant fungal infections, and numerous types of cancer. His work resulted in a number of impactful studies, patents and foundation of companies. In his talk, Anders will broadcast his latest ventures in using RNA therapeutics in combating human diseases.

Date: 13 December 2021Time: 3pm

Venue (format hybrid): SciLifeLab, lunchroom, y2The ZOOM link is: https://ki-se.zoom.us/j/68353175106?pwd=[REDACTED]

Meeting ID: 683 5317 5106Passcode: [REDACTED]

Cryo-EM 2021 user meeting & Integrated Structural Biology user day
2021-12-13 09:00 - 2021-12-14 15:30 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
The Integrated Structural Biology welcomes you to these two events. You can join either event – or both – and you can choose to participate online or on site in Air&Fire at SciLifeLab Campus Solna.

We invite you to either or both of our events:

3rd Cryo-EM Facility National Meeting – December 131st Integrated Structural Biology platform user meeting – December 14

3rd Cryo-EM Facility National Meeting

Welcome to join this meeting with users to discuss results and needs from the community.

Program – December 13

9.00News from the Cryo-EM facility nodes in Stockholm and Umeå10.00Fika10.20PReSTO for Cryo-EM, Torben Rasmussen, Linköping10.40Chameleon sample preparation for cryo-EM,Sacha de Carlo, SPT Labtech11:00Recent advances in the field of CryoEM Gaurav Sharma, Thermo Fisher Scientific.11:20Structural proteomics for studying protein interactions and dynamicsSimon Ekström, Lund University11:40Big and dynamic – An ancient and universal NMP kinaseTobias Sparrman12:00Lunch13:00Cryo-EM user discussion, previous in-person meeting (drop-in service, booking system, cryoScreeeNET) and sensing the interest for potentiating new applications (electron diffraction, FIB cryoET, cryo-CLEM)15:00Wrap-up16:00End of Meeting

Register to attend this event

1st Integrated Structural Biology platform user meeting

The purpose of this meeting is to show complementary techniques available at SciLifeLab Infrastructure and to encourage interactions.

Program – December 14

8:45General introduction to ISB platform9.00Presentation of Protein Production Sweden (PPS)Malin Bäckström9.15MicroED for structure determination of biomolecules, Laura Pacoste, SU9.35NMR studies on VIM-2, Hermina Wieske, Uppsala University9.55Proteome-wide crosslinking mass spectrometry of host-pathogen interactions, Lotta Happonen, Lund University10.15Coffee Break11.00Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome, Luka Bacic, Uppsala University11.20Structural basis of DegP-protease temperature-dependent activation, Darius Šulskis, University of Gothenburg11.40The interface study of M1-protein and M1-specific IgG via structural mass spectrometry, TX-MS and HDX-MS, Di Tang, Lund University12.00Lunch13.00Cryo-EM structural study of the P5-type ATPases” Ping Li, Kopenhagen University, LU13.20Characterizing proteins in their native environment: Advances in in situ NMR, Johannes Thoma, University of Gothenburg13.40Unravelling the molecular basis of cell protection by Bcl-2 proteins, Gerhard Gröbner, Umeå University14.00Bruker on UF-MAS and structural biology14.30Discussion – user feed back15.20Final notes15:30End of Day

Register to attend this event

Validating antibodies for research applications
2021-12-09 13:30 - 14:30 | Online event via Zoom
Will Howat, Senior director of Antibody Validation and Characterization at Abcam

Abstract

Validation of antibodies for use in scientific research is a tricky and time-consuming process which can stifle scientific progress. During this seminar, I will demonstrate why we need validation and the tools that are available to help.

Biography

Will Howat leads Abcam’s approach to product validation and technical quality globally as Senior Director of Antibody Validation & Characterization. Prior to joining Abcam in 2018, he worked at AstraZeneca as Team Leader of its Molecular Pathology Group, where his team developed biomarker assays for preclinical, Phase 1 and Phase 2 clinical trials. Before that he was at the Cancer Research UK’s Cambridge Institute, where he set up and ran the Histopathology/ISH core facility for 9 years. He has also worked at the Wellcome Sanger Institute on the Atlas of Protein Expression and was responsible for R & D within the Immunohistochemistry group.

