SciLifeLab

EASI-Genomics stakeholder meeting
2023-03-07 09:00 - 2023-03-08 12:30 (Europe/Stockholm) | Inghesalen, Tomtebodavägen 18a,, Solna, 171 65 171 65, Sweden
EASI-Genomics is an EU-funded consortium of sixteen partners, including eleven of the largest genomic facilities in Europe, which provides easy and seamless access to state-of-the-art DNA sequencing technologies to researchers from academia and industry within a framework that ensures compliance with ethical and legal requirements, as well as FAIR and secure data management (https://www.easi-genomics.eu).

On March 7th-8th, EASI-Genomics will organize a hybrid event for stakeholders from the scientific community (https://www.easi-genomics.eu/stories/events). The event will feature speakers from Transnational Access-user, industry and EASI-Genomics facilities. Participation is free of charge.

Registration

Event homepage

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824110

Networking Meeting Between the Wallenberg Programs WASP-HS and Data-Driven Life Science (DDLS)
2023-03-06 14:00 - 16:00 | Online event via Zoom
The purpose of this on-line 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. The meeting is divided in two parts, one with focus on information, where an upcoming call for seed-money for cross-program research collaborations will be announced and one part with focus on networking.

AGENDA

14:00-15:00 Information

Presentation of WASP-HS, Bodil Formark (Program Coordinator WASP-HS) and DDLS, Erik Kristiansson (DDLS Steering Group)

Information about the new call for seed-money, Erik Kristiansson (DDLS Steering Group)

Presentation of previous call, Francis Lee (WASP-HS Management Team)

Q/A

15:00-15.30 Networking

Possibilites to interact with researchers within the fields of WASP-HS and DDLS Heidi Howard (ELSI-expert DDLS)

Register here

Open Hearing: Gothenburg Phenomics – Proof of Concept Project Invitation
2023-03-01 13:00 - 15:00 | Arvid Carlsson Lecture Hall, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 3, Gothenburg, Sweden
The aim is to establish proof-of-concept for life science research with expressed (pre-)clinical relevance. This will be achieved by forming a closed loop from biomedical research question (initiated by pre-clinical researchers) to returning actionable biological results, in terms of mechanisms and potential biomarkers and targets.

In this open hearing we would like to identify preclinical and clinical research questions where samples and data are available for proof of concept for a combined metabolomics/proteomics/data analysis study. We will coordinate data deliveries from platforms to data storage via inferential analysis and extraction of biomarkers and mechanisms of interest go from compute and back to the biomedical researcher (question owner).

Registration and more information

OpenUC2: From Ideas to Globally Accessible Instruments
2023-02-28 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Benedict Diederich, Leibniz IPHT Jena

Pandemics, extinction of species, and antibiotic crises: These are not dystopian scenarios of the distant future, but current, observable problems that people globally are now trying to deal with. Science is responsible here for guiding the path, researching connections on a global level and disseminating its findings. However, technical expertise and financial investments in laboratory equipment and experiments are often limiting factors. What follows from this is the lack of accessibility to the scientific tools necessary for researching socially relevant topics.

“Frugal Science” thinks of scientific instruments from a whole new perspective. Limited by the available budget and parts, one has to get creative to solve a scientific question posed by society. Following this idea, we have applied this method to the – in many situations – costly field of microscopy to provide a deeper insight into the microcosm for everyone, everywhere. With our modular, open-source optics toolbox UC2 (You.See.Too.), we provide teaching materials in STEM subjects and put powerful optical tools in the hands of those who need them most: Biologists, Chemists, Physicists, Computational scientists, and students. We prove its capabilities as a rapid prototyping tool for optics by rapidly developing a new method to capture large amounts of plankton in 3D using a light sheet and a holographic setup. The “HoLiSheet” costs less than the laptop that processes the data and is fully open-source.

Campus Solna Seminar Series: Matilda Holm and Stefan Wennmalm & Steven Edwards
2023-02-23 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Matilda Holm

Cecilia Williams – alpha 2

Exploring the impact of intestinal ERβ on the colonic immune microenvironment.

Stefan Wennmalm & Steven Edwards

Hans Blom – gamma 3

Single molecule analysis of membrane proteins with FCS-FRET and Expansion microscopy using genetic code expanded bioorthogonal labelling

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

Identification of novel functional and genetic interactions of the Bloom syndrome helicase
2023-02-23 09:30 - 10:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Andrew Blackford, Associate Professor at University of Oxford

MAX IV new users: introduction and updates - Alexandr Talyzin
2023-02-21 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 2023. 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 2023 here.

