Planetary Biology Workshop
2022-05-16 08:00 - 2022-05-17 17:00 (Europe/Stockholm) | EMBL Heidelberg, Meyerhofstraße 1, Heidelberg, Germany
EMBL-SciLifeLab workshop on the theme Planetary Biology

The purpose of the workshop is to enhance connectivity between researchers at both, SciLifeLab and EMBL, to identify new collaboration ideas, and to promote joint technology and infrastructure resource development within Planetary Biology.

This is one of many workshops that will follow the conclusion of the MoU between SciLifeLab and EMBL in 2021.

The workshop is a hybrid event. Physical location is the EMBL Heidelberg campus, where in-person attendance is limited. Allocation of spaces is on a first-come first-served basis.

Please note: there are two separate registration links for on-site or virtual participation. In case you sign up for on-site participation but your availability changes, please make sure to inform the responsible contacts.

The workshop will include talks on a broad set of themes including:

Biodiversity Genomics & Reference Genome SequencingEcology & EvolutionBiogeochemistry & EcosystemsData-driven Planetary Biology,

As well as invited keynote speakers and panel discussions.

read more and sign up here

Day 1, Monday 16th May, 2022

13:00Welcome and opening remarksEdith HeardDirector General of EMBLOlli KallioniemiDirector of SciLifeLab13:10Introduction and overview of Planetary BiologyDetlev ArendtPlanetary Biology Co-Chair, Senior Scientist, Group Leader, EMBLOlga Vinnere Pettersson & Stefan BertilssonCo-Leads Planetary Biology Capability, SciLifeLab13:30Session 1: Biodiversity Genomics & Reference Genome Sequencing (15 mins + 5 mins Q&A per speaker in each session)ModeratorPeter Harrison, Genome Analysis Team Leader, EMBL-EBISpeakersFergal Martin, Vertebrate Annotation Coordinator, EMBL-EBIKerstin Lindblad Toh (remote), Professor in Comparative Genomics, Uppsala University, Scientific Director of Vertebrate Genome Biology, Broad InstituteDetlev Arendt, Planetary Biology Co-Chair, Senior Scientist, Group Leader, EMBLOve Nilsson, Group Leader Control of Flowering Time and Tree Phenology, Umeå Plant Science Center14:50 Coffee break15:10Session 2: Ecology and EvolutionModeratorOlga Vinnere Pettersson, Co-Lead Planetary Biology Capability, SciLifeLabSpeakersLove Dalén, Professor of Evolutionary Genetics, Swedish Museum of Natural History, Research Leader at Center for Palaeogenetics, StockholmMichael Dorrity, Group Leader Structural and Computational Biology, EMBLJames Sharpe (remote) , Head of EMBL Barcelona, Group Leader in Tissue Biology and Disease ModellingAnna Rosling, Group Leader Ecology and Evolution in Soil Fungi, Uppsala University16:30Keynote by Mark BlaxterWellcome Sanger Institute17:15Summary and Q&A

Day 2, Tuesday 17th May, 2022

09:00Arrival and Coffee09:30Keynote by Martin PolzUniversity of Vienna10:20Session 3: Biogeochemistry & Ecosystems(15 mins + 5 mins Q&A per speaker in each session)ModeratorStefan Bertilsson, Co-Lead Planetary Biology Capability, SciLifeLabSpeakersMichael Zimmermann, Group Leader in Structural and Computational Biology, EMBLFlora Vincent, Incoming Group Leader in Developmental Biology; Post Doctoral Fellow at Weizmann Institute of Science, RehovotSara Hallin, Professor at the Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesMark Dopson, Professor at the Department of Biology and Environmental Science, Linnaeus University11:40 Break12:40Session 4: Data-driven Planetary BiologyModeratorOliver Stegle, Associate Group Leader in Genome Biology, EMBLSpeakersTomas Roslin (remote), Professor at the Department of Ecology, Swedish University of Agricultural SciencesPeer Bork, Director of EMBL Heidelberg, Group Leader in Structural and Computational Biology, EMBLAnders Andersson, Group Leader in Environmental Genomics, Royal Institute of TechnologyAnna Kreshuk, Group Leader in Cell Biology and Biophysics14:00Summary and Q&A14:15Coffee break14:45Panel Discussion 1: Technological Infrastructure Needs for PB ResearchModeratorStefan Bertilsson, Co-Lead Planetary Biology Capability, SciLifeLabPanelistsYannick Schwab, Team Leader Volume Correlative Light and Electron Microscopy and Head of Electron Microscopy Core Facility, EMBLTimo Zimmermann, Team Leader Advanced Light Microscopy Technology Development and Service Provision, EMBLLinda Sandblad, Scientific Platform Director Cellular and Molecular Imaging, Umeå University, SciLifeLabOlga Vinnere Pettersson, Project coordinator at Department of Immunology, Genetics and Pathology, Uppsala University; Co-Lead Planetary Biology Capability, SciLifeLabAnnika Johansson, Head of Swedish Metabolomics Centre, Umeå University, SciLifeLab16:00Short break16:10Panel Discussion 2: Data Collection in PB ResearchModeratorOlga Vinnere Pettersson, Co-Lead Planetary Biology Capability, SciLifeLabPanelistsRainer Pepperkok, Director of Scientific Core Facilities and Scientific Services, Team Leader Membrane traffic and Organelle Biogenesis, EMBLStefan Bertilsson, Professor in Functional Ecology of Freshwaters, Swedish University of Agricultural Sciences; Director of the Swedish Infrastructure for Ecosystem Science (SITES); Co-Lead Planetary Biology Capability, SciLifeLabFredrik Ronqvist, Professor in the Department of Bioinformatics and Genetics, Swedish Museum of Natural History; Swedish Biodiversity Data Infrastructure (SBDI)16:40Panel Discussion 3: Data Management and Processing in PB ResearchModeratorFergal Martin, Eukaryotic Annotation Team Leader, EMBL-EBIPanelistsGuy Cochrane (remote), Team Leader Data Coordination and Archiving, EMBL-EBIBlokeshwaran Manoharan, Expert in Metagenomics; National Bioinformatics Infrastructure Sweden (NBIS)Johan Rung, Head of Data Center, SciLifeLab17:00Conclusion and Closing Remarks

Scientific committee SciLifeLab

Stefan Bertilsson, SLUOlga Vinnere Pettersson, Uppsala University

AI / Data-driven life science
2022-05-16 09:15 - 16:30 | Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, Sweden
Life science research is becoming increasingly dependent on data, and never before has so much data been generated today. The amount and complexity increase exponentially, and when this data becomes open to researchers around the world, more scientific discoveries are made possible. The rapid technological development in life sciences, combined with innovations in computing and AI, will play an increasingly important role in research and development and affect virtually all areas of medicine and science.