Will has a BSc (Hons) in Immunology & Pharmacology from the University of Strathclyde and a PhD in Pathology from the University of Southampton. His publications span key journals such as The Lancet, Nature, Science, Nature Genetics, American Journal of Pathology, and the Journal of Pathology.

Hosts

Fabio Socciarelli MD, Henrik J. Johansson PhD

Campus Solna Seminar Series: Gabriele Pozzati and Alex Petri
2021-12-09 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Simultaneous folding and docking: a new approach for modelling protein complexesGabriele Pozzati (Arne Elofsson, alpha 6)

De novo construction of Isoforms from Long-read data (isONform)Alex Petri (Kristoffer Sahlin, gamma 6)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

FAIR principles in life science research practice
2021-12-09 09:00 - 16:00 | Online event via Zoom
Location: Online via Zoom

This online workshop will showcase how to put the FAIR principles into practice and is specifically designed to cater to life science researchers at all career stages. It is organised by SciLifeLab Data Centre and NBIS and include international speakers, presenters from the SciLifeLab community and optional hands-on exercises guided by experts from NBIS and SciLifeLab Data Centre.

The workshop aims to highlight some of the strongest motivators for adopting the FAIR principles and demonstrate how to operationalise them in your projects’ data management practices. While the intended audience is the full spectrum of researchers from experienced principal investigators to early career PhDs the registration open to everyone involved in life science research. To serve participants with varying roles and priorities the day is divided into two companion sessions and you can sign up for one or both at your leisure. The morning session covers the principles and a selection of case studies on how to operationalise them. The afternoon session is based on practical exercises and will provide an opportunity to gain hands-on experience of making research data FAIR.

The overall issues that the sessions aim to address is the fact that an increasing number of policymakers and funders are expecting research projects to adopt the FAIR principles for scientific data management. While the acronym is composed of words that are commonly associated with assessing secondary data—that is that they are Findable, Accessible, Interoperable, and Reusable—it might not be obvious how to prepare your data to be FAIR.

Acceptance to this workshop is on a first come, first served basis. Registration is required to receive the Zoom link. The afternoon session is limited to 20 participants.

Morning session (09:00–12:00)

Invited speakers include international experts on supporting research projects in adopting the FAIR principles and a selection of projects from the SciLifeLab community that illustrate aspects of putting FAIR in practice.

Erik Schultes – Lead FAIR Implementation at the GO FAIR Foundation and a member of the Leiden Center for Data Science.Rob Hooft – Technical Coordinator for the Dutch ELIXIR Node and Programme Manager Data Stewardship at the Dutch Techcentre for Life Sciences (DTL).

Afternoon session (13:00-16:00)

Join the local data management experts from SciLifeLab’s national bioinformatics support platform (NBIS) and SciLifeLab Data Centre in guided, hands-on exercises on data organisation, reproducibility and good data management practices that you can apply in your own projects.

Register here

View the full agenda here

SciLifeLab Drug Discovery Seminar & DDD Exit event: Thomas Helleday
2021-12-08 14:00 - 15:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress

Professor Thomas Helleday, Karolinska Institutet

SciLifeLab Drug Discovery Seminars, hosted by the DDD platform, is a series of educational lectures about recent developments, technologies, and trends in drug discovery and development that aims to enlighten, and spark a discussion, within the Swedish drug discovery community.

Abstract

The folate metabolism enzyme MTHFD2 is consistently overexpressed in cancer but its roles are not fully characterized and current candidate inhibitors have limited potency for clinical development. Here we demonstrate a role for MTHFD2 in DNA replication and genomic stability in cancer cells, and present optimised potent and selective nanomolar MTHFD2 inhibitors (MTHFD2i); protein co-crystal structures demonstrated binding to the active site of MTHFD2 and target engagement and that works in vitro and in vivo.

The results demonstrate a functional link between MTHFD2-dependent cancer metabolism and replication stress that can be exploited therapeutically with this new class of inhibitors. The work, done in collaboration with the SciLifeLab DDD platform, is accepted in the journal Nature Cancer and is the base for the creation of a new company: One-carbon therapeutics AB.

registration

Symposium: Science & SciLifeLab Prize for Young Scientists
2021-12-08 09:30 - 15:00 | Humanities Theater, Engelska parken, Uppsala, 75238, Sweden
SciLifeLab and AAAS/Science magazine have joined forces in creating the Science & SciLifeLab Prize for Young Scientists to promote young scientists early in their careers. The Prize is awarded annually to four recent Ph.D. graduates for outstanding life science research.