On February 21st, 12:00-13:00, SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents:

MAX IV for new users: introduction and updates

by Alexandr Talyzin, Associate professor at the Department of Physics, Umeå University

Abstract

The main purpose of my presentation is to encourage more users (physics, chemistry and bioscience) to submit proposals to the MAX IV synchrotron facility. I will provide short summary of available beamlines and access schemes and give some advice related to the preparation of proposals. Some recent research highlights will be used to illustrate the possibilities of MAX IV in all branches of science. The presentation is addressed first of all to new users, but it could be of interest to everybody interested in exploring research possibilities at MAX IV. The next call has a deadline on the 7th of March 2023, and it is now the right time to prepare proposals. Currently, 16 beamlines are opened for standard proposals. Some beamlines are still under construction, and some beamlines are expanding the range of their experimental possibilities with every call. Therefore, it is important to follow updates and learn about current opportunities.

Join for 30 min presentation, followed by 15 min questions.

Registration: Sign up (latest by Monday, 20 February, 10 a.m.) for on-site attendance to reserve your free lunch sandwich:

Registration

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

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

FAIRPoints-FAIRPoints ‘Ask me Anything’ (AMA)
2023-02-21 11:00 - 12:30 | Online event via Zoom
Location: Online via Zoom

FAIRPoints ‘Ask Me Anything’ on Software and Workflows

This event is part of a series of “Ask Me Anything”-style events featuring keynote speakers from the RDA, and EOSC groups focused on RDA activities and EOSC solutions in relation to FAIR implementation and Open practices in Science.

February

The theme of this session is “FAIRPoints ‘Ask Me Anything’ on Software and Workflows.” We will be discussing the FAIRification of software and workflows and how it looks like, the available tools/infrastructures that support this process, why FAIRification is important and how it is applicable to researchers. Speakers include Carole Goble and Paula Martinez.

The events will bring together speakers from the RDA Groups and speakers from a related EOSC service to describe how their work aligns, how it connects to the research community, and how it benefits the research community in a way that is directly related to the implementation of FAIR and Open research practices. The events are beginner-friendly, laid-back, and easy to follow, with moderators driving the discussion, posing questions to our speakers, and inviting audience questions. Finally a selection of questions will be gathered and turned into Google Educational Q&A flashcards (https://schema.org/QAPage) for future reference.

FAIRPoints ‘Ask me Anything’ (AMA) event series on FAIR implementation and Open practices in Science, is hosted by FAIRPoints and supported by RDA, EOSC, FDO, GOFAIR-US & SciLifeLab-DataCentre.

ThemeTypeDateSpeakerModeratorFAIR software and WorkflowsEventFebruary 21st 2023Carole GoblePaula MartinezTBATBAIdentifiersRecordingJanuary 26th 2023Maggie HellströmNabil KsibiMatthew BuysNatasha SimonsPeter WittenbergPatricia HerterichMachine Centric Science PodcastJanuary 2023Christophe Blanchi listen hereDonny WinstonFAIR Data PodcastPodcastJanuary 18th 2023Tibor Kalman and Sven Bingert listen hereRory MacneilRegulatory Processes and GovernanceEventApril 27th 2023TBATBAMachine ActionabilityEventMay 25th 2023TBATBAEquitable and Transparent Access to Information and KnowledgeEventSeptember 28th 2023

Register here

Sign up for future events here

Twitter: @FAIR_Points

Ultrasensitive-and-digital sequencing and infrastructure activities within Genomic Medicine Sweden
2023-02-17 14:00 - 15:00 | Online event via Zoom
During this seminar, Prof. Anders Ståhlberg, Professor in Clinical Genomics at University of Gothenburg, will showcase the applications of ultrasensitive and digital sequencing. Per Sikora, Co-Chair of the Informatics and and Infrastructure at Genomic Medicine Sweden (GMS) as well as part of the GMS management group, will give us an update of the GMS working package related to Informatics and Infrastructure

Read more

The presenters:

Anders Ståhlberg: Professor in Clinical Genomics at GU, has an extensive expertise within cancer, diagnostics and molecular techniques, especially NGS and single cell analysis. Anders leads the Translational Genomic Platform that aims to implement ultrasensitive DNA and RNA analyses in clinical routine

Per Sikora: Co-Head of Bioinformatics and Data Center at GU, Head 1st engineer at the Sahlgrenska University Hospital and Co-Chair of the Informatics and and Infrastructure at GMS as well as part of the management group in Genomic Medicine Sweden

Host/moderator

Marcela Dávila, Co-Head of the Bioinformatics and Data Centre and Head of Clinical Genomics Gothenburg

Campus Solna Seminar Series: Mariam Haffa and Davide Buzzao
2023-02-16 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Mariam Haffa

Brinton Seashore-Ludlow – alpha 4

Cancer – adipocyte interactions: Targetable vulnerabilities in ovarian cancer?

