SciLifeLab

AI-driven genomic precision diagnostics in hematologic malignancies
2022-04-29 14:00 - 15:00 (Europe/Stockholm) | Online event via Zoom
In this webinar, jointly organized by the Clinical Genomics platform and Genomic Medicine Sweden, Dr. Aziz Nazha will present AI-based solutions to improve the diagnosis, prognosis, and selection of therapy in hematologic malignancies. The talk will also cover the clinical implication of AI/ML in diagnostic hematology, current challenges and potential future opportunities.

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Host: Thoas Fioretos, Director Clinical Genomics platform

Short bio: Aziz Nazha, MD, is currently a Global Tech Business Development for Healthcare Solutions at Amazon Web Services. Prior to joining Amazon, Dr. Nazha was the director of the Cleveland Clinic Center for Clinical Artificial Intelligence and an Associate Medical Director at Enterprise Analytics. He is also an internationally recognized expert in treating patients with leukemia. His research focuses on the use of artificial intelligence, machine learning, and deep learning to translate genomic and complex healthcare data into useful clinical tools that can improve patient outcomes.

Matchmaking Event – Data Science and Medical/Clinical Research
2022-04-28 17:00 - 19:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to a matchmaking event between researchers within Data Science and Medical/Clinical research at KTH and Region Stockholm. The event is related to the project call: Health, Medicine and Technology 2023.

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Region Stockholm and KTH opened the yearly call for collaboration in Health, Medicine and Technology 14 April, 2022. A key requirement to apply for this call is that one of the partners should be from KTH and one from Region Stockholm. With this event, we hope to encourage collaborations between experts in data science and clinical research, at KTH and Region Stockholm. The event is open for all researchers from KTH and from Region Stockholm who are eligible to submit a grant proposal for the Health, Medicine and Technology Project Call. Postdoctoral researchers who can be co-PI are also encouraged to attend the event. Should you have any questions, please contact: lifescienceplatform@kth.se ordigitalizationplatform@kth.se

The event is organised by the KTH Life Science Platform and KTH Digitalization Platform

Campus Solna Seminars
2022-04-28 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.

Casper Winsnes

Emma Lundberg, alpha 2

Multi-scale mapping of cell structures using protein images and interactions

Sergio Perez Conesa

Lucie Delemotte, gamma 3

K-Ion channel inactivation and lipid dependence through free energy surfaces

Nordic Precision Medicine Forum
2022-04-28 08:00 - 2022-04-29 17:00 | Hotel Birger Jarl, Birger Jarlsgatan 61, Stockholm, Sweden
Just prior to the pandemic Sweden launched its first ever national Life Science Strategy in eight priority areas covering the strengthening of academic research, facilitating collaboration between academia and industry, attracting more industry initiated clinical trials, and the continuous skills development needed for precision medicine and highly advanced production of pharmaceuticals and medtech devices. Across the Nordic countries precision medicine and technology developments continue at pace, truly putting them in a favourable position when it comes to taking on the opportunities and challenges of implementing precision medicine, with its promise to really transform future healthcare as well as the entire life science sector.

Since 2016 we have convened the regions leading scientists, healthcare practitioners, and industry pioneers at our annual meeting. For 2022 you can expect a whole lot more interaction as we finally get back to in-person events.

Read more

We very much hope to see you in Stockholm in April 2022 and hope that you and your loved ones remain safe and healthy throughout these troubling times.

Developmental origins of cell heterogeneity in the human lung
2022-04-27 14:00 - 15:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
HDCA Seminar Series 2022 | Lung
Christo Samakovlis and Alexandros Sountoulidis
The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a first comprehensive topographic atlas of early human lung development. We report 83 cell states, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatial transcriptomics into a web-based, open platform for interactive exploration. To illustrate the utility of our approach we show distinct states of secretory and neuroendocrine cells, largely overlapping with the programs activated either during lung fibrosis or small cell lung cancer progression. We define the origin of uncharacterized airway fibroblasts associated with airway smooth muscle in bronchovascular bundles, and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