Join us, to celebrate the 2020 and 2021 winners of the Science & SciLifeLab Prize for Young Scientists at the Scientific Symposium, December 8, 09:30-15:00.

The bus from Tomtebodavägen 23 to Humanistiska Teatern departs at 07:45 and from Uppsala to Solna at 15:15.

Hybrid event

On-site, Humanistiska Teatern, Uppsala: The Symposium will include the Prize winner’s presentations, a keynote lecture, lunch, and coffee with the possibility to meet and mingle with the winners and your SciLifeLab colleagues. Many people are interested in meeting IRL again but the seats are limited (100p). Register today! First-comes first served! Please cancel if you can’t come so that the spot can be available for someone else. We have bus transportation from Tomtebodavägen 23 at 07:45.

We need you to register for the on-site event by November 30, at the latest for catering reasons. The registration will be open until we reach the maximum participants (100p), but we cannot guarantee lunch or coffee after November 30. If you have questions, please contact events@scilifelab.se.

Registration

Program

Remote: The event will be broadcasted on the SciLifeLab YouTube channel. You don’t have to register for the YouTube broadcast. But if you do, you will get a reminder and a direct link to the event. Don’t miss this scientific symposium where you will meet the 2020 and 2021 year´s laureates and hear about their award-winning research.

The Prize is awarded in the following categories:

Cell and Molecular BiologyResearch in this category includes cellular and molecular processes at levels ranging from single molecule to single cell to tissue and organ systems.Genomics, Proteomics and Systems BiologyResearch in this category focuses on genomics, proteomics, integrative omics and systems biology approaches to facilitate comprehensive understanding of living cells, organisms and species.Ecology and EnvironmentResearch in this category encompasses interactions between organisms and their environment, and how these processes are influenced by human activity.Molecular MedicineResearch in this category aims at building on the molecular understanding of disease in humans to develop preventive, diagnostic and therapeutic approaches, including individualized medicine.

Short facts:

Date: December 8, 2021

Time: 09:30-15:00

Venue: Humanistiska teatern, Engelska Parken, Uppsala and streaming to SciLifeLab YouTube channel.

Registration deadline For lunch and coffee, register by November 30, at the latest. Limited seats on site, unlimited participants online

About the Prize

Science/AAAS and SciLifeLab, have joined forces in creating the Science & SciLifeLab Prize for Young Scientists. Both Science/AAAS and SciLifeLab recognize that global economic health is dependent upon a vibrant research community and we need to incent our best and brightest to continue in their chosen fields of research. Considering the difficult economic environment, we feel it is important to provide extra encouragement to young scientists as they begin their scientific careers. Each year, the grand prize winner will receive a prize of US$30,000; each of the three category winners will receive US$10,000. The grand prize winning essay will be published in Science and essays from the three category winners will be published online. The prize is jointly operated by Science and SciLifeLab and is generously sponsored by the Knut and Alice Wallenberg Foundation.

Read more about the prize here.

Watch this video to hear from the 2020 Grand Prize Winner and Category Winners!

About Science/AAAS

The American Association for the Advancement of Science (AAAS) is the world’s largest general scientific society, and publisher of the journals, Science, Science Translational Medicine, Science Signaling, Science Advances, Science Immunology, and Science Robotics. AAAS was founded in 1848, and includes some 254 affiliated societies and academies of science, serving 10 million individuals. Science, founded by Thomas Edison, has the largest paid circulation of any peer-reviewed general science journal in the world, with an estimated total readership of 570,400.

The non-profit AAAS—www.aaas.org—is open to all and fulfills its mission to “advance science and serve society” through initiatives in science policy, international programs, science education, and more. Science further participates in various efforts to provide free access for scientists in the world’s poorest countries.