Davide Buzzao

Eric Sonnhammer – gamma 7

A generalized benchmark for all types of enrichment analysis methods.

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

FunCoup network analysis workshop
2023-02-14 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Network biology is a new paradigm to understand the complex interactions of the molecules in an organism using an integrative and systems approach. This workshop is intended for scientists interested in learning more about and applying network analysis in their research. We will describe and demonstrate the comprehensive network database FunCoup (https://funcoup.sbc.su.se/) and show how it can be used to answer various research questions at the systems biology level.

PROGRAM:

1. Introduction to FunCoup and its unique features for analyzing functional coupling between genes/proteins, as well as accompanying analysis tools such as PathBIX and MaxLink.

2. Demonstration of FunCoup and accompanying tools, as well as programmatic usage of FunCoup in an R notebook.

Registration

Link to zoom

TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics
2023-02-14 10:00 - 12:00 | Online event via Zoom
We present TissUUmaps, browser-based tool for GPU-accelerated visualization and interactive exploration of tens of millions of datapoints overlaying tissue samples. Users can visualize markers and regions, explore spatial statistics and quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. TissUUmaps provides instant multi-resolution image viewing, can be customized, shared, and also integrated in Jupyter Notebooks. It is also possible to directly connect spatial markers with markers in feature space, such as UMAP plots, to interactively relate feature space with physical space. TissUUmaps was created in collaboration between BIIF and the Wählby lab. You can read more about it and test the software on its web page: https://tissuumaps.github.io/

During the seminar, we will specifically showcase new features of TissUUmaps 3.1, such as:

HDF5 / AnnData files loading

Network diagram visualization

Multiple datasets displayed on a grid

Plugin engine

The webinar will be given by Christophe Avenel and Fredrik Nysjö.

[Clinical Talks] A co-creation engine for the next Generation Life Science ventures
2023-02-10 09:00 - 09:30 | Online event via Zoom
Bobby Kaura

Seed Investment, Global Entrepreneurial & Ecosystem Development @ Illumina For Startups

Illumina Inc.At Illumina, we’re committed to unlocking the power of the genome, and we know we can’t do it alone. Illumina for Startups is our way of accelerating innovation in the entrepreneurial community by partnering with leading venture capital investors and entrepreneurs to create, launch and grow genomics startups. Together, we’re advancing breakthrough applications in genomics, including therapeutics, diagnostics, agriculture, synthetic biology, software and direct-to-consumer applications.

Illumina Accelerator is a company creation engine co-located with Illumina research and development sites in San Francisco Bay Area and Cambridge, UK. Since inception, Illumina Accelerator has invested in 70+ genomics startups from across the globe, which have collectively raised over $1 billion in venture capital funding. Approximately 93% of Illumina Accelerator investments have gone on to raise additional capital from leading investors.

Other global models to catalyse genomics startups include the following initiatives: Sequoia Capital China Intelligent Healthcare Genomics Incubator powered by Illumina, Illumina for Start-ups Australia, Illumina for Start-ups Singapore, Illumina for Start-ups Grants, and Illumina for Start-ups Networks.

MultiplAI HealthMultiplAI is a biotech startup developing universal genomic screening for cardiovascular diseases using RNA sequencing and machine learning. They are bringing liquid biopsy to cardiovascular disease. They have a proprietary laboratory-validated prototype and are conducting pilot clinical studies aiming to achieve initial clinical validation of their whole-blood liquid biopsy approach in the cardiovascular space. MultiplAI is based in London, UK, with clinical and lab operations in Cambridge, UK, and Buenos Aires, Argentina. MultiplAI Health has attended the Illumina Accelerator program.