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Human developmental cell atlas (HDCA) is the Swedish effort within the human cell atlas (HCA), one of the largest international scientific projects. The project aim is to create a comprehensive molecular atlas of human prenatal development at the molecular resolution using state-of-the-art multi-omic technologies such as single-cell RNA-seq, Spatial Transcriptomics, in situ sequencing in order to provide deeper insight into how variations and deviations contribute to health and disease.
The HDCA Seminar Series 2022 invites you to join us on a journey of early human organogenesis of several organs at the single-cell and spatial resolution. Seminars will be held at SciLifeLab Gamma building on Wednesdays at 14:00 or 15:00 and also via Zoom. After each seminar, we will have up to 30 min round up discussions with the speaker on how you can contribute to the atlas!
Warm Welcome!

registration

Workshop on Data Visualization in R - Lund
2022-04-27 08:00 - 2022-04-29 17:00 | Retina D227, Biologihuset, Sölvegatan 35, Lund, 223 62
National course open for PhD students (prioritized), postdocs, researchers and other employees within all Swedish universities interested in learning to plot using different packages in R.

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

Responsible teachers: Lokeshwaran Manoharan, Louella Vasquez, Markus Ringner

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

aPPLY HERE

COURSE WEBSITE

Important dates

Application open: Jan 31, 2022

Application deadline: Mar 18, 2022

Confirmation to accepted participants: Mar 25, 2022

Course fee

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

*Please note that NBIS cannot invoice individuals

Course description

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

Course content

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

In particular, you will learn:

· how to format the data necessary for ggplot

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

· how to make PCA plots in ggplot

· how to use R packages for heatmaps

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

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

· how to make interactive plots in R using Rshiny

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

Learning outcomes

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

· handle data in R for visualizations

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

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

· write your own simple Rshiny app

· deploy Rshiny apps in public servers.

Entry requirements

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

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

Selection criteria

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

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

Measuring metabolites, the building blocks of biology
2022-04-26 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 April 26th, 12:00-13:00, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

“Measuring metabolites, the building blocks of biology”

by Annika Johansson, Head of the Swedish Metabolomics Centre (SMC) facility.

The presentation will give an introduction to metabolomics and small molecule analysis by mass spectrometry. We will present our different services and also give examples of different research projects in which SMC has been involved.

Learn more about the Swedish Metabolomics Centre on its homepage.

Sign up (latest by April 25th, 10 a.m.) for on-site participation or follow online via Zoom: https://umu.zoom.us/j/63138997026

registration

New developments in upstream bioprocessing technologies seminar
2022-04-26 09:30 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Presentation och demonstration av nya single use bioreactors (SUB) för mammalieceller.

register to attend

Program:

9:30-10:15 Matthijs Neimeijer, Cultivating red blood cells in singe-use bioreactors

10:15-10:45 Fika och demonstration

10:45-11:30 Michel Kensler, Comparisons in scale up and down scale

11:30-12:00 Questions

NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
2022-04-25 09:00 - 2022-04-29 15:30
NBIS / ELIXIR-SE course is open for PhD students, postdocs, group leaders and core facility staff interested in making their computational analysis more reproducible. International applications are welcome, but we will give approximately half of the participant slots to applicants from Swedish universities at minimum, due to the national role NBIS plays in Sweden.

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

Responsible teachers: John Sundh, Erik Fasterius

Contact information: edu.trr@nbis.se

APPLICATION

COURSE WEBSITE

Important dates

Application open: Feb 1, 2022

Application deadline: Mar 25, 2022

Confirmation to accepted participants: Apr 1, 2022

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 2,000 SEK.

*Please note that NBIS cannot invoice individuals

Course description

One of the key principles of proper scientific procedure is the act of repeating an experiment or analysis and being able to reach similar conclusions. Published research based on computational analysis, e.g. bioinformatics or computational biology, have often suffered from incomplete method descriptions (e.g. list of used software versions); unavailable raw data; and incomplete, undocumented and/or unavailable code. This essentially prevents any possibility of attempting to reproduce the results of such studies. The term “reproducible research” has been used to describe the idea that a scientific publication based on computational analysis should be distributed along with all the raw data and metadata used in the study, all the code and/or computational notebooks needed to produce results from the raw data, and the computational environment or a complete description thereof.

Reproducible research not only leads to proper scientific conduct but also provides other researchers the access to build upon previous work. Most importantly, the person setting up a reproducible research project will quickly realize the immediate personal benefits: an organized and structured way of working. The person that most often has to reproduce your own analysis is your future self!