About SciLifeLab

As a national hub for molecular biosciences in Sweden, SciLifeLab develops and maintains unique research infrastructure, services and data resources for life science. SciLifeLab coordinates research communities in health and environmental science, recruitment and training of young scientists, and fosters collaboration with industry, health care, public research organizations and international partners. The overall aim of SciLifeLab is to facilitate cutting-edge, multi-disciplinary life science research and promote its translation to the benefit of society.

SciLifeLab is jointly operated by its four founder universities: KTH Royal Institute of Technology, Karolinska Institutet, Stockholm University and Uppsala University. About 200 research groups, 1500 researchers and 40 national infrastructure units are associated with SciLifeLab. The two main research centers are located in Stockholm and Uppsala, but national SciLifeLab units exist at all major Swedish universities.

Affinity proteomics Uppsala present a seminar about the latest developments of the in situ proximity ligation assay
2021-12-07 13:00 - 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Topic: Navinci in Situ Proximity ligation assay, new developments, applications, and user presentations.

SciLifeLab Affinity Proteomics Uppsala offer full service of in situ proximity ligation assays (PLA) in fixed cells or tissue sections to image, with enhanced specificity, the presence of specific proteins, interactions and/or post-translational modifications to e.g. characterise acts of protein signaling in tumor tissues, or to evaluate effects of drug treatment. Our latest addition is the PLA technology offered by Navinci and we would like to present this technology together with research presentations by users in a hybrid event (in-person and online). After the event there will be time for questions and refreshments at Mötestorget in Navet.

Welcome!

Register here

Agenda

Seminar 13:00 – 15:00, SciLifeLab, Trippelrummet and Zoom

13:00 Welcome and introduction (Mikael Åberg, SciLifeLab Affinity Proteomics and Robert Gunnarsson, Navinci)

13:15 Agata Zieba Wicher, Navinci: Introduction to Navinci technology

13:40 Amanda Lindberg, Uppsala University: Detection of activated PDGFRb receptor in NSCLC using NaveniFlex combined with a TSA-based detection method

14:00 Nicolle Heinzl, Oncolabs 14:00 Nicolle Heinzl, Oncolabs: “p53 prions” – A new promising cancer biomarker meets a disruptive technology

14:20 Johan Heldin, Uppsala University: Differential impact of lipid raft depletion on platelet-derived growth factor (PDGF)-induced ERK1/2 MAP-kinase and AKT signaling

14:40 Brian Perrino, University of Nevada : TBD

15:00 – 17:00 Mingle with bubbles and canapés and open house with a vernissage at Navinci, SciLifeLab Navet, Mötestorget/ Navinci facilities

BioImage Informatics Call4Help
2021-12-07 09:00 - 11:00
Every 1st week of the 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?

We prefer if you prepare a short presentation and upload it together with some example images according to the steps 1 and 2 below. This makes it easier for us when we have to prioritize between projects and allows us to prepare for the meeting. But if time permits, we can also accept participants without this info.

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, December 7, 2021, 9.00-12.00. Deadline for application: Friday, December 3, 2021.

DDLS fellow candidates' seminars at Linköping University
2021-12-06 16:30 - 2021-12-08 18:30 | Online event via Zoom
Welcome to listen to the seminars and discussions of the candidates for DDLS fellow position in I) Cell and Molecular Biology and in II) Precision Medicine and Diagnostics at Linköping University. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative funded with a total of 3.1 billion SEK from the KAW.

Read more

MTLS Alumni Network Speaker Day
2021-12-03 10:00 - 15:00 | Widerströmska Huset, Tomtebodavägen 18, Solna, Sweden
The joint master’s programme in Molecular Techniques in Life Science fosters graduates for a professional research career in life science. It has a strong focus on molecular techniques for disease therapies and diagnostic tools, coupled with substantial training in data analysis (bioinformatics and programming). The programme is a collaboration between Karolinska Institutet, KTH and Stockholm University at the Science for Life Laboratory in Stockholm, offering students the unique opportunity to study at all three institutions.

Facts

Date: Friday, December 3rdTime: 10:00-15:00Location: Widerströmska Huset, KI Campus Solna (Next to Scilifelab)

We are looking forward to welcoming alumni from Academia, Industry, and other science fields to this event, where they will share their wisdom and experience with current students.