Bobby Kaura, MScBobby has supported the creation of Illumina For Startups, a platform and portal for entrepreneurial and ecosystem development initiatives, with startups, entrepreneurs, investors and lifesciences stakeholders. He co-launched Illumina Accelerator Cambridge UK, the flagship initiative under Illumina For Startups, and the second location for Global Illumina Accelerator which is a genomics and VC backable company creation engine. In his current role, he looks to grow the life sciences and genomics ecosystem, supporting UK Plc., and globally, by partnering with entrepreneurs, investors and individuals within the innovation/entrepreneurial community, to support entrepreneurs with access to funding, sequencing, coaching and facilities and to create new models of innovation. Previously, he was responsible for heading commercial market and business development for Illumina EMEA. His focus was on how the application of genomics enables precision health.

Before joining Illumina, he worked in the NHS to deliver sustainable transformation programs, early founder team for US based startup and spent several years working in the pharma industry.

He is a member of the advisory board at Praesens Foundation (non-profit), Expert in Residence at Cambridge Judge Business School & Oxford University Translational Research Office and member of NHS Innovation Accelerator panel. In addition, he advises health, tech and blockchain startups.

Bobby read his B.Sc in Biology, with a focus on neuroscience and genomics, and an M.Sc in IT from the Queen Mary University of London.

Dr. Santiago Miriuka, MD MSc PhDSantiago is the co-founder and CEO/CTO of MultiplAI Health. He is a Medical Doctor with 20+ years in clinical cardiology. Director of a basic and translational lab working on cutting-edge cellular and molecular biology. Data scientist and coder looking to innovate in medicine.

register to receive zoom link

Moderator: Michael Akhras, Colibri Ventures

Clinical Talks

Clinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record, we have barely scratched the surface of all the amazing work our clinical, academic and industry Life Science community has to offer. More about the upcoming events is available here.

These events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab, and brought to you by Colibri Ventures.

Campus Solna Seminar Series: Patrick Bryant and Jan Schlegel
2023-02-09 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Patrick Bryant

Arne Elofsson – alpha 6

Structure prediction of protein-nucleic acid complexes.

Jan Schlegel

Erdinc Sezgin – gamma 3

A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens.

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

Data-driven hallmarks of acute myeloid leukemia: biological, prognostic and therapeutic implications
2023-02-09 08:00 - 17:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Tom Erkers

Assistant professor, Department of Oncology-Pathology, Karolinska Institutet

Hosts: CBCS-KI and PhenoTarget Research Community Program

February 9 at 3.30 pm

Gamma 2 Lunch Room & on Zoom

Omics Integration and Systems Biology - Online
2023-02-08 09:00 - 2023-02-10 17:00 | Online event via Zoom
The National Bioinformatics Infrastructure Sweden (NBIS) is pleased to announce the workshop in Omics Integration and Systems Biology. This workshop is open for PhD students, postdocs, group leaders and core facility staff from Swedish academic institutions looking for an introduction to multi-omics data analysis and integration of biological data. This course will include lectures and hands-on exercises from NBIS / Scilifelab experts from Stockholm, Lund and Gothenburg.

Application

Course website

Important dates

Application opens: 15 December 2022

Application closes: 25 January 2023

Confirmation to accepted applicants: 1 February 2023

Course fee

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK. * Please note that NBIS cannot invoice individuals.

Course content

The aim of this course is to provide an integrated view of data-driven hypothesis generation through machine learning integration methods, biological graph / network analysis and genome-scale metabolic models. A general description of different methods for analyzing different omics data (e.g. transcriptomics and genomics) will be presented with some of the lectures discussing key methods and pitfalls in their integration. The techniques will be discussed in terms of their rationale and applicability. The course will also include hands-on sessions and seminars by invited speakers.Some of the covered topics include:

Data pre-processing and cleaning prior to integration;

Application of machine learning for multi-omics analysis including deep learning;

Multi-omics integration, clustering and dimensionality reduction;

Biological network inference, community and topology analysis and visualization;

Condition-specific and personalized modeling through Genome-scale Metabolic models for integration of transcriptomic, proteomic, metabolomic and fluxomig data;

Identification of key biological functions and pathways;

Identification of potential biomarkers and targetable genes through modeling and biological network analysis;

Application of network approaches in meta-analyses;

Similarity network fusion and matrix factorization techniques;

Integrated data visualization techniques

Further details about the course content may be found on the course website.

Entry requirements

This course is open for PhD students, postdocs, group leaders and core facility staff from Swedish academic institutions. Please note that NBIS training events do not provide any formal university credits. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Practical exercises can be performed using R or Python, so we only accept students with previous experience in one of those programming languages. We will not discuss how to process specific omics, and the students are referred to other NBIS courses for this matter.

