SciLifeLab

Evolution in Sweden 2023
2023-01-10 09:00 - 2023-01-12 17:00 (Europe/Stockholm) | Friessalen, Evolutionsbiologiskt centrum, EBC Norbyvägen 14-18, Uppsala, 752 36
Evolution in Sweden is a biannual meeting, which broadly gathers evolutionary biologists working in Sweden. The meeting was held in Uppsala 2014, Lund 2016, Stockholm 2018, and Gothenburg 2020. The host for 2023 is Evolutionary Biology Centre, at Uppsala University. The meeting is aimed to be a broad meeting on every aspect of evolutionary biology of all forms of life on Earth. However, please note that the meeting is restricted to scientists active in Swedish academic departments.

This year the Evolution in Sweden conference is organized together with the Evolution and Biodiversity research area from the Data-driven life science program (DDLS), part of a 12-year SEK 3.1 billion initiative from the Knut and Alice Wallenberg Foundation. Please find more information about the DDLS program here. We encourage researchers working with analysis of large data sets in the fields of evolution and biodiversity to attend.

Keynote speakers:

Luis-Miguel Chevin, Centre d’Ecologie Fonctionnelle et Evolutive, CNRS Montpellier, France, Paul Hohenlohe, University of Idaho, USA and Tanja Schwander, University of Lausanne, Switzerland.

Registration:

Registration and check-in will open at 09:30 on Tuesday, January 10, followed by self-catered lunch. No registration fee, fika will be provided. Lunch, Dinner, and Hotel are not included in the registration.

Posters:

We ask you kindly to hang your poster during the registration, pins will be provided. Make sure to stand by your poster at the Poster session. The poster board area is 119×89 (excl frame), in standing format.

Lunches:

The lunches will be self-catered. There is a restaurant at EBC, Hassans, and restaurants close by, for instance, Blåsenhus or Segerstedthuset (see Google maps). There will be pub evenings (at your own expense) and an informal dinner on January 11.

Informal Conference dinner on January 11:

The registered participants have received a separate invitation to attend the informal dinner on January 11. Attendance is optional, and the cost is the participant’s responsibility. A Lebanese buffet (195 kr not including beverages or coffee) will be offered at Hassans at EBC. Follow the instructions in the invitation to register, and remember to pay the restaurant in advance using Swish.

Conference Pub and Hotel:

The Conference Pub, on January 10, is Bishop Arms. Keynote speakers are staying at the Elite Hotel Academia. We have not pre-negotiated any hotel rooms for the participants.

Conference book:

A link to the Conference book is sent to all registered participants, with a detailed program, information about the keynote speakers, abstracts, and a List of participants.

Cancellation of attendance:

email events@SciLifeLab.se

Brief program

The detailed program is published in the Conference Abstract book, and emailed to all participants.

January 10

09:3012:00On-site registration opens outside Friessalen and Ekmansalen, EBC12:00Lunch (self-catered)12:45Welcome (parallel in Fries and Ekman)13:00Keynote: (parallel in Fries and Ekman)Adaptive capacity in wildlife populations: a case study of a unique diseasePaul A. Hohenlohe, University of Idaho, USA14:0017:00Two parallel afternoon sessions (Friessalen and Ekmansalen, EBC) with coffee at 15:15-15:4518:00Conference pub; Bishop Arms (map)

January 11

09:0012:00Two parallel morning sessions (Friessalen and Ekmansalen, EBC) with coffee at 10:15-10:4512:00Lunch (self-catered)13:30Keynote: (parallel in Fries and Ekman)Evolution and consequences of parthenogenesis: Insights from stick insectsTanja Schwander, University of Lausanne, Switzerland14:3017:30Two parallel afternoon sessions (Friessalen and Ekmansalen, EBC) with coffee at 15:45-16:1517:30Poster session, cash bar on 2nd floor.19:15Dinner buffet at Hassans, EBC (more information sent to the Conference participants)23:00EBC closes, and everyone has to leave the Campus building for security reasons.

January 12

09:0012:00Two parallel morning sessions incl. DDLS (Friessalen and Ekmansalen, EBC) with coffee at 10:15-10:4512:00Lunch (self-catered)13:30Keynote: (parallel in Fries and Ekman)Predictability of ecology and evolution in randomly fluctuating environmentsLuis-Miguel Chevin, Centre d’Ecologie Fonctionnelle et Evolutive, CNRS Montpellier, France14:30Final remarks, future meeting thoughts15:00Meeting closesUpdated: December 12.