Agenda:10:00-12:00 Session 112:00-13:00 Lunchbreak and Mingle13:00-15:00 Session 2

We will announce the speaker list closer to the event.

Learn more about the master’s programme here.

Campus Solna Seminar Series: Tojo James and Karl Olofsson
2021-12-02 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Single-cell transcriptional changes associated with drug response in AMLTojo James (Päivi Östling, alpha 4)

Multicellular tutor diskoids: A 3D cell culture geometry optimised for microscopyKarl Olofsson (Martin Viklund, gamma 3)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

SciLifeLab COVID-19 seminars: Ralf Bartenschlager and Kristian Sandberg
2021-12-01 15:15 - 16:45 | Online event via Zoom
Topic: Drug screening and emerging viruses

The last of the five SciLifeLab COVID-19 seminars this autumn starts with Ralf Bartenschlager, Professor, Department of Infectious Diseases, Molecular Virology, Heidelberg University & Virus-associated Carcinogenesis, German Cancer Research Center, Heidelberg, talking about Architecture and biogenesis of ER-derived viral replication organelles.Kristian Sandberg, PhD, Associate Professor., and SciLifeLab Drug Discovery and Development Platform Co-Director at Uppsala University, then continues the seminar with his talk on Establishing a drug discovery platform for corona virus disease at SciLifeLab

Moderator: Marianna Tampere, KI

Registration is mandatory to get the Zoom link for the event

REGISTRATION

BIOS & ABSTRACTS

Uppsala PhD&Postdoc seminars: Weifeng Lin & Liza Löf
2021-11-30 11:00 - 11:50 | Online event via Zoom
Welcome to SciLifeLab Uppsala PhD&Postdoc seminars!We are very happy to host exciting talks by PhD students and Postdocs from a great variety of fields within SciLifeLab.The seminars will take online place every Tuesday from 11:00 to 11:50

For this occasion the seminars will be: Weifeng Lin, PhD student in Globisch labTitle: Unique chemoselective probes for discovery and investigation of metabolites in human samples with enhanced mass spectrometric sensitivityLiza Löf, Postdoc in Landegren Lab (Molecular Tools)Title: Development of methods to characterize the impact on signaling pathways by targeted therapy in chronic myeloid leukemia

Link to seminar

Swedish Microfluidics in Life Science 2021
2021-11-30 10:30 - 2021-12-01 15:00 | Lund University, Lund, Sweden
The Swedish Microfluidics in Life Science meeting gathers researchers in the field of micro- and nanofluidics. The meeting offers an opportunity to present your research, to network with researchers at Swedish universities, institutes and companies , and to listen to invited talks by a panel of well reputed research leaders. Confirmed speakers are Stefan Löfås (Innovido AB), Edith Hammer (Lund University), Christoph Merten (Ecole Polytechnique Fédérale de Lausanne), Anja Boisen (‎Technical University of Denmark) and Madhavi Krishnan (University of Oxford)

Save the date and please help spread this information in your groups and local networks.

Read more

Clinical Talks: The road towards precision medicine in Sweden
2021-11-26 09:00 - 09:30 | Online event via Zoom
On November 26, we will host Karolinska Institutet (KI) Professor Richard Rosenquist Brandell. In addition to his academic research and clinical work, he also co-founded the Genomic Medicine Sweden (GMS) initiative and serves as the Director of GMS. Richard will share his insights on Sweden’s national strategy to implement precision medicine into our healthcare environment and pave the way for the amazing potential the approach has to offer. To benefit from the sustainable advantages of tailored and efficient use of diagnostics and treatment options, Sweden needs to prepare our society for the legal challenges and infrastructures necessary to support and enable this transformation.

Read more about clinical talks

Richard Rosenquist Brandell, MD, PhD, is Professor of Clinical Genetics at Karolinska Institutet, Senior Physician at Karolinska University Hospital and director of Genomic Medicine Sweden, a national infrastructure for implementation of precision medicine. He obtained his MD degree in 1996, and later his PhD in Medicine in 1998, from Umeå University. In 2000 Richard joined Uppsala University Hospital (“Akademiska Sjukhuset”) and in 2007 became a Professor at the Department of Immunology, Genetics and Pathology, Uppsala University. In April 2017, he relocated to the Karolinska University Hospital as a Senior Physician and Professor. Richard’s work focuses on hematological malignancies and utilizing high-throughput sequencing technologies, his team has identified novel prognostic and predictive biomarkers that have significantly improved patient risk-stratification. Dr Rosenquist Brandell is also a member of the Nobel Assembly at Karolinska Institutet.