Required

Basic knowledge in R or Python;

Basic understanding of frequentist statistics;

A computer with a web camera, Zoom, and permissions for installing software.

Desired

Experience with analysis of NGS and other omic data;

Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “Introduction to biostatistics and machine learning”

Basic conda and git knowledge

This workshop can accommodate a maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria including entry requirements, motivation to attend the course as well as gender and geographical balance.

Contact information

For questions about this workshop please contact: edu.omics-integration@nbis.se

SciLifeLab Metabolomics platform - Metabolomics for the masses
2023-02-07 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Otto SavolainenMetabolites reflect the interaction between the gene cascade and surrounding exposures and are therefore essential components in all living organisms. Metabolites can be used to identify biomarkers of both health conditions and environmental exposures. The SciLifeLab Metabolomics platform offers a range of services for researchers interested in metabolomics.

Registration

SciLifeLab Gothenburg Lunch Seminar Series (hybrid) 2022-2023

SciLifeLab (www.scilifelab.se) is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital. This seminar series is started with an overview of the site, followed by presentations by the individual units.

On-site location: Assembly Room “Birgit Thilander”, Medicinaregatan 3A light lunch will be offered during the talks.It is also possible to participate online via Zoom. The link will be sent out after registration.

KTH's Kommunikatörer på SciLifeLab
2023-02-07 08:30 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Välkommen på Kommunikatörsträff på SciLifeLab i Solna!

Plats: SciLifeLab, Tomtebodavägen 23, SolnaDatum: tisdag 7 februari 2023Tid: 08:30-16:00

Har ni fått nya kommunikatörskollegor så vidarebefordra gärna inbjudan!Program

08:30 Frukostfika09:00 Programpunkter kopplade till arbetet med stödområde kommunikation, grupparbeten och diskussion12:00 Lunch13:00 Uppföljning förmiddagens arbete, vad händer nu?13:30 Vad är SciLifeLab? Kommunikationsarbetet på SciLifeLab; utmaningar och prioriteringar14:15 Fikapaus14:30 Rundvandring med visning av lokaler och det arbete som pågår15:30 Universitetsdirektör Kerstin Jacobsson kommer och pratar om vårt samordnade verksamhetsstöd16:00 Slut för dagen

Vi återkommer med ett mer detaljerat program längre fram!

Introduction to bioinformatics using NGS data - Lund, Umeå and Uppsala
2023-02-06 09:00 - 2023-02-10 17:00
This intense one-week workshop provides an introduction to the analysis of next generation sequencing data. The workshop is open to PhD students, post-docs, and other researchers affiliated to Swedish academia and healthcare. It is organised by the National Bioinformatics Infrastructure Sweden (NBIS) and National Genomics Infrastructure (NGI).

Important dates

Application opens: 21-Nov-2022Application closes: 31-Dec-2022Information to accepted students will be sent: Week 2, 2023

Venues

This workshop runs in parallel on-site in Uppsala, Umeå and Lund. Lectures will be streamed online from our Uppsala site (mainly) to the other classrooms. Several teaching assistants will be present in the Umeå, Lund and Uppsala classrooms all week to help with exercises and questions. When registering you will be asked to select a preferred site.

UppsalaTrippelrummet (E10:1307-1309)Entrance C11Biomedical Centre (BMC) / SciLifeLab / Uppsala UniversityHusargatan 3752 37 Uppsala

UmeåUB341Universitetsbibioteket plan 3Umeå University901 87 Umeå

LundSölvegatan 35Lund University223 62 Lund

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

website & Application

Contact

Email: edu.intro-ngsMalin Larsson, Martin Dahlö, Roy Francis

Course fee

This on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals.

Course content

Briefly, the workshop covers the followings major topics:

Working on the UNIX/LINUX command line

Bioinformatic/NGS data formats and QC

DNA variant calling workflow essentials

RNA sequence analysis workflow essentials

Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.

Please note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop.

Campus Solna Seminar Series: Krzysztof Jurdzinski and Keyi Geng
2023-02-02 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Krzysztof Jurdzinski

Anders Andersson – alpha 3

Metabarcoding-based biodiversity monitoring along the Swedish coastline.

Keyi Geng

Claudia Kutter – gamma 5

Cas9-mediated genome engineering exaggerates collateral deletion at the PTEN gene locus mimicking cancer profiles.