Course content

Topics covered:

Good practices for data analysisVersion control and collaborative code developmentPackage and environment managementWorkflow managementDocumentation and reportingContainerized computational environments

Learning outcomesBy the end of the course the student will be able to:

Organize and structure computational projectsTrack changes and collaborate on code using GitInstall packages and manage software environments using CondaStructure computational steps into workflows with Snakemake and NextflowCreate automated reports and document their analyses with RMarkdown and JupyterPackage and distribute computational environments using Docker and Singularity

Entry requirements

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

Familiarity with using the terminal (e.g. be familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.)A computer with a webcamYou will be asked to install the video conferencing software zoom (https://zoom.us/) to be able to participate in the courseSome knowledge in R and/or python is beneficial but not strictly required

Selection criteria

The course can accommodate 20 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance. Academic affiliated registrants are prioritized prior to participants from the industry.

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

[Clinical Talks] Introduction to AI-driven image analysis in pathology: from preclinical research to clinical diagnostics
2022-04-22 09:00 - 09:30 | Online event via Zoom
Dr. Sami Blom leads Aiforia’s application development team with an ambition to build impactful image analysis solutions to advance histopathology. He has a background in the fields of translational cancer research and pathology and he has extensive expertise in staining and imaging methods for histology specimens. Dr. Blom joined Aiforia in 2016 to develop and advance Aiforia’s applications, products and services.

Introduction to AI-driven image analysis in pathology: from preclinical research to clinical diagnostics

Aiforia equips pathologists and scientists with powerful deep learning artificial intelligence for translating images into discoveries, decisions, and diagnoses. The cloud based Aiforia software aims to escalate the efficiency and precision of preclinical and clinical medical image analysis from oncology to neuroscience and more. Deep learning artificial intelligence enables increased speed, accuracy and consistency in medical image analysis.

Aiforia was founded in 2013 and our mission is to provide the highest quality solutions for AI-assisted image analysis to enable personalized and democratized care for patients. Year 2021 was historic for the company: Aiforia was listed on Nasdaq Helsinki First North Market Finland in December 2021. In connection with the listing, the Company raised approximately 29 million euros in gross assets. This, together with the B-financing round implemented earlier in the same year, provides a strong foundation for Aiforia’s growth.

Register to receive zoom link

“Clinical Talks” has been renewed for yet another exciting, innovative, and enlightening season. This season will focus on sustainable innovations within Life Sciences, that have the potential to contribute to a better climate friendly future for our future generations. Also new this year is that the seminar is co-organized in a collaboration between SciLifeLab and KI Innovations .

Season 5, will be held September 2021 until March 2022 with scheduled Talks, during Friday mornings 09-09:30 am via ZOOM (with some time-zone friendly adjustments for our international speakers). Each session consists of a talk given by our invited speaker followed by Q&A. The seminar is an open educational seminar series for our ever-expanding Life Science community.

FAIRPoints-Things you need to know about Data Access Statements
2022-04-21 15:00 - 16:00 | Online event via Zoom
Location: Online via Zoom

See Event in your Time Zone

Speaker: Juliane Schneider & Chris Erdmann

Speakers Juliane Bio, Chris Bio

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.

Data access statements (DAS), also known as data availability statements, are key elements that can be used in multiple diverse disciplines and have a huge impact in providing essential information as it outlines where and how any underlying data may be accessed and reused, listing specific restrictions (if any) and authorization requirements. It is therefore integral to the FAIRification process.

Join us in this talk to discover how an effective data access statement should look like!

Register here

Sign up for future events here

Twitter: @FAIR_Points

Career in Life Science - MTLS Networking Event
2022-04-21 14:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
The MTLS Alumni Network is a student-led initiative to connect current students and alumni of the Joint Master’s Programme in Molecular Techniques in Life Science (MTLS). The programme was created through a collaboration between Karolinska Institutet, Stockholm University, and KTH Royal Institute of Technology. Launched in 2015, it has since reached a network of over 150 alumni and 60 current students.

At the ‘Careers in Life Science – MTLS Networking Event’, you will meet recruiters from biotech and pharma as well as representatives from diverse life science companies. It is a great opportunity for current students and graduates of MTLS to network and to look for employment post-grad, summer internships, and even master thesis projects. There will also be speakers from “alternative” life science career paths, such as science communicators, facility managers, and policy makers. Getting to engage with this unique “human library” is sure to inspire you if what you are looking for is an unconventional career path in the life sciences!