During this day, you will meet prominent international and local researchers, take part in current research, and discuss open data, AI, ethics, and visualization related to life science.

Contacts: Carolina Wählby and Bent Persson.

Venue: Ångströmslaboratoriet, Lägerhyddsvägen 1, Uppsala

Registration opens at the end of March.

Program and registration will be published here!

The event is part of Uppsala University’s multidisciplinary theme week in technology and science from May 16 to 20, at the Ångström Laboratory. During the week, you will be able to take part in current research in AI / Data-driven life science, the universe and mathematical physics, materials, energy, and climate change.

The Svedberg seminar: Simon Elsässer
2022-05-16 17:15 - 18:15 | Online event via Zoom
Register and get the link here

Simon Elsässer is Associate Professor at Karolinska Institutet, Department of Medical Biochemistry and Biophysics. He has studied at University of Tübingen and Harvard University, and received his Ph.D. from The Rockefeller University in 2012. He has performed postdoctoral research at MRC Laboratory of Molecular Biology and was recruited to Karolinska Institutet as a SciLifeLab Fellow in 2015. His research combines synthetic biology methods to probe and manipulate proteins in the living cell with quantitative ‘omics readouts, focusing on stem cells, gene expression regulation and epigenomics.

Title of the seminar: Exploring the dynamics of the pluripotent epigenome and lineage choice in development

Short Abstract:

The first lineage choice made in human embryo development separates trophectoderm from the inner cell mass, which proceeds to form the pluripotent epiblast and primitive endoderm. We discovered that Polycomb repressive complex 2 (PRC2) maintains naïve pluripotency and restricts an intrinsic capacity of pre-implantation pluripotent stem cells to give rise to extraembryonic lineages. Through quantitative ChIP-seq and single-cell transcriptomics, we demonstrate that PRC2-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development.Webpage: http://www.elsaesserlab.org

Handling Pandemic Omics Data in the Nordics
2022-05-18 09:00 - 2022-05-19 13:00 | Online event via Zoom
Dates: 18 & 19th May (9:00-13:00)

Location: online via Zoom

The current COVID-19 pandemic has understandably received considerable attention worldwide over the last few years. As it spread across the globe, the pandemic posed significant challenges for society, governmental bodies, healthcare systems, and research communities. Unprecedented efforts were necessary to generate, handle, and report the sheer amount of complex data required to be able to understand how SARS-CoV-2 was spreading, and develop efficient policies to fight the pandemic.

SciLifeLab Data Centre, ELIXIR Norway and ELIXIR Estonia have organised an online event exploring how Nordic countries handled omics data related to the SARS-CoV-2 pandemic. We invite bioinformaticians, data stewards, research scientists, and anyone else interested in this topic to attend. We will focus in particular on how sequencing efforts were coordinated, how data was managed and shared, and how data was used and communicated to different groups. We will also discuss the importance of the FAIR principles in pandemic data management, and which tools and pipelines facilitated efforts. We hope that this will shed light on best practices that could be adopted across the Nordics for future pandemics, and how we might best prepare for them. We also hope to identify key resources that have wider applicability and can be reused further.

The programme is available at:

https://nordic-compbio.iscbsc.org/omics-data.

For any queries about the meeting, please email nazeefaf@uio.no

Register Here

Campus Solna Seminar
2022-05-19 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Seminars are back in person!

The speakers for Thursday 19 May:

1) Erik Wernersson (Magda Bienko’s group, alpha4):“deconwolf: free and open source deconvolution for widefield microscopy.”

2) Carlos Gallardo Dodd (Claudia Kutter’s group, gamma5):“Cell type-specific deployment of codons and anticodons in mammals.”

Time: 12:00-13:00

Place: Air&Fire, SciLifeLab Campus Solna

Towards characterizing the human 3D-proteome - Nobel Symposium
2022-05-19 14:00 - 18:00 | Beijersalen, Kungl. Vetenskapakademien, Lilla Frescativägen 4A, Stockholm, Sweden
Public keynote lectures: 14:00-18:00

No registration necessary, but when the room is full, it is full

Read more

Program

14:00 Introduction – Arne Elofsson14:15 Demis Hassabis, DeepMind, Using AI to model biology14:45 Sarah Teichmann, Wellcome Sanger Institute, TBD15:15 Sergey Ovchinnikov, Harvard, Inverting protein structure prediction models to solve problems in biology.For this talk I’ll describe some exciting applications of protein structure prediction models such as TrRosetta, RoseTTAFold and AlphaFold. More specifically, I’ll describe how we can invert these models for protein design, generation of multiple sequence alignments and navigating the conformational landscape to predict structure(s) from single sequence

15:45-16:15 Coffee

16:15 Debora Marks, Harvard, TBD16:45 Alice Y Ting, Stanford, Spatial proteomics and transcriptomics via enzyme-catalyzed proximity labelingWhere a protein is localized in the cell exerts tremendous influence over its function, interaction partners, dynamics, and modifications. Enzyme-catalyzed proximity labeling (PL) has emerged as a powerful and generalizable method to map the locations and interactions of endogenous proteins in the context of living cells, applicable to even membraneless organelles and transient interactions that are inaccessible to traditional methods such as affinity purification. I will give a brief account of PL method development, including directed evolution of the PL enzymes APEX and TurboID, and then describe new efforts to extend PL to RNA and proteome trafficking.

17:15 John Jumper, DeepMind, TBD17:45 Final Comments

The Nobel Foundation’s symposium activities were initiated in 1965. Over the years, they have achieved a high international standing. The symposia are devoted to science areas where breakthroughs are occurring.

This symposium aims to bring together experts from various fields with the explicit goal of outlining a joint worldwide strategy to obtain a structural map of the human proteome. In addition to determining the structure and composition of all human proteins and their interactions, it would also require understanding the flexible and dynamic supra-molecular structures in living cells, such as multi-component membraneless organelles. A few key findings from the last years make us believe that this goal is achievable. First, detailed knowledge of composition (splice forms, PTMs) and expression levels in different cells are becoming available. Secondly, Cryo-EM has revolutionized the structural determination of large protein complexes. Finally, using co-evolution and advances in deep learning, it is now possible to predict the structure of many individual proteins and complexes directly using no other information than the sequences and their evolutionary history. In the next few years, combining the progress in these three areas will provide an opportunity to provide unprecedented molecular insights into the function of cells. Theoretical methods combined with ever-increasing sequence information will enable an understanding sequence and structural variation within populations, both in humans and in disease-causing organisms.