Genomic Medicine Sweden (GMS) started as a bottom-up initiative within the national Clinical Genomics Platform (previously named the Diagnostics Development platform) at the Swedish Science for Life Laboratory (SciLifeLab). In 2017 and 2018 discussions with funding agencies, decision-makers, healthcare providers, patient organisations, universities, and industry led to the founding of GMS as a national venture. GMS strategic mission is to foster collaboration between healthcare providers, academia, patient organizations and industry and realize precision medicine by effectively utilizing the rapidly advancing sequencing technologies to provide the highest standards of genomic testing in routine clinical care throughout Sweden.

Registration

Campus Solna Seminar Series: Casper Winsnes and Morteza Aslanzadeh
2021-11-25 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Casper Winsnes (Emma Lundberg, alpha 2)

The impact of miRNAs on Variation and Covariation of Proteins in Single CellsMorteza Aslanzadeh (Marc Friedländer, gamma 5)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

Uppsala PhD&Postdoc seminars: Gang Pan & Adrian Garcia Concejo
2021-11-23 11:00 - 11:50 | Online event via Zoom
Welcome to SciLifeLab Uppsala PhD&Postdoc seminars!We are very happy to host exciting talks by PhD students and Postdocs from a great variety of fields within SciLifeLab.The seminars will take online place every Tuesday from 11:00 to 11:50

For this occasion the seminars will be: Gang Pan, Researcher in Claes Wadelius´ research groupTitle: Trs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 ExpressionAdrian Garcia Concejo, Postdoc in Dan Larhammar´s research groupTitle: Regulation of memory receptors by protein kinase C

LINK to Seminar:

SciLifeLab AI Seminar Series: A sneak peek into the future of AI-assisted life science
2021-11-23 10:00 - 11:00
SciLifeLab Data Centre hosts a seminar series on the topic of applied AI in life science research. SciLifeLab AI Seminar Series combines scientific highlights from SciLifeLab-affiliated researchers and invited experts on the general topic of AI applications in Life Science.

The seminar will be held physically at SciLifeLab Gamma 7 lunch room in Solna and online via Zoom. Physical participation is recommended since some AI models are not allowed to be shown via streaming and there will be no recording after the seminar according to the live demonstration policy of OpenAI.

Contact: Prof. Ola Spjuth, AI coordinator, SciLifeLab Data Center.

Speaker: Wei OUYANGKTH Royal Institute of Technology and Science for Life Laboratory

Abstract

Have you imagined how AI may one day help you with your research by proposing new ideas, running experiments, analyzing data, and even writing manuscripts? While current AI systems are too weak for those tasks, we are closer than ever before!

In June 2020, OpenAI revealed the most advanced AI model in the world, GPT-3. It is the largest natural language processing model ever created with 175 billion parameters, trained on about 45TB of text data, and it cost $12 million for a single training run that may be utilized and reused for many tasks. Not only are these numbers impressive, its “text in, text out” interface can be used as a general purpose tool for almost any language task with impressively good performance. With the newly released Codex model (a descendant of GPT-3), it can even generate source code in popular programming languages by following instructions in natural languages, e.g., English. GPT-3 not only brings us to a new paradigm of AI-assisted coding, but it also has a great potential to address long-standing challenges in deep learning about generalization and interpretability.

We are excited to share with you what we have learned so far about GPT-3 and its applications in life science. In this talk, we will give you an overview and discuss the promises and pitfalls of GPT-3. You will also see live demos in biomedical applications, such as processing genomic sequences, analyzing microscopy images, and creating user-friendly software with graphical user interfaces (GUIs). Hopefully, this session will serve as inspiration for your own research, serve as a basis for discussion about AI in life science, and convey how these tools may accelerate data-driven life science at SciLifeLab.