Agenda

14:00-17:00 Networking, mingle with recruiters and representatives, and “human library” speakers

15:00-16:00 Zoom Session with Illumina and Randstad in Water

Read more about the program

Campus Solna Seminars
2022-04-21 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.

Olena Berkovka

Janne Lehtiö, alpha 1

To stay or to leave? – (p)ppGpp signaling determines bacterial lifestyle decisions during distinct starvation conditions

Ruben Soares

Mats Nilsson, gamma 4

Lock on target: padlock probes and rolling circle amplification towards next-gen pathogen diagnostics and genotyping at the point-of-care

WGS & WTS – gamechangers in AML and ALL diagnostics
2022-04-21 11:00 - 12:00 | Online event via Zoom
Speaker: Manja Meggendorfer, Head of Molecular Genetics at MLL Munich Leukemia Laboratory

The webinar is jointly organized by the Unit of Clinical Genetics at the Department of Molecular Medicine, KI, the Clinical Genomics platform and Genomic Medicine Sweden.

Register to receive zoom link

Campus Solna Seminar - Martin Kosar and Ryan Hull
2022-04-14 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.

Martin Kosar

Jiri Bartek-group, alpha 5

TRole of nucleoporin Tpr in the maintenance of genomic integrity

Ryan Hull

Vicent Pelechano-group, Gamma 5

5PSeq-TS: Capturing the degradome in humans and single-cells

SciLifeLab COVID-19 seminar: Jinal Bhiman and Vicent Pelechano
2022-04-13 15:15 - 16:45 | Online event via Zoom
Topic: Detection of virus

The second SciLifeLab COVID-19 seminar this spring starts with Jinal Bhiman, PhD and Scientific lead for the Global Immunology and Immune Sequencing South Africa (GIISER-SA), talking about SARS-CoV-2 viral evolution in South Africa and hybrid immunity profiles. Vicent Pelechano, PhD, SciLifeLab and Wallenberg Academy Fellow and Principal Researcher at Karolinska Institutet, then continues the seminar with his talk on Development of LAMP-based point of care strategies for simplified SARS-CoV-2 detection

Schedule

15:15- 16:00 – SARS-CoV-2 viral evolution in South Africa and hybrid immunity profiles Jinal Bhiman, PhD and Scientific lead for the Global Immunology and Immune Sequencing South Africa (GIISER-SA)16:00-16:45 – Development of LAMP-based point of care strategies for simplified SARS-CoV-2 detection Vicent Pelechano, PhD, SciLifeLab and Wallenberg Academy Fellow and Principal Researcher at Karolinska Institutet

Registration is mandatory to get the Zoom link for the event

REGISTRATION

BIOS & ABSTRACTS

γδSTO workshop – Mini-symposium of Stockholm’s γδ T cell community
2022-04-12 00:30 - 01:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
A workshop on the May 5, on gamma delta T cells for our scientific community in Stockholm. Different labs from SciLifeLab, KI (Solna and Fleminsberg) and Stockholm University are invited.

Program:

13:15 / Introduction

Taras Kreslavskiy(KI): Transcriptome-wide screen for γδTCR specificities identifies a novel superantigen-like ligand candidate for Vγ7 γδTCRs

Lola Boutin (KI): Evaluation of the potential of using non-conventional (NC) T cell- based immunotherapy in Medulloblastoma

Patrick Sandoz (KTH): Dynamics of Vγ9Vδ2 T cell cytotoxic functions at the single-cell level

14:30 / Coffee break

Faisal Alagrafi (KI):γδ T cells reconstitution in long term survivors after hematopoietic stem cell transplantation

ClàudiaArasa(SU): Functional characteristics of γδ T cells in prematurity and early life, and their response to staphylococcal enterotoxins

Julius Lautenbach (KI): Systems level analysis indicates an interplay between cytophilic antibodies, monocytes, and γδ T cells in malaria tolerance

16:15 / Drinks and Discussion (γ2 lunchroom)

Decreased levels of oxygen radicals cause autoimmune disease.
2022-04-11 15:15 - 16:15 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Prof. Rikard Holmdahl

Karolinska Institute, Sweden

Register HERE

Rikard Holmdahl made his PhD (1985) and MD (1987) at Uppsala University. Professor in medical inflammation research Lund University 93-07. Professor at Karolinska Institute from 2008