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

Single cell RNAseq data analysis
2023-01-30 08:00 - 2023-02-03 14:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data. The total course duration is 5 days, including the lectures and practical exercises that will be held on site in Stockholm.

Application

Application open: 2022-11-25

Application deadline: 2022-12-21

application form

Course Leaders

Paulo Czarnewski

Åsa Björklund

Contact: edu.sc@nbis.se

Course fee

This workshop has a fee of 2000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner.

Course content

Overview of the current scRNAseq technologies

Basic overview of pipelines for processing raw reads into expression values

Quality control and normalization

Dimensionality reduction techniques

Data integration and batch correction

Differential gene expression

Clustering techniques

Celltype prediction

Trajectory inference analysis

Analysis of spatial transcriptomics datasets

Comparison of different analysis pipelines such as Seurat, Scran and Scanpy

Who can apply?

This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff within all Swedish universities. Even if we do accept application from other countries, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries.

Practical exercises will be performed using either R or Python, so we only accept students that fulfil the entry requirements below.

Entry requirements

You are used to program in either R and/or Python

You already understand the basis of NGS technologies

You are able to analyse bulk RNA-sequencing data

You are used to navigate and use UNIX command line (bash)

Have full access to your computer (admin permissions). Instructions on installation will be sent by email to accepted participants.

Due to limited space the course can accommodate 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.

WASP and DDLS networking event January 2023
2023-01-27 11:00 - 14:00
The second WASP-DDLS joint call for research project: Information and networking event
This networking event welcomes everyone that wants to learn more about the second WASP-DDLS joint call for research projects. The event will start with an open Zoom meeting that will give an introduction to the new call and also highlight lessons learned from previous approved projects. The digital introduction will be followed by on-site network meetings at different university sites.
11:00-12:00 Open Zoom meeting: Introduction and information about new call, lessons from ongoing projects, Q&A

Danica Kragic, Co-director Co-director for external relations WASP
Olli Kallioniemi, Director SciLifeLab
Erik Kristiansson member of ScilLifeLab and DDLS steering group

12:00-14:00 Mingle and networking at university sites (light lunch will be provided).

KTH, host Joakim Jaldén
Chalmers, host Rebecka Jörnsten and Erik Kristiansson
LiU, host Andreas Kerren
UmU, host Martin Rosvall
Lund, host Bo Bernhardsson

Deadline for registration January 18th

Register

Read more

Campus Solna Seminar Series: Hong Yang and Kyra Kuhnigk
2023-01-26 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Hong Yang

Adil Mardinoglu – alpha 6

Novel insights into ChREBP regulation in Glycogen Storage Disease Type 1a Liver Disease.

Kyra Kuhnigk

Björn Önfelt – gamma 3

Modulation of lytic molecules restrain serial killing in γδ T cells.

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

FAIRPoints-FAIRPoints ‘Ask me Anything’ (AMA)
2023-01-26 11:00 - 13:00 | Online event via Zoom
Location: Online via Zoom

See event in your timezone

FAIRPoints ‘Ask Me Anything’ on Identifiers

This event is part of a series of “Ask Me Anything”-style events featuring keynote speakers from the RDA, and EOSC groups focused on RDA activities and EOSC solutions in relation to FAIR implementation and Open practices in Science.

January

The theme of this session is “FAIRPoints ‘Ask Me Anything’ on Identifiers.” We will be discussing the different types of identifiers available, their importance in creating FAIR Digital Objects, and how they can be applied and integrated into research practices. Speakers include Maggie Hellström, Peter Wittenberg, Matthew Buys, and moderated by Natasha Simons, Nabil Ksibi, Patricia Herterich.

The events will bring together speakers from the RDA Groups and speakers from a related EOSC service to describe how their work aligns, how it connects to the research community, and how it benefits the research community in a way that is directly related to the implementation of FAIR and Open research practices. The events are beginner-friendly, laid-back, and easy to follow, with moderators driving the discussion, posing questions to our speakers, and inviting audience questions. Finally a selection of questions will be gathered and turned into Google Educational Q&A flashcards (https://schema.org/QAPage) for future reference.

FAIRPoints ‘Ask me Anything’ (AMA) event series on FAIR implementation and Open practices in Science, is hosted by FAIRPoints and supported by RDA, EOSC, FDO, GOFAIR-US & SciLifeLab-DataCentre.

For more information please visit https://eoscfuture-grants.eu/meet-the-grantees/rda-eosc-future-ambassador-ask-me-anything-style-events-fair-implementation-and.