Biography

Wei OUYANG is a researcher in Prof. Emma Lundberg’s group at the Science for Life Laboratory and KTH Royal Institute of Technology. He has a diverse background across several different fields including material science, computer science and advanced microscopy imaging. In 2018, Dr. Ouyang obtained his PhD in computational image analysis at Institut Pasteur, Paris where he mainly focuses on applying deep learning for super-resolution microscopy. During this period, he developed a deep learning method called ANNA-PALM which massively accelerates super-resolution localization microscopy by 100x. To address the challenges in the dissemination of AI tools, he developed an open-source computational platform, ImJoy, which makes deep learning tools easier to build and more accessible to the user. He is actively involved in consortiums and community activities for promoting more open, scalable, accessible and reproducible scientific tools. Dr Ouyang has been focusing on AI augmented microscopy imaging and data-driven whole cell modeling. More recently, he is excited about the recent progress in the field of AI and has a knee interest in exploring the next generation of data-driven life science powered by AI, robotics, blockchain and decentralized applications.

Register here

The Svedberg seminar series: Prof. Tuuli Lappalainen
2021-11-22 15:15 - 16:30 | Online event via Zoom
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden

New York Genome Center, New York, USA

LINK TO SEMINAR

Tuuli Lappalainen is a Professor in Genomics at KTH Royal Institute of Technology, an Associate Faculty Member at the New York Genome Center, and the Director of the National Genomics Infrastructure of SciLifeLab. She is also an Adjunct Professor at the Department of Systems Biology at Columbia University.

Her research focuses on functional genetic variation in human populations and its contribution to traits and diseases. She has pioneered the intergration of large-scale genome and transcriptome sequencing data to understand how genetic variation affects gene expression, providing insight to cellular mechanisms underlying genetic risk for disease.

Functional variation in the human genome: lessons from the transcriptome

Detailed characterization of molecular and cellular effects of genetic variants is essential for understanding biological processes that underlie genetic associations to disease. A particularly scalable approach has been linking genetic variants to effects in the transcriptome that is amenable for scalable measurements in human populations and in experimental settings, including at the single cell level. Our multi-omic analysis in human cohorts in the TOPMed project has identified genetic and environmental effects on molecular variation together with their complex interplay with clinical phenotypes. Furthermore, in this talk I will discuss how CRISPRi silencing of regulatory elements followed by single-cell analysis provides novel insights of mechanisms of genetic associations to complex traits. Altogether, these diverse approaches for integration genome and transcriptome data uncover functional genetic architecture of human traits, and enhances our understanding of both basic biology and precision medicine applications.

Host: Jessica Nordlund, Uppsala University

DDLS Conference: Strategic research areas - postponed!
2021-11-22 08:30 - 17:00
Join us at the first conference within The SciLifeLab and Wallenberg national program for Data-Driven Life Science!

The practice of life science is continuously becoming more data-dependent. The amount and complexity of data is growing exponentially, and more scientific discoveries are enabled when data is openly available to researchers across the world. This is the basis for the SciLifeLab and Wallenberg National Program on Data-Driven Life Science (DDLS).

The program focuses on four strategic areas for data-driven research, all of which are essential for improving the lives of people as well as animals and nature, detecting and treating diseases, protecting biodiversity and creating sustainability:

Cell and molecular biologyEpidemiology and infection biologyEvolution and biodiversityPrecision medicine and diagnostics

The conference will focus on enthusing research within the four research areas and aims to bring together researchers within the field for discussion and sharing the latest within the research areas. The meeting will offer an exciting compilation of keynotes, special lectures within the four fields and opportunities to meet and discuss with prominent researchers.

Anyone with interest in the data-driven research field is welcome to participate. The full-day conference will be virtual (Zoom).

The program with confirmed speakers will be available shortly.

The conference is part of the SciLifeLab and Wallenberg national program for the DDLS program, funded by the Alice and Knut Wallenbergs Foundation.

Introduction to bioinformatics using NGS data - ONLINE
2021-11-22 08:00 - 2021-11-26 17:00
National workshop for PhD students, postdocs, researchers, and other employees within Swedish academia. This workshop is organized by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI).

Due to the Covid-19 situation, this workshop will be held online.