Venue: Hybrid meeting – Trippelrummet, Navet and zoom

Title of the seminar: Finding and understanding genes associated with common diseases; decreased levels of oxygen radicals cause autoimmune disease

A long-standing challenge is to understand which genes that cause common complex diseases, such as rheumatoid arthritis, atherosclerosis or cancer, and thereby understand the disease causes. However, even though we know the human sequence and can genotype millions of individuals it is very difficult to conclusively identify the single nucleotide variants that cause the diseases. We have taken another approach through animal models. Both genetics and diseases show similarities with humans, and we have shown that it is possible to not only identify the loci associated with disease but also exactly position the polymorphic nucleotides for common autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE).

I will focus on the first gene that we cloned, Ncf1, which regulate immune tolerance through different levels of oxygen radicals, or more precisely hydrogen peroxide. It is the major gene causing SLE and is important in Sjögren’s syndrome and RA and most likely most autoimmune disease.

To understand the role of Ncf1 is also complicated as peroxide seem to regulate many different pathways leading to autoimmune diseases. I will discuss how we think it regulates RA and SLE but also how it could explain our normal behaviour, thus explaining why Ncf1 variants are common in both rat and human population.

Read more about ikard Holmdahl´s research http://ki.se/en/mbb/research-division-of-medical-inflammation-research

[Clinical Talks]Seeing is believing, unraveling the discovery of a centimeter-long macro-bacteria
2022-04-08 09:00 - 09:30 | Online event via Zoom
On April 8, Dr. Jean-Marie Volland, Scientist at Berkeley Lab and Laboratory for Research in Complex Systems (LRC Systems), and Shailesh Date, CEO of LRC Systems (Adj. Assoc. Professor at UCSF),will talk about their recent discovery and characterization of the macro-bacteria Ca. Thiomargarita magnifica. The threadlike single-cell bacterium, commonly found in the Caribbean Mangroves, is visible to the naked eye, and able to grow up to 2 centimeters in length. In a recent effort, an international team studied the “magnificent” organism using fluorescence, x-ray, and electron microscopy, and fully sequenced the genome.

Through a unique strategy of polyploidy, along with compartmentalization of genomic material and protein synthesis in membrane-bound organelle, the organism has been able to grow orders of magnitude over the theoretical limits for bacterial cells. The traditional view, which has almost become dogmatic, is that prokaryotes (bacteria and single-cell microbes) have free-floating DNA, whereas eukaryotes (yeast and multicellular organisms) package their DNA in a nucleus. This new model organism blurs that line and offers amazing potential insights into biological evolutionary strategies, many of which are as yet unexplored. One can only wonder at the type and number of new clinical innovations that will emerge as we continue exploring the frontiers of biology and biological complexity.

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Jean-Marie Volland is a Scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and at Laboratory of Research in Complex Systems (LRC Systems) in Menlo Park California. He obtained his PhD at the Université des Antilles, in the French West Indies, studying biology and tropical ecology in the Indian Ocean and Caribbean. Jean-Marie then continued to pursue his Postdoctoral research at University of Vienna, Austria during 2012-2017. Initially in the Monika Bright´s Lab at the Department of Limnology and Biological Oceanography studying symbiosis in chemosynthetic ecosystems, and then also in the Silvia Bulgheresi´s Lab at the Archea Biology and Ecogenomics Division studying tropical ecology pathways of microorganisms. In 2018 Jean-Marie joined the Berkeley Lab as an affiliate Scientist to continue working on uncovering highly divergent forms of life together with LRC Systems. The story of the discovery of Thiomargarita magnifica dates back a decade ago, when marine biologist Olivier Gros, from the Université of Antilles, first discovered microbial filaments on leaves buried in the mangrove of Guadeloupe. Gros lab member and microbiologist colleague Silvina González-Rizzo identified it to be in fact be one bacterium. Jean-Marie, together with his Université of Antilles colleagues and LRC Systems set forth to methodologically study and categorize the new organism.