ThemeTypeDateSpeakerModeratorIdentifiersEventJanuary 26th 2023Maggie HellströmNabil KsibiMatthew BuysNatasha SimonsPeter WittenbergPatricia HerterichMachine Centric Science PodcastJanuary 2023Christophe Blanchi listen hereDonny WinstonFAIR Data PodcastPodcastJanuary 18th 2023Tibor Kalman and Sven Bingert listen hereRory MacneilFAIR software and WorkflowsEventFebruary 23rd 2023TBATBARegulatory Processes and GovernanceEventApril 27th 2023TBATBAMachine ActionabilityEventMay 25th 2023TBATBAEquitable and Transparent Access to Information and KnowledgeEventSeptember 28th 2023

Register here

Sign up for future events here

Twitter: @FAIR_Points

3D context analysis of multicellular systems by CUBIC cell-omics technology
2023-01-24 14:00 - 15:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Professor Etsuo Susaki

Department at Biochemistry and Systems Biomedicine, Juntendo University Graduate School of MedicineVisiting Scientist at Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research

Three-dimensional biological tissue and multicellular systems should primarily be analysed by 3D information technology. Tissue clearing and lightsheet microscopy allow 3D analysis and can be combined with multiomics analysis for full biological context investigations.

OligoNova Hub - National resource for development of oligonucleotide therapies
2023-01-24 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Pär MatssonWe will present OligoNova Hub and the capabilities we provide for academic researchers to transform their scientific discoveries into new oligonucleotide therapies.

registration

SciLifeLab (www.scilifelab.se) is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital. This seminar series is started with an overview of the site, followed by presentations by the individual units.

On-site location: Assembly Room “Birgit Thilander”, Medicinaregatan 3A light lunch will be offered during the talks.It is also possible to participate online via Zoom. The link will be sent out after registration.

Project support in chemical biology and drug discovery
2023-01-24 10:00 - 10:45 | Online event via Zoom
The chemical biology unit (CBCS) and the Drug discovery and development (DDD) platform at SciLifeLab have calls out for projects.

CBCS is looking for projects in Chemical Biology which includes assay development for small molecule screening and profiling, as well as enabling chemistry. For more information, please visit www.cbcs.se.

The DDD platform has a call looking for new project proposals for drug discovery. All therapeutic modalities that can be developed in collaboration with the DDD platform at SciLifeLab are of interest, including small molecules, antibodies, oligonucleotides and new modalities.

Some users and projects are at the intersection between chemical biology and drug discovery.This webinar aims to guide users to the call that best suits the needs of their project.

Documentation

DDD Call for Projects

Webinar Slides CBCS

Webinar Slides PPP

Web-editing Workshop for Unit Website Editors
2023-01-19 12:30 - 14:30 | Online event via Zoom
Current or future editors of unit websites on the SciLifeLab.se website are welcome to join this workshop.

Register

Workshop will be managed by David Gotthold from the Operations Office. The Workshop will contain:

Account set-up and permissions

How to Log-in

Introduction to Word Press

Editing Basics

Suggestions for headlines at all unit websites

Other resources on the SciLifeLab

The workshop will end with a 30 minute co-working session where you work individually and can get individual assistance

David GottholdProject leaderEvent management, visits coordination, webmaster, communicationsdavid.gotthold@scilifelab.se +46 (0) 72 858 91 03

Uppsala University Pharmaceutical Profiling in Drug Discovery and Development Symposium
2023-01-19 08:00 - 17:00 | Humanities Theater, Engelska parken, Uppsala, 75238, Sweden
Every year, the Drug Delivery group at the Department of Pharmacy (headed by Prof. Per Artursson, Prof. Christel Bergström and Dr. Pawel Baranczewski) organizes a one day symposium on pharmaceutical profiling. On January 19th, 2023, the 12th Uppsala University Pharmaceutical Profiling in Drug Discovery and Development Symposium will be arranged. This twelfth edition of the symposium will focus on new modalities with respect to their development and formulation to overcome biological barriers and achieve targeted therapies.

Past symposia have been highly attended by faculty and students at Uppsala University and other Swedish and international universities, as well as by researchers from the local biotech and pharma industry and from regulatory agencies. Previous keynote speakers included among others Prof. Langer (MIT), Prof. Alonso (USC CIMUS Research Institute), Prof. Porter (Monash University), Prof. Leroux (ETH Zürich) and Dr. Hochman (Merck). The symposia provide excellent opportunities for academia-industry networking and for scientific discussions on current research at our platform for drug optimization and pharmaceutical profiling as well as in the Drug Delivery research group at the Department of Pharmacy.