If you have questions regarding the workshop, please email: edu.intro-ngs@nbis.se

Important dates

Application opens: August 16, 2021

Application closes: October 10, 2021

Confirmation to accepted students: October 15, 2021

Responsible teachers

Malin Larsson, Martin Dahlö, Roy Francis

Course 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 2000 SEK.

Please note that NBIS cannot invoice individuals

Course content

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.

After this workshop you should be able to:

Describe the basic principles of next generation sequencing.Use the Linux command line interface to manage simple file processing operations, and organize directory structures.Connect to and work on a remote high performance compute cluster.Apply programs in Linux for analysis of NGS data.Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.Explain common NGS file formats.Interpret quality control of NGS reads.Explain the steps involved in variant calling using whole genome sequencing data.Independently perform a basic variant calling workflow on example data.Explain the steps involved in differential gene expression using RNA seq data.Independently perform differential gene expression analysis on example data.

Entry requirements

A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable. To get the maximum benefit from the workshop we would like you to

Have relevant previous experience in sequencing or analysis.Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.

Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance.

Link to application

The application opens on August 16, 2021.

Nurturing wellbeing in academia
2021-11-18 14:15 - 15:45 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
DEI committee continues series of events “Our community, ourselves” dedicated to raising awareness and improving mental health in Academia. The following event “Nurturing wellbeing in academia” is brought to us by Deborah Rupert and Frida Rångtell, well-being coaches from “Dear Academia”. Dear Academia offers interactive seminars and holistic workshops focused on individual mental wellbeing, burnout prevention, peer-to-peer support and creation of healthy environment in academic settings.

More information here: https://deborahrupert.com/dear-academia/

We are each other’s working environment. Nurturing taking care of ourselves and of each other is one key aspect of cultivating a healthy academic work environment – together with active conscious leadership.

At an interactive webinar where we will explore how to create a human friendly work environment covering how to:

Improve your sleep and implement healthy routinesDevelop strategies to manage your stress and grow resilienceBe an ally to cultivate wellbeing at work

Taking care of our mental health is paramount to the individual wellbeing, performance and to a healthy working culture.

join zoom meeting 18 November 14:15

Speakers:

Deborah Rupert, PhD

Wellbeing and career coach, Dear Academia

Déborah Rupert is the founder of Dear Academia and is a wellbeing and career coach. She is certified from the International Coaching Federation and holds a PhD in biological physics from Chalmers Technical University, Sweden. She is dedicated to burnout prevention and supporting researchers with mental clarity and career strategy. She is a career coach for researchers in career transition at Trygghetsstiftelsen and the nordic director of Enkindle Global, focusing on burnout prevention for individual change makers and leaders within organisations.

Frida Rångtell, PhD

Sleep and habits educator, Dear Academia

Frida Rångtell has a PhD in sleep and memory from Uppsala University, Sweden. Today she works as a sleep and habits educator, scientific advisor and runs Slumra of Sweden.

Campus Solna Seminar Series: Haris Babacic and Gustavo Jeuken
2021-11-18 13:00 - 14:00
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 13:00-13:50 and following current regulations, they will be broadcast via zoom.

This week

Plasma proteome alterations in glioblastoma: preliminary resultsHaris Babacic (Janne Lehtiö, alpha 1)

Pathway Activity-based Survival AnalysisGustavo Jeuken (Lukas Käll, gamma 6)

Registration

Register to receive the zoom-link. The same zoom link applies for all Campus Solna Seminar Series, i.e. only one registration is necessary.

Uppsala PhD&Postdoc seminars: Niki Sarri & Ankit Gupta
2021-11-16 11:00 - 11:50 | Online event via Zoom
Welcome to SciLifeLab Uppsala PhD&Postdoc seminars!We are very happy to host exciting talks by PhD students and Postdocs from a great variety of fields within SciLifeLab.The seminars will take online place every Tuesday from 11:00 to 11:50

For this occasion the seminars will be: Niki Sarri, PhD student in Carl-Henrik Heldin’s research groupTitle: Deubiquitinating enzymes USP4 and USP17 fine-tune the trafficking of PDGFRβ and affect PDGF-BB-induced STAT3 signallingAnkit Gupta, PhD student in Wählby lab, Division of Visual Information and InteractionTitle: SimSearch: A Human-in-the-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images