Shailesh Date is the CEO and Founder of Laboratory for Research in Complex Systems (LRC Systems). He is also Adjunct Professor of Biology at San Francisco State University and an Associate Adjunct Professor of Epidemiology and Biostatistics at the University of California San Francisco (UCSF). Shailesh obtained his PhD at The University of Texas, Austin in Molecular Biology in 2004, and completed a postdoctoral fellowship at the University of Pennsylvania School of Medicine in 2008, focusing on computational biology of infectious diseases. Between 2008-2015, Shailesh worked as a scientist at Genentech, and during a brief sabbatical in 2013, completed the prestigious Ignite Program at the Stanford Graduate School of Business. He left Genentech in 2015 to join Global Viral (GV), a nonprofit organization with roots in public health research. He founded the LRC Systems in 2019, transforming Global Viral into a new organization focused on complex systems research in a wide variety of areas.

About Global Viral and LRC SystemsGlobal Viral was founded by Nathan Wolfe in 2007 as the Global Viral Forecasting Initiative (GVFI), focusing on public health and field epidemiology while supporting programs like HIV prevention run by USAID, WHO and other similar organizations in Africa and South East Asia.In 2012, the organization split into Metabiota, a for-profit company that took over epidemiology and forecasting-related work, and Global Viral, a nonprofit that retained and concentrated on basic research.In 2019, under the leadership of a new Chief Executive and a new board, the organization reoriented its research towards complex systems and adopted the “Laboratory for Research in Complex Systems (LRC Systems)”, which was initially founded as a new division within GV, as its new name.https://www.lrc.systems

“Clinical Talks” has been renewed for yet another exciting, innovative, and enlightening season. This season will focus on sustainable innovations within Life Sciences, that have the potential to contribute to a better climate friendly future for our future generations. Also new this year is that the seminar is co-organized in a collaboration between SciLifeLab and KI Innovations .

Season 5, will be held September 2021 until March 2022 with scheduled Talks, during Friday mornings 09-09:30 am via ZOOM (with some time-zone friendly adjustments for our international speakers). Each session consists of a talk given by our invited speaker followed by Q&A. The seminar is an open educational seminar series for our ever-expanding Life Science community.

Campus Solna Seminar Series - Joel Hallgren
2022-04-07 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.

Joel Hallgren

Kristina Jonas-group, gamma 5

To stay or to leave? – (p)ppGpp signaling determines bacterial lifestyle decisions during distinct starvation conditions

Sustainability in Science: My Green Lab
2022-04-05 15:30 - 16:30 | Online event via Zoom
Cristalle Ruiz

Market Development Representative, My Green Lab

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.

My Green Lab is an internationally recognised non-profit organisation run by scientists aimed at introducing sustainable laboratory practices across the globe. We can find out more about My Green Lab’s mission, the highly successful ‘Ambassador programme’ and other resources available from Cristalle Ruiz, Market Development Representative of My Green Lab. The talk is intended to provide valuable insight into sustainability in science and the steps that could be implemented in our labs.

Cristalle Ruiz is the Market Development Representative for My Green Lab, the leading global nonprofit supporting laboratory sustainability. Her role is to bring awareness to the benefits of sustainable practices across laboratories and manufacturers of laboratory products through My Green Lab’s market-leading programs. In her previous position, Cristalle advocated for implementing renewable energy in the United States. She holds a bachelor’s degree in Environmental Business and Economics from Rutgers University. She will discuss and provide resources to build a culture of sustainability in the science industry.

PhD & Postdoc council (phd-council@scilifelab.se)

Unbiased characterization of cells using the single-cell facility
2022-04-05 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”, Johan Henriksson, Research fellow at the Dept. of Molecular Biology & Molecular Infection Medicine Sweden (MIMS), will present the Single-cell facility. If you want to learn how you can benefit from single-cell analysis, join for 30 min presentation of cases & opportunities, followed by 30 min discussion of practicalities & project design.

Presenter:Johan Henriksson, Dept. Molecular Biology / Molecular Infection Medicine Sweden (MIMS)

Registration:To register your physical attendance and reserve your free sandwich, please go to the Registration Link

Registration

Physical Attendance:Glasburen seminar roomChemical Biological Centre (KBC) BuildingUmeå University

Online Attendance:You can join the seminar on Zoom:https://umu.zoom.us/j/63138997026

BioImage Analysis support - Call4Help
2022-04-05 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, April 5, 2022, 9.00-12.00. Deadline for application: Friday, April 1, 2022.