This year’s confirmed speakers and the titles of their talks:

Prof. Olivia Merkel (Ludwig-Maximilians-Universität München, Germany): Treatment of lung diseases via siRNA inhalation delivery

Prof. Paola Luciani (University of Bern, Switzerland): Targeting fibrosis in multiple organs via lipid-based drug delivery systems

Prof. Ola Söderberg (Uppsala University, Sweden): Development of novel molecular biology tools for medical research

Assist. Prof. Daniel Fürth (Uppsala University, Sweden): A chemoselective in vivo sequencing chemistry

Prof. Yvonne Perrie (University of Strathclyde, Scotland): Formulation strategies for the delivery of mRNA vaccines

Prof. My Hedhammar (KTH Royal Institute of Technology/Spiber Technologies AB, Sweden): FN-silk membrane as mimic of basement membrane in tissue barrier models

Assoc. Prof. Daniel Espes (Uppsala University, Sweden): Novel imaging techniques and drugs for targeting human pancreatic islets

Prof. Per I Arvidsson (Karolinska Institutet, Sweden): Explorations and innovations at the academia-industry interface – tales from the SciLifeLab DDD infrastructure

Prof. Jens Carlsson (Uppsala University, Sweden): Antiviral drug discovery by virtual screening of ultra-large chemical libraries

There will be also a panel discussion about “Impact of European drug delivery science”, led by Dr. Björn Arvidsson.

Uppsala University Pharmaceutical Profiling in Drug Discovery and Development Symposium
2023-01-19 08:00 - 17:00 | Humanities Theater, Engelska parken, Uppsala, 75238, Sweden
Every year, the Drug Delivery group at the Department of Pharmacy (headed by Prof. Per Artursson, Prof. Christel Bergström and Dr. Pawel Baranczewski) organizes a one-day symposium on pharmaceutical profiling. On January 19th, 2023, the 12th Uppsala University Pharmaceutical Profiling in Drug Discovery and Development Symposium will be arranged.

registration

This twelfth edition of the symposium will focus on new modalities with respect to their development and formulation to overcome biological barriers and achieve targeted therapies. Past symposia have been highly attended by faculty and students at Uppsala University and other Swedish and international universities, as well as by researchers from the local biotech and pharma industry and from regulatory agencies.

Previous keynote speakers included among others Prof. Langer (MIT), Prof. Alonso (USC CIMUS Research Institute), Prof. Porter (Monash University), Prof. Leroux (ETH Zürich) and Dr. Hochman (Merck). The symposia provide excellent opportunities for academia-industry networking and for scientific discussions on current research at our platform for drug optimization and pharmaceutical profiling as well as in the Drug Delivery research group at the Department of Pharmacy.

This year’s confirmed speakers and the titles of their talks:

Prof. Olivia Merkel (Ludwig-Maximilians-Universität München, Germany): Treatment of lung diseases via siRNA inhalation delivery

Prof. Paola Luciani (University of Bern, Switzerland): Targeting fibrosis in multiple organs via lipid-based drug delivery systems

Prof. Ola Söderberg (Uppsala University, Sweden): Development of novel molecular biology tools for medical research

Assist. Prof. Daniel Fürth (Uppsala University, Sweden): A chemoselective in vivo sequencing chemistry

Prof. Yvonne Perrie (University of Strathclyde, Scotland): Formulation strategies for the delivery of mRNA vaccines

Prof. My Hedhammar (KTH Royal Institute of Technology/Spiber Technologies AB, Sweden): FN-silk membrane as mimic of basement membrane in tissue barrier models

Assoc. Prof. Daniel Espes (Uppsala University, Sweden): Novel imaging techniques and drugs for targeting human pancreatic islets

Prof. Per I Arvidsson (Karolinska Institutet, Sweden): Explorations and innovations at the academia-industry interface – tales from the SciLifeLab DDD infrastructure

Prof. Jens Carlsson (Uppsala University, Sweden): Antiviral drug discovery by virtual screening of ultra-large chemical libraries

There will also be a panel discussion about “Impact of European drug delivery science”, led by Dr. Björn Arvidsson.

Organizers:

Drug Delivery group, Uppsala University

SciLifeLab

UDOPP