The Svedberg seminar: Tanja Slotte
2022-05-23 15:15 - 16:15 | Online event via Zoom
Tanja Slotte, Assoc. Prof.Stockholm University, Sweden

Register and get the Link

Assoc. Prof. Tanja Slotte is a population geneticist who is interested in the genetic causes and genomic consequences of plant mating system shifts and the evolution of mating system supergenes. She received her PhD from Uppsala University in 2007, followed by a postdoc at University of Toronto. She started her own group at Uppsala University in 2010 and moved to Stockholm University to take up a SciLifeLab Fellow position in 2014. She is currently Associate Professor in Ecological Genomics at Stockholm University.

Title of the seminar: Sequencing the supergene that governs Darwin’s different forms of flower

Supergenes are responsible for a wide variety of balanced polymorphisms in nature, yet our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene. Recent studies have shown that the Primula distyly S-locus supergene is hemizygous due to structural variation at the supergene. If this genetic architecture is common to other distyly supergenes, it could have major implications for the evolution and loss of distyly. To shed further light on this question we have characterized the genetic architecture and evolution of the distyly supergene in Linum, one of the plant systems where Dawin first described distyly. We have generated multiple high-quality genome assemblies of Linum species as a genomic framework for evolutionary studies. Here, we leverage this framework to identify the distyly S-locus supergene and study its evolution and expression. Our results show that hemizygosity and thrum-specific expression are major features of the Linum distyly supergene, and suggest that the supergene has arisen in a stepwise manner. Our findings demonstrate remarkable convergence in the genetic architecture, origin and evolution of the distyly supergene among systems with independently derived distyly, and shed light on the evolution of the classic supergene that governs Darwin’s “different forms of flowers”.

Solid tumours as dynamic cellular ecosystems
2022-05-24 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Dr. Alex Swarbrick, Garvan Institute for Medical Research, Australia

Location: Air/FireDate: 10.00 24th of May

Abstract: A well-established principle in developmental biology is that cellular context governs cell fate, differentiation, proliferation and survival. There is emerging evidence that solid tumours are also complex cellular systems, or ecosystems, in which interactions between neoplastic, stromal and immune cells govern the natural history of disease and response to treatment. In this seminar Dr Swarbrick will discuss his latest research applying cellular genomics to understanding breast cancer ecosystems, with the aim of making new discoveries relevant to disease stratification and treatment.

SciLifeLab Uppsala PhD&Postdoc seminar
2022-05-24 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.

Speaker 1: Hongxing Zhao, Researcher at Ulf Landegren Lab (Molecular Tools), Dept. of Immunology, Genetics and Pathology

Title: Detection of SARS-CoV-2 antibodies from dried blood spots of vaccine individuals by proximity extension assay Summary: We have developed a solution-phase assay for sensitive detection of SARS-CoV-2 antibodies in serum or dried blood spots (DBS) from infected or vaccinated individuals. Detection probes were prepared by conjugating the recombinant S1-RBD or nucleocapsid (NC) to either of a pair of oligonucleotides. Upon incubation with COVID-19 patient serum or DBS from vaccinated individuals, the multivalency of the antibodies brings pairs of oligonucleotides that have been conjugated to the viral proteins in proximity. The oligonucleotides can then undergo enzymatic DNA extension via a proximity extension assay (PEA), and the resulting amplicons are sensitively detected by real-time PCR or end-point read out using ELISA mechine. This antibody PEA (AbPEA) test uses only 1 µl neat or diluted serum or one ø1.2 mm disc cut from a DBS. All 100 investigated sera and 21 DBS collected prior to the COVID-19 outbreak were negative, demonstrating a 100% specificity. The sensitivity of the assay for infected patient after 10 days symptom reached 99.8% [95% confidence interval: 0.9935-1]. Anti-S1 antibodies could be detected directly in punched-out discs from self-sampled DBS 11 days after vaccination, and it reached a maximum at 3 weeks after a first inoculation. Examination of a serially collected DBS from 14 individuals all showed similar trends of antibody responses after both a first and second vaccination, although antibody levels varied between individuals.

Speaker 2: Manon Dubol, PhD. Postdoctoral Researcher at Erika Comasco Neuropsychopharmacology Group, Dept. of Women and Children’s Health

Title: Grey matter morphometry and MRI data-driven classification of premenstrual dysphoric disorder (PMDD) Summary: Premenstrual dysphoric disorder (PMDD) is recognized in the DSM-5 as a hormone-related depressive disorder, specific to women’s mental health 1. Women who suffer from PMDD experience affective, cognitive, and physical symptoms that peak during the late luteal phase of the menstrual cycle, and remit shortly in the beginning of the next cycle 2. The key affective symptoms of PMDD point to anatomical and functional brain impairment, suggesting an impaired top-down inhibitory process involving limbic brain structures 3. However, very little is known about brain morphological alterations in PMDD. The present study aimed at investigating the grey matter structures that distinguish women with PMDD from healthy controls, by use of multiscale structural MRI analyses. Differences in grey matter structure between the groups were investigated by use of Voxel- and Surface Based Morphometry. Furthermore, machine learning and multivariate pattern analysis was performed using a leave-one-fold-out cross-validation procedure, to test whether MRI measures (volume, thickness, gyrification, sulcal depth and cortical complexity) could distinguish women with PMDD from healthy controls. The findings point to PMDD-specific grey matter structure in regions of corticolimbic networks, in line with the hypothesis of an impaired top-down inhibitory circuit involving limbic structures in PMDD. Furthermore, the results include widespread cortical regions and cerebellar areas, suggesting the involvement of distinct networks in PMDD pathophysiology. These effects prominently involved volumetric and cortical thickness measures, as further highlighted by multivariate pattern classification analyses. Such differences in brain structure may help explaining the variations in brain function previously reported in women with PMDD during the symptomatic phase.

NGS at NGI
2022-05-24 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 2022 in turn with IceLab Lunch Pitches. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Take the chance to get information on facilities, possibilities and services that infrastructure, both SciLifeLab-associated and local, can offer! Learn more about the seminar series and Schedule for Spring 2022 here.