Introduction to Data Management Practices
2022-04-05 08:00 - 2022-04-07 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
National course open for PhD students, postdocs, researchers and other employees within all Swedish universities. This course will introduce important aspects of Research Data Management through a series of lectures and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data.

Note: We follow the recommendations and guidelines from Swedish authorities and Folkhälsomyndigheten. The course is designed to be an interactive face-to-face event. However, we follow the situation carefully and will deliver the course online if needed.

COURSE WEBSITE

APPLICATION

Contact: edu.intro-dm@nbis.se

Important dates

Application is open now

Application closes: 2022-03-15

Confirmation to accepted students: 2022-03-21

Course fee

1500 SEK paid by invoice to NBIS. This includes lunches, coffee and snacks. Please note that NBIS cannot invoice individuals.

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.

Entry requirements

No previous programming experience is required but you are required to bring your own laptop with the required software pre-installed.

Installation instructions will be provided before the course starts.

Course content

Topics covered will include:

• Open Science and FAIR in practice

• Organising data, files and folders in research projects

• Versioning data, documents and scripts with Git

• Describing data with metadata

• Cleaning tabular data and metadata with OpenRefine

• Submitting data to public data repositories

• Writing basic recipes for data analysis and visualisation with R

(Links to an external site.)

Learning objectives:

• To get acquainted with, and reflect upon, the principles of Open

Science and FAIR

• To understand the importance of metadata, and how it affects

“FAIRness”

• To learn how to organise files to make project work more efficient

• To learn to clean up messy tabular data and metadata

• To learn how to find, and submit to, relevant public repositories for

data publication

• To learn to apply simple version control practices on files

• To learn to start using R to analyse data

Information Meeting: Call for therapeutic oligonucleotide projects
2022-04-04 14:00 - 15:00 | Online event via Zoom
This digital information meeting will be held April 4, 2022 at 14.00–15.00. At this meeting, there will be a presentation of the call and you as an applicant will have the opportunity to ask questions about the call and the application process.

register here to receive zoom link

Apply in the call here

The mission of the Drug Discovery and Development Platform at SciLifeLab is to support researchers in developing new drugs, transforming academic ideas into new treatments. To this end, the DDD platform provides state-of-the-art drug discovery technologies to scientists across the country. Therapeutic oligonucleotides are a recent addition to the DDD platform’s capacity, complementing the previous focus on small molecule and protein drugs. Oligonucleotide drugs have different modes of action, and a potentially faster development compared to other drug types. Therapeutic oligonucleotide development is supported by the OligoNova Hub, based in Gothenburg and part of SciLifeLab’s DDD platform.

In this call, we are looking for project ideas for new therapeutic oligonucleotides that can be developed at DDD and OligoNova Hub. Approved project ideas will be developed in close collaboration between the academic laboratory and drug development experts at DDD and OligoNova Hub. The costs of the projects will mainly be covered by OligoNova, but academic partners will be expected to contribute by paying for reagent costs.

The call is open for scientists with a doctoral degree at a Swedish university or higher institution. English should be used when filling out this application. You are responsible for ensuring that the application is complete. Incomplete applications will not be processed. Attach only material that we explicitly request. SciLifeLab DDD/OligoNova will not accept additional information after the closing date for applications, except for information we ourselves explicitly request. Applications are reviewed by a review committee with international representation.

Call Announcement FlyerDownload

The call is open March 28, 2022 to May 13, 2022.

Information meeting – Call for Therapeutic Oligonucleotide Projects at OligoNova Hub / SciLifeLab DDD
2022-04-04 14:00 - 15:00 | Online event via Zoom
The mission of the Drug Discovery and Development Platform at SciLifeLab is to support researchers in developing new drugs, transforming academic ideas into new treatments. Therapeutic oligonucleotides is a recent addition to the Drug Discovery and Development platform’s capacity, available through the OligoNova Hub in Gothenburg.

Now, the first call for therapeutic oligonucleotide projects is opening (March 28 – May 13, 2022).

At this online information meeting, there will be a presentation of the call and you as an applicant will have the opportunity to ask questions about the call and the application process.

The call text will be published via the SciLifeLab and OligoNova websites on March 28.