On May 24th, 12:00-13:00, you are welcome to participate in the seminar

NGS at NGI

by Kristina Benevides, Project coordinator, National Genomics Infrastructure (NGI), SciLifeLab, and research engineer in bioinformatics and sequencing, UPSC Bioinformatics Facility, Department of Plant Physiology, Umeå University

Seminar description

Got samples? We’ve got the sequencing! NGI(https://ngisweden.scilifelab.se/) is one of the largest platforms at SciLifeLab and provides both established and cutting-edge genomics technologies to diverse user groups across Sweden and internationally. There’s a wide range of applications as NGI is equipped with both short- and long read technologies, as well as SNP genotyping- and DNA methylation arrays. The platform assists users in project design, data generation, analysis and management of data in order to support genomics research in all subject areas.

Prepare for your next (generation) sequencing experiment as we’ll get into the nitty-gritty of some different methods, sample types and requirements.

There will be a fun online science quiz at the end – participate to win some swag!

Registration

Sign up (latest by May 23rd, 10 a.m.) for on-site attendance to reserve your free lunch sandwich:

sign up

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

Organisers

SciLifeLab Site Umeå and Chemical Biological Centre (KBC)

A novel, antibody-based radiopharmaceutical for advanced thyroid cancer
2022-05-25 13:00 - 14:00 | Online event via Zoom
Presenter: Dr Marika Nestor, Department of Immunology, genetics and pathology, Uppsala University, Sweden

Molecular radiotherapy is increasingly becoming a powerhouse in the field of cancer- and radiation therapy. By targeting a structure that is abundant on tumor cells but scarce in healthy tissues, a cancer-targeting molecule labeled with a therapeutic radionuclide can mediate the delivery of radioactivity specifically to cancer cells. This creates a targeted, localized form of radiotherapy that combines the advantages of systemic therapy with therapeutically effective radiation.

In a collaboration with the Drug Discovery & Development platform at Science for Life Laboratory, we have developed an antibody-based radiopharmaceutical for molecular radiotherapy of advanced thyroid carcinoma. The project spans over the whole early development chain; from preclinical innovation in the lab, dosimetry and proof-of-concept in animal models, to upscaled production and preparations for first-in-man studies.

Dr Nestor in her presentation will discuss the process from innovation to implementation of the project, both from a research and a commercialization perspective.

sign up here

Marika Nestor leads a translational research group at the Department of Immunology, Genetics and Pathology, Uppsala University. Her research group focuses on radionuclide targeting and radiosensitization of cancer cells. She obtained her PhD at Uppsala University in 2006, and became an Associate Professor in 2012. In 2013 she was awarded the Göran Gustafsson prize for young scientists, in 2016 the Junior Investigator Award from the Swedish Cancer Society, and in 2020 the Senior Investigator Award. In 2019, she was awarded a grant from Sweden’s innovation agency VINNOVA to facilitate clinical translation of her findings, as well as an Attractive Innovation Award by UU Innovation.

New Imaging and Fluctuation Methods: Super-Resolution, Light-Sheet, STED-FCS and FRET-FCS
2022-05-30 08:00 - 2022-06-10 17:00 | Online event via Zoom
Web-based PhD-level course, 3 hp credits, by the ALM facility at Scilifelab.

Flyer_220119

Light-Sheet Imaging

Long time-lapse imaging of live modelorganisms with low phototoxicityCombined light-sheet andsuper-resolution

Super-Resolution Imaging in Living Cells – MoNaLISA

Smart probes50 nm resolution at 1-2 Hz100 x 100 um field of view time lapse imaging

STED-FCS

Fluctuation spectroscopy with 30 nm resolutionSub-diffraction dynamics in living cells

FRET-FCS

Easy detection of protein-protein interactions in living cellsHighly sensitive detection of rare oligomers in living cells

Lecturers

Andreas BodénErdinc SezginIlaria TestaStefan Wennmalm, stewen@kth.se

Registration

Please register by sending an e-mail with your contact details to: stewen@kth.se.Registration deadline: May 20, 2022

FAIRPoints-Enhancing Sample Provenance and Experimental Reproducibility
2022-05-30 16:00 - 17:00 | Online event via Zoom
Location: Online via Zoom

See Event in your Time Zone

Speaker: Rory Macneil

Lack of reliable information about sample usage, location, provenance, metadata and experimental use is a core barrier to experimental reproducibility and general FAIRification of data. This presentation will describe how these issues are being addressed in the design and development of a sample management module within the RSpace electronic lab notebook, focusing on three specific challenges: (1) Incorporating sample data into experimental documentation; (2) Associating PIDS like IGSNs and RRIDS into sample metadata; and (3) Export of sample metadata in required formats to different domain repositories and databases.

FAIRPoints is an event series highlighting pragmatic measures developed by the community towards the implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) data principles, in collaboration with GoFAIR US, SDSC, AGU, and SciLifeLab Data Centre.

Speaker bio:

Rory Macneil is CEO of Research Space, which provides RSpace, an electronic lab notebook and research data management platform, and host of the FAIR Data Podcast. In these roles, and through participation in organizations and forums like the Research Data Alliance, numerous conferences and events, and conversations with researchers, research data managers, policy makers, funders, and tools developers, he enjoys exploring practical ways in which FAIRification of data can be advanced.

Register here

Sign up for future events here

Twitter: @FAIR_Points

Webinar: Funding and support from Novo Nordisk Foundation and BioInnovation Institute
2022-05-31 13:00 - 14:00 | Online event via Zoom
SciLifeLab invites the Novo Nordisk Foundation and the BioInnovation Institute (BII) to a webinar where they will present organizations, grant and funding instruments, upcoming programs and tips and tricks for a successful application.

MAY 31, at 13:00 – 14:00

The Novo Nordisk Foundation is an international foundation focusing on improving people’s lives and sustainability of the society. The Foundation awards grants for research projects based on applications it receives in open competition and for strategic projects for which the Foundation takes the initiative. The Foundation has two grant instruments within Innovation, the Pioneer innovator Grant and the Distinguished Innovator Grant, both of which are open for researchers in the Nordic countries.

BioInnovation Institute (BII) is an international commercial foundation with a non-profit objective supported by the Novo Nordisk Foundation. BII operates an incubator to accelerate world-class life science innovation that drives the development of new solutions through the creation of life science start-ups for the benefit of people and society. BII offers help to early-stage projects and start-ups in health tech, bio-industrials and therapeutics through their various programs. They can provide funding up to 2.5m euros. They are open for applications twice a year. September is the next deadline for applications.

Register for the Webinar, May 31

Registration

Following event:

SciLifeLab BII pitch days

June 16, 14:00-17:00 and June 17, 10:00-12:00

The webinar on May 31, is followed by two pitch days where researchers are given the opportunity to pitch their ideas to the BII team. The purpose is to get feedback and guidance from business developers on your idea and to learn if your project could be a fit for their different innovation programes and funding instruments.

Read more

Swedish Microfluidics in Life Science (SMILS) 2022
2022-06-01 08:00 - 2022-06-02 17:00 | Ångström Laboratory, Lägerhyddsvägen 1, Uppsala, Sweden
The Swedish Microfluidics in Life Science meeting gathers researchers in the field of micro- and nanofluidics, and 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.

ABSTRACT DEADLINE: APRIL 15, 2022

REGISTRATION DEADLINE: MAY 25, 2022

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

Registration

Read more

Serial biomarker measurements and cardiovascular disease
2022-06-01 10:00 - 11:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Datum: 1 juni, kl. 10.00 Plats: Biomedicinskt centrum Navet BMC E10:3309, SciLifeLab Uppsala. Föreläsare: Isabella Kardys Kontaktperson: Agneta Siegbahn Seminarium

Biomarkers of Clinical Relevance – The ABC Risk Scores in Cardiovascular Diseases
2022-06-01 13:00 - 17:00 | Martin H:son Holmdahlsalen, Dag Hammarskjöldsväg 8, Entrance 100, Akademiska sjukhuset, Uppsala
Symposium on the ABC study

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.

We kindly ask those who plan to attend the coffee break and evening mingle to register by May 20.

REGISTRATION

PROGRAM

POSTPONED - SciLifeLab COVID-19 seminars: Drug repurposing and Precision Medicine - Philip Gribbon & Päivi Östling
2022-06-01 15:15 - 16:45 | Online event via Zoom
This seminar is unfortunately postponed due to illness – new date not decided yet

Philip Gribbon & Päivi Östling

The fourth SciLifeLab COVID-19 seminar this spring starts with Philip Gribbon, Head of Discovery Research, Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany, talking about ” Compound repurposing in COVID-19, target and phenotypic-based approaches“. The second talk, “Exploring the morphology of the host cell to open new possibilities in drug repurposing” will be given by Päivi Östling, Department of Oncology-Pathology, Karolinska InstitutetModerator: Annika Jenmalm Jensen, SciLifeLab Infrastructure Director

Register here to Get the Link to the seminar

Schedule

15:15- 16:00Compound repurposing in COVID-19, target and phenotypic-based approaches Philip Gribbon Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany16:00-16:45Exploring the morphology of the host cell to open new possibilities in drug repurposingPäivi Östling Department of Oncology-Pathology, Karolinska Institutet

BIOS and ABSTRACTS

The Fair Journal: Science Cartoons for the People
2022-06-02 10:00 - 11:00 | Online event via Zoom
Jonas N. Søndergaard

The Fair Journal is run by active scientists passionate about spreading recent scientific findings in an understandable and truthful manner to kids and non-scholarly educated adults (https://thefairjournal.com). Their specialty is making cartoons explaining the essence of research articles to kids, with a focus on storytelling and making it fun. They also publish a written summary in a language that non-scholarly educated people can understand. In this BAM presentation, Jonas will talk about how the Fair Journal’s system works, how they produce the cartoons, and how scientists can earn from their own layman summaries.

join zoom meeting

Jonas Søndergaard is current an Assistant Professor at Osaka University in Japan. Previously, he performed research in Sweden (SciLifeLab), Netherlands, Denmark, and the US. His main research focus is immunology, but he is also interested in all fields of science ranging from engineering, to medical sciences, and social sciences. He envisioned the idea for the Fair Journal while working at SciLifeLab.

Researchers in all stages of their career are welcome to attend and could find the talk useful. Kindly feel free to extend the invitation to your home universities.

Flyer-BAM-Jonas.N.Söndergaard_editedDownload

Campus Solna Seminar - Isabelle Leo and Shan Chen
2022-06-02 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to 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 the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-12:50 and in Air&Fire, SciLifeLab Stockholm.

Isabelle Leo

Janne Lehtiö, Alpha 1

Using proteomics to understand biology and biomarkers in childhood acute lymphoblastic leukemia.

Shan Chen

Ola Larsson, Gamma 6

PABP prevents the untimely decay of select mRNA populations in human cells

BioImage Analysis support - Call4Help
2022-06-07 09:00 - 12:00 | Online event via Zoom
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?

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, June 7, 2022, 9.00-12.00. Deadline for application: Friday, June 3, 2022.

SciLifeLab Uppsala PhD&Postdoc seminar
2022-06-07 11:00 - 12:00 | Online event via Zoom
ZOOM link

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.

Speaker 1: Gustav Arvidsson, Researcher at Jessica Nordlund Lab (Molecular Precision Medicine), Dept. of Medical Sciences
Title: B-cells in primary Sjögren’s syndrome studied by scRNA-seqSummary: Primary Sjögren’s syndrome (pSS) is an autoimmune disease where the main clinical indication is an increased lymphocyte infiltration to the salivary and lacrimal glands, leading to a dry mouth and dry eyes. Auto-antibodies to SSA or SSB are present in the majority of the cases and these can often be detected long before symptoms arise. The disease primarily affects middle aged women and while the disease manifestation is mild for most patients about a third develop more severe systemic symptoms and 5% of the patients develop B-cell lymphomas. Given the prominent role of B-cells in the onset and progression of pSS the present study aims to interrogate differences in B-cell subtype composition, clonotype distribution and gene expression differences between patient subgroups for different B-cell subtypes by means of scRNA-seq. For this purpose, we have generated gene expression and targeted B-cell receptor libraries for ~230 000 unique purified B-cells from 24 patients and healthy controls which we hope can broaden the understanding of the role of B-cells in pSS.
Speaker 2: David Lagman, Researcher at Dan Larhammar Lab(Pharmacology), Dept. of Medical Cell Biology
Title: Evolution of genes important for nervous system function in vertebrates with a focus on visionSummary: Whole genome duplications (WGDs) at the base of the vertebrate lineage have over the years been shown to be responsible for the expansion of many gene families that are important in vertebrate central nervous system function. We have previously resolved the evolution of many of these genes in relation to these WGDs, especially those involved in neuronal, neuroendocrine, and visual function. Here, I will describe our latest results regarding the evolution of cyclic nucleotide gated cation (CNG) channel genes in metazoans. The CNG channels play an important role in vision in vertebrates by being responsible for the hypopolarization of cone and rod photoreceptor cells after the detection of light. Using extensive datamining we have managed to identify four previously unknown CNG channel genes in several invertebrate lineages. We have also managed to, through detailed analyses of conserved synteny, accurately assign vertebrate CNG genes to related chromosomal regions providing strong evidence for an expansion in the early vertebrate WGDs. These analyses open up the door for investigations into the function of the novel CNG genes identified in invertebrate genomes. Finally, I will describe our current endeavor into understanding the evolution of genes involved in long term memory formation and maintenance in vertebrates.