Register here

OligoNova Hub is a national facility providing academic researchers in Sweden with support and capabilities to convert ideas and discoveries into potential new oligonucleotide therapies. OligoNova Hub is part of the SciLifeLab Drug Discovery and Development platform, and is located at the AZ BioVentureHub campus in Gothenburg. The OligoNova Hub offers full capacity for the design, synthesis, evaluation and optimization of therapeutic oligonucleotides to academic researchers. The hub has been made possible through support from the Knut and Alice Wallenberg foundation, SciLifeLab, University of Gothenburg, Region Västra Götaland, and a donation from Carl Bennet.

Campus Solna PhD&Postdoc Seminar Series – Emma Persson and Hjalmar Brismar
2022-03-31 12:00 - 12:50 | 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.

InParanoid-DIAMOND for Big Data orthology detection

Emma Persson

Erik Sonnhammer group, gamma 7

Na+,K+-ATPase forms Oligomers in The Plasma Membrane of Living Cells

Hjalmar Brismar (gamma 3)

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

Please select a valid form

Legal aspects of SARS-CoV-2 genome data processing and sharing across Europe
2022-03-30 10:00 - 12:00 | Online event via Zoom
Location: Online via Zoom

This online workshop will showcase how to address the legal aspects of mobilising SARS-CoV-2 genome data across Europe and is specifically designed to cater to organisations acting as regional or national coordinators tasked with brokering data across healthcare systems, research infrastructures and publicly accessible data sharing platforms. It is organised by ELIXIR CONVERGE WP9 in collaboration with SciLifeLab and includes speakers on GDPR and local legislation as well as presentations of solutions adopted and developed by project members.

Participants should be aware that the workshop will not provide legal advice. The workshop will provide participants with examples of legal contexts for data processing and contracts between organisations within a selection of national legal frameworks. The workshop also aims to illustrate how legal aspects come into play when genetic, personal and phenotypic patient information is processed, masked and shared across data producers, data brokers and data sharing platforms.

Before the workshop, participants will be encouraged to answer a short survey related to the workshop’s content.

Registration is required to receive the Zoom link.

Workshop outline (10:00–12:00)

Introduction and survey results (10 min)Legal aspects of mobilising SARS-CoV-2 genome data (20 min)Examples of implementations in organisations across Europe (20 min)Break (10 min)Examples of implementations in organisations across Europe (30 min)Sharing data through the European COVID-19 data portal (20 min)Closing remarks (10 min)

Register here

NGI and Nanopore; tech update seminar
2022-03-30 09:30 - 12:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Note! The event was originally planned for January but was postponed. This is the new date!

National Genomics Infrastructure has now increased capacity for methylation calling, direct RNA sequencing, sequencing of ultra-long fragments to resolve structural variation. Do you want to hear more? We invite you to an event where you will be able to hear the latest tech updates from Oxford Nanopore Technologies as well as hearing from NGI and the following local and international users about their research using nanopore sequencing.

The event will be a hybrid event with the possibility to attend on-site in Trippelrummet, Navet, BMC, Uppsala or via zoom. This event is free to attend, but registration is required.

Registration

AGENDA

09:30Welcome09:35Introduction to Oxford Nanopore SequencingJakob Ørtvig, Oxford Nanopore Technologies09:50Nanopore sequencing at NGIAnna Petri, National Genomics Infrastructure10:10Coffee break10:40Interrogating the effects of CRISPR-Cas9 genome editing by long-read sequencingIda Höijer, National Genomics Infrastructure11:00Using ONT-sequencing to gain insight into genome structure and functionCarl-Johan Rubin, Uppsala University11:20Developing an end-to-end solution to deliver long read whole genome sequencing for cancerMelanie Tanguy, Genomics England11:40Q&A12:00End of day

Fluorescence In Situ Hybridization (FISH) – Advanced Technologies for Single Cell Visualization and Identification
2022-03-29 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”, Natuschka Lee, Research fellow at the Department of Ecology and Environmental Sciences, UmU, will present the Fluorescence In Situ Hybridization (FISH) infrastructure.

Presenter:Natuschka LeeResearch fellow at Department of Ecology and Environmental Sciences

More information about the infrastructure: Homepage

Registration:To register your physical attendance and reserve your free sandwich, please go to the Registration Link

registration

Physical Attendance:Glasburen seminar roomChemical Biological Centre (KBC) BuildingUmeå University

Online Attendance:You can join the seminar on Zoom:https://umu.zoom.us/j/63138997026