Networking meeting between the Wallenberg programs Data-driven Life Science (DDLS) and WASP-HS
2022-06-08 10:00 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
The purpose of the meeting is to explore opportunities for joint and multidisciplinary research ventures between researchers working within data-driven life science and researchers from the humanities and social sciences working on Artificial Intelligence and Autonomous Systems. Information regarding an upcoming call for seed-money for cross-program research collaborations will also be announced at the meeting. Apart from thematic parallel networking sessions, the program will include a study visit to SciLifeLab. Coffee and lunch will be served.

Deadline: Registration closes on June 1st at 23:00

For questions about WASP-HS, please contact tatyana.sarayeva@umu.se

For questions about DDLS, please contact ddls@scilifelab.se

Registration

Program

10:00Site visit to SciLifeLab12:00Lunch13:00WelcomePresentation of the programsWASP-HS: Francis Lee Associate Professor in Science and Technology Studies Chalmers University of TechnologyDDLS: Erik Kristiansson Professor Mathematical Sciences, Chalmers University of Technology13:20Networking session 1 (select one)1.1. Data Challenges Moderators:WASP-HS: Amanda Lagerkvist, Professor of Media and Communication Studies, Uppsala UniversityDDLS: Helga Westerlind, Assistant professor, Computational epidemiology, Karolinska Institutet1.2 Implementation and UseModerators:WASP-HS: Helena Lindgren. Professor in Computer Science, Umeå UniversityDDLS: Janne Lehtiö, Professor in medical proteomics, Karolinska Institutet14:20Break14:50Networking session 2 (select one)2.1 Prediction and Modeling Moderators:WASP-HS: Francis Lee, Associate Professor in Science and Technology Studies, Chalmers University of TechnologyDDLS: Erik Kristiansson¸ Professor, Chalmers University of Technology2.2 Governance and EconomicsModerators:WASP-HS: Liane Colonna, Assistant professor in law and information technology, Stockholm UniversityDDLS: Heidi Howard, Researcher, Medical Ethics, Lund University15:50Closing words16:00End of day

Theme descriptions DDLS/WASP-HS networking meeting

Data Challenges

WASP-HS: Amanda Lagerkvist, Professor of Media and Communication Studies, Uppsala University

DDLS: Helga Westerlind, Assistant professor, Computational epidemiology, Karolinska Institute

This theme centers around the ethical, organizational, and social challenges around data work. Questions could include for instance: What are the challenges in creating representative datasets for diverse populations? In making data travel between project or countries. Or when old historical data are used to model contemporary phenomena? How do the categories of databases shape the collection of life science data?

Implementation and Use

WASP-HS: Helena Lindgren. Professor in Computer Science, Umeå University

DDLS: Janne Lehtiö, Professor in medical proteomics, Karolinska Institute

This theme centers on the ethical, organizational, and social challenges around implementation and use. Questions could include for instance: How can the generated medical knowledge be implemented in medical education and clinical practice? What are the legal and ethical implications thereof? How can a patient-centered, holistic perspective on a patient’s health situation be maintained (balancing data-driven bio-centric assessments with clinical findings)?How can the computational instruments explain their grounds for output (classification, assessment, diagnosis, or prediction) to a clinician or patient?

Prediction and Modeling

WASP-HS: Francis Lee, Associate Professor in Science and Technology Studies, Chalmers University of Technology

DDLS: Erik Kristiansson, Professor, Chalmers University of Technology

This theme centers on the ethical, organizational, and social challenges around prediction and modeling. Questions could include for instance: What are the ethical and social issues in modelling and forecasting.What are the challenges for model reuse from different domains? What are the challenges of using ”ground truth datasets” to assess model fit for real data cases.

Governance and Economics

WASP-HS: Liane Colonna, Assistant professor in law and information technology, Stockholm University

DDLS: Heidi Howard, Researcher, Medical Ethics, Lund University

This theme centers on the legal, organizational, and governance challenges around data-driven life science. Questions could include for instance: Legal aspects of data (use, reuse, transfer, sharing etc) What is/could be/should be the big picture (non-technical) model of data governance at DDLS? What are the fundamental assumptions, expectations and procedures accepted by stakeholders?

SciLifeLab COVID-19 seminars: Male sex bias in severe COVID-19 outcomes- Claire Deakin and Jan Dumanski
2022-06-08 15:15 - 16:45 | Online event via Zoom
The last SciLifeLab COVID-19 seminar this spring starts with Claire Deakin, Director of Research and Biostatistics at OPAL Rheumatology, Australia, and part-time Senior Research Associate in the Centre for Adolescent Rheumatology Versus Arthritis at University College London, talking about Male sex bias in severe COVID19 outcomes and sex differences in infection, immunity and autoimmunity. The second talk, Loss of Y in leukocytes as a risk factor for critical course of COVID-19 in men, will be given by Jan Dumanski, Professor, Uppsala UniversityModerator: Disa Larsson Hammarlöf, SciLifeLab Research Coordinator

Register here to Get the Link to the seminar

Schedule

15:15- 16:00Male sex bias in severe COVID19 outcomes and sex differences in infection, immunity and autoimmunityClaire Deakin, Director of Research and Biostatistics at OPAL Rheumatology, Australia16:00-16:45Loss of Y in leukocytes as a risk factor for critical course of COVID-19 in menJan Dumanski, Uppsala University

BIOS and ABSTRACTS

Campus Solna Seminar - Alejandro Gijon and Boyang Guo
2022-06-09 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to 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 the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-12:50 and in Air&Fire, SciLifeLab Stockholm.

Alejandro Gijon

Janne Lehtiö, Sarahi Garcia, gamma5

The genomospace: a new ecological perspective based on microbial genomes.

Boyang Guo

Per-Olof Syrén, gamma5

The perfect fit: Enzyme and Substrate conformations in plastic degradation.

The Tara Oceans Expedition: Swimming in environmental genomics data
2022-06-10 13:00 - 14:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Prof. Pascal Hingamp

Aix-Marseille University

The National Graduate School for Medical Bioinformatics welcomes you to a seminar by Pascal Hingamp, from Aix-Marseille University.

Title: “The Tara Oceans Expedition: swimming in environmental genomics data.”

Hope to see you there!

Join Virtually

https://stockholmuniversity.zoom.us/j/2207537839

RaukR, Advanced R for Bioinformatics - Online workshop
2022-06-13 08:00 - 2022-06-17 17:00 | Online event via Zoom
International workshop. The workshop is open for researchers at university or in industry such as PhD students, postdocs, group leaders, core facility staff and analysts.

Join us online this June to improve your R skills and have a nice time!In Life Science and Bioinformatics, R is increasingly being used to transform and analyse data, perform statistical analysis and produce publication-ready visualisations. This workshop will focus on advanced R functionality, to increase the participants skillset and understanding of what is possible to do today.

While we still cannot gather in Visby due variability of pandemic restrictions internationally, we will have the workshop online! We hope that, like last year, we will learn a lot and have fun coding together! See you there!

The workshop is organised by NBIS.

Responsible teachers: Marcin Kierczak, Sebastian DiLorenzo, Roy FrancisContact: RaukR@NBIS.se

You are very welcome to apply or see the website for more information. Please, help us spread the word to interested participants!

APPLICATION

WEBSITE

Important dates

Application deadline: Fri, 13.05.2022, 24:00GMT

Notification of acceptance/decline: Fri, 20.05.2022

Workshop fee

Academic: no fee this year. However, if you register and will be admitted but you will not attend the event without a valid reason, you will be charged a no-show fee (4000 SEK).

Participants from outside of academia should contact us for a fee quote.

The fee does not include travel costs.

Guest speakers

Jenny Bryan (software engineer at RStudio, Data science professor at UBC) Yihui Xie (software engineer at RStudio) Christophe Dervieux (software engineer at RStudio)

Content

reproducible research in R (rmarkdown, knitr),collaborative work using git and GitHub, CD/CI,R code style guidelines,code debugging, optimization and profiling,parallelization and vectorization in R,writing own functions – best practices,understanding and using the system of R classes: S3, S4, R6 and RC,anatomy of an R package: writing your own package from scratch,code debugging, profiling and optimization,tidy data flow with tidyverse,using the language of graphics, ggplot2,developing simple web applications using shiny,R and Python integration using reticulate

Entry requirements

The workshop is aimed at both Ph.D. students and researchers within Life Sciences who are already using R for basic bioinformatics analyses and who would like to start using R at a more advanced level. In order for you and other participants to benefit the most, you should consider yourself eligible if you are comfortable with reading and transforming data, installing and using third-party packages and plotting using standard R graphics.

We offer places for participants from all over the world, but there is a number of places reserved for participants from Sweden.

Selection criteria

This year, we can accommodate ~30 participants. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance.

SciLifeLab Group Leader Retreat
2022-06-14 08:00 - 2022-06-15 16:00 | Aronsborg Konferenshotell, Helgövägen 7, Bålsta, 746 30
We warmly welcome all SciLifeLab Group Leaders to take part in the SciLifeLab’s Group Leader Retreat 2022, June 14-15, at the Aronsborg conference center in Bålsta.

In December 2019, the SciLifeLab Board defined the criteria for being a SciLifeLab Group Leader. Currently, there are close to 250 Group Leaders with a strong affiliation to SciLifeLab research and infrastructure. The Group Leaders are the core of the SciLifeLab community, and are essential to the scientific development of our organization.

This two-day retreat is the first to bring together the expanding SciLifeLab Group Leader community from all SciLifeLab sites. The organizing committee (Anniina Vihervaara, Sarahi Garcia, Prashant Singh, Jean Hausser, Ellen Sherwood, Mats Nilsson and Per Ljungdahl) has developed a program aimed at stimulating interactions and networking between Group Leaders, catalyzed through activities such as speed dating, research discussions, and a sci-hack. In addition, there will be workshops & discussions focused on a broad array of themes tailored for the Group Leader community, e.g. planning a research project and/or improving the impact section of your research application, how research can connect with infrastructure through training activities, SciLifeLab capabilities, the DORA declaration, and more.

The hope is that the retreat will have lasting positive effects by involving everyone in a productive manner. The clear ambition of gathering everyone is that the new contacts made during the retreat will facilitate new collaborations leading to exciting scientific progress. The retreat activities are meant to inspire this!

We highly encourage your participation and hope that you will prioritize this Group Leader Retreat!

On behalf of

Olli Kallioniemi , Director & Mia Phillipson, Co-Director

June 14

TimeActivity08:45Registration and Coffee09:15Visionary Introduction with SciLifeLab Directors10:00Networking activity: Speed dating 10:55Coffee Break11:15Speed dating (cont.)12:00LunchSpa reserved for SciLifeLabWorkshops13:00Planning for Research Impact13:15Connecting Research with Infrastructure using Training activities: a brainstorming exercise13:15How can SciLifeLab group leaders and infrastructures contribute to the clinical implementation of Precision medicine?14:15Coffee break14:45Networking activity: Group Research Discussions17:30Check in / Free time18:30Mingle & Dinner

June 15

TimeActivity07:00Breakfast and check-outSpa reserved for SciLifeLab09:00Research Excellence through Collaboration:SciLifeLab Capabilities09:30Networking activity: SciHack 09:45Coffee break10:15SciHack (cont.)12:15LunchWorkshops13:00Data Centre Compute & Storage for DDLS and infrastructure13:00From research to innovation and commercialization: how to get funding and support13:00DORA13:00Developing the Campus Solna research community13:45Coffee Break14:05Complex problem solving and creative leadership15:30Concluding remarks16:00End of retreat

“Our” premises at Aronsborg

Printable Program

Group Research Discussions

This session is designed for you to get inspired with new views on your scientific challenge, stimulate your thinking by learning about ongoing research in the SciLifeLab community, and make personal connections in this community, across areas of research at SciLifeLab.

Think about and formulate a research challenge or problem you are presently facing. You will have up to 10 minutes to present your challenge, followed by 15 minutes for feedback and discussions with the other group members. That is 25 minutes of dedicated brain time of four accomplished scientists focused on your challenge.

To make the best of this

Prepare and train for your presentation. Presentations will be in an analog format, e.g. no slides, no screens, to encourage high-level, conceptual thinking. Flip chart and board markers will be available.Make sure your presentation is accessible to researchers across the SciLifeLab areas.

SciHack

The overarching idea with this exercise is to enable participants to apply themselves, allowing them to think across disciplines, and perhaps even sparking new collaborations.

How? Identify a problem of interest together with the group members – it could be for example a research challenge or problem brought up in the group research discussions (day 1), or a grand challenge in one of the group member’s research field. Prepare a poster outlining a proposal to solve this problem, leveraging the expertise of all group members. You will have 40 min for this part of the exercise.

Each groups presents their poster 4-5 min in a super-group of 6 SciHack groups. The winning solution from each super-group will be selected, and posted in Upplandssalen.

Workshops

Planning for Research Impact
Hillevi EnglundSusanne Bredenberg

This workshop will provide practical knowledge around research impact and a useful tool to structure your thoughts. The tool will help you who struggle to make a credible impact plan for your grant applications, and you who have a strong drive to create societal impact but don’t know where to start. The practical exercise will be individual. Preparation: Decide on a new or existing research project to work with during the practical exercise, and start thinking of what the potential long term use of future/existing results could look like.

Connecting Research with Infrastructure using Training activities – a brainstorming exercise
Jessica LindvallNina Norgren

This workshop will provide practical knowledge around research impact and a useful tool to structure your thoughts. The tDo you as a SciLifeLab groupleader have ideas on how to connect Research with Infrastructure using Training? Are you as an expert within your specific domain engaged and enthusiastic regarding training and education? Do you like to contribute to training and education for the life science community and train the next generation? If it is a yes to any of these question we would like to welcome you to this Brainstorming exercise. Here we want to find engaging ways using Training to further connect the SciLifeLab Research community with the Infrastructure activities. We believe Training activities, which in the widest sense could mean building a community of trainers across Research and Infrastructure to the ideas of specific course topics where Resaerch and Infrastructure contribute to the activity, is one of the paths to build synergies across SciLifeLab. With this Groupleader retreat at Aronsborg, we take the opportunity to invite SciLifeLab groupleaders i.e. PIs and Heads of Unit to this brainstorming exercise to get the best ideas on the table on how to connect Research with Infrastructure and capitalize on both pillars expertise and training enthusiasm. Welcome!

How can SciLifeLab group leaders and infrastructures contribute to the clinical implementation of precision medicine?
Åsa JohanssonJanne LehtiöPäivi ÖstlingEva Berglund

Precision medicine (PM) has potential to significantly improve human health, and is an important part of the Swedish life science strategy as well as the SciLifeLab roadmap for 2020-2030. The vision of the SciLifeLab PM Capability is that SciLifeLab plays an important role in the implementation of PM in Sweden by providing cutting-edge technologies to world-leading PM research and to clinical trials. In this workshop, we will discuss the proceedings of SciLifeLab’s roadmap for PM and collect your input. Topics to be discussed include the definition of PM research, and how the PM Capability can contribute to enable cutting-edge PM research at SciLifeLab.

Campus Solna
Per Ljungdahl

SciLifeLab Campus Solna (CS) is a shared extra campus of the Stockholm Trio universities and the largest SciLifeLab site. CS was established twelve years ago and has been a great success. But, what about the future?In 2019 our IAB pointed out that an active and exceptional research environment at CS is critical to the future success of SciLifeLab, and this notion was reemphasized in their most recent report. Additionally, the IAB pointed out that CS has an important role in educating researchers in the fine art of analyzing biological problems that can only be answered using high data-density approaches.There are many challenges facing CS and maintaining an exceptional research and educational environment depends on constant input from the community and an active leadership in tune and well-synchronized with the core activities.After a brief introduction, together we will seek to identify the principles that should be guiding and to establish common goals required to shape a concrete vision for the CS of the future. Specifically, the goals we define should have a steering function, support planning activities, be motivational and useful when evaluating progress.

Merit assessments DORA
Katarina Gustafsson

Stockholm university signed the DORA declaration in 2019. The workshop, lead by Katarina Gustafsson, Excecutive Officer at the office of Science (SU), will focus on how employment of teaching positions and promotion matters are handled at SU, based on DORA. How are these processes prepared and implemented, ie how are experts appointed, what instructions go out to experts, the current premises under which employment committees and promotion committees work, balance between scientific and pedagogical skills.

Data Centre
TBA

TBA

From research to innovation and commercialisation – how to get funding and support
13:00Welcome words and presentationsAlexandra Patriksson, SciLifeLab13:05An overview of the Swedish innovation support system and presentation of Vinnova, including relevant calls and funding opportunitiesLars Hammarström, Vinnova13:15Presentation of WALP, including your offer to KAW-funded research and researchersSandor Albrecht,13:25Presentation of BII, including your programmes and callsMatthias Wulf, BII13:35Questions

CONTACT FOR PRACTICAL QUESTIONS

Campus Solna Seminar - Emelie Flaberg and Charlotte Stadler
2022-06-16 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to 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 the alpha and gamma buildings. The format will be 2 short 15 min talks (1 speaker from alpha and 1 from gamma), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-12:50 and in Air&Fire, SciLifeLab Stockholm.

Towards precision treatment of advanced bladder cancer – characterization of the cellular landscape by multiplex immmunofluoresence

Emelie Flaberg, Päivi Östling-group, Alpha 4

An update from the Spatial Proteomics facility.

Charlotte Stadler, Spatial Proteomics, Alpha 2

SciLifeLab BII pitch days
2022-06-16 14:00 - 2022-06-17 12:00 | Online event via Zoom
SciLifeLab is offering Swedish researchers the opportunity to pitch their innovative ideas to a team of business developers from the Danish BioInnovation Institute. The purpose is to get feedback and guidance on your idea and to learn if your project could be a fit for their different innovation programs and funding instruments.

BioInnovation Institute (BII) is an international commercial foundation with a non-profit objective supported by the Novo Nordisk Foundation. BII operates an incubator to accelerate world-class life science innovation that drives the development of new solutions through the creation of life science start-ups for the benefit of people and society. BII offers help to early-stage projects and start-ups in health tech, bio-industrials and therapeutics through their various programs. They can provide funding up to 2.5m euros. They are open for applications twice a year. September is the next deadline for applications.

Two pitch days will be offered:

June 16, 14:00-17:00

June 17, 10:00-12:00

A pre-selection will be made by BII among the researchers and projects registering their interest for the pitching. Projects selected to pitch will be given a time slot of 30 minutes on the preferred day. The slot should be used for a 15 minutes pitch followed by 15 minutes discussion.

Registration of interest

Deadline to register is June 12, 23:59.

For questions, contact externalrelations@scilifelab.se