Paul Hohenlohe, Abstract and Bio
Adaptive capacity in wildlife populations: a case study of a unique disease

Wildlife populations face threats from climate change, invasive species, habitat modification, disease, and other factors. Evolutionary biology and genomics provide powerful tools for assessing the capacity of populations to adapt and persist. As a case study for adaptive capacity, I focus on a unique disease that threatens the persistence of Tasmanian devils. Devil facial tumor disease (DFTD) is a transmissible cancer that has spread across the species range. Using genomic techniques, we have found evidence of rapid evolution in response to DFTD as well as a genetic basis for disease-related phenotypes. Recently a second independently derived transmissible cancer was discovered in devils, raising the possibility that this is a recurrent selective force. We have found widespread evidence of both historical and contemporary selection in the devil genome, but no evidence that genes currently responding to DFTD were under recurrent selection in the past. These results help us assess the capacity of devil populations to adapt to threats, including transmissible cancers, and can help guide the management of both wild and captive devil populations.

Bio

Paul A. Hohenlohe is an Associate Professor of Biological Sciences at the University of Idaho, USA. He earned his Ph.D. in Zoology from the University of Washington and worked as a conservation biologist for the U.S. federal government. During his postdoctoral work at the University of Oregon, he was part of the team that developed RAD sequencing as a tool for population genomics. His current research program focuses on evolutionary genetics and genomics with applications to conservation of biodiversity, across a wide range of plant and animal taxa. He is also the director of the Bioinformatics and Computational Biology graduate degree program at UI.

Tanja Schwander, Abstract and Bio
Evolution and consequences of parthenogenesis: Insights from stick insects

Parthenogenesis is predicted to have many evolutionary consequences, since gamete production and the restoration of somatic ploidy levels via fertilization no longer take place, and because male phenotypes are not exposed to selection. The empirical evidence for most predictions remains however scarce, largely because in case studies of isolated parthenogenetic species, putative effects of parthenogenesis are confounded with species specific patterns. To fill this knowledge gap, we study independently evolved asexual arthropod species and their sexual relatives. I will discuss the insights we developed from genome andtranscriptome comparisons of sexual and asexual stick insect species as well from comparisons across new and previously published genomes of parthenogenetic animals.

Bio

Tanja Schwander earned her PhD at the University of Lausanne 2007 and then got postdoctoral and independent researcher fellowships at Simon Fraser University (CA), University of Groningen (NL) and the Wissenschaftskolleg zu Berlin (DE). Tanja returned to Lausanne with a SNSF starting grant in 2013 and got a tenure track position there in 2014. Since 2018, Tanja is an associate professor at University of Lausanne.

Luis-Miguel Chevin, Abstract and Bio
Predictability of ecology and evolution in randomly fluctuating environments

Most natural environments exhibit some component of random variation or noise, which can only be predicted in a probabilistic sense. Current anthropogenic change, beyond causing trends in mean environments, also modifies the patterns of these fluctuations, so there is a need to better understand their influences on ecology and evolution. Population responses to environmental noise depend not only on the magnitude of fluctuations, but also on their alternation pattern, as captured by their temporal autocorrelation. However, a major challenge when investigating these effects is that their inherent stochasticity requires abundant replication, which is often unfeasible in nature. I will argue that a powerful strategy towards this goal is to use a combination of approaches: theory, experimental evolution, and analyses of natural populations. I will illustrate this by confronting results from our long-term experiments with the microalga Dunaliella salina under randomly fluctuating salinity to theoretical predictions about changes in population size, genetic composition, phenotypes, and fitness. I will end by considering how ecological interactions, within and between species, may alter these population responses to randomly fluctuating environments.

Bio

Luis-Miguel Chevin did his PhD at University Paris South (2005-2008) then a postdoc at Imperial College London in Silwood Park (2009-2011). Luis-Miguel was hired in 2011 as a permanent CNRS researcher at the Center for Functional and Evolutionary Ecology in Montpellier, where he is now a CNRS research director.

For more information, feel free to contact events@scilifelab.se or the organizers:

Scientific Committee

Arild Husby, Evolutionary Biology Centre, Uppsala University

Frank Johansson, Evolutionary Biology Centre, Uppsala University

Pascal Milesi, SciLifeLab, Uppsala University

Andreas Wallberg, Biomedical Centre, Uppsala University

Matthew Webster, Biomedical Centre, Uppsala University

Tanja Slotte, Stockholm University

[Clinical Talks] Functional precision medicine using AI drug discovery
2022-12-16 09:00 - 09:30 | Online event via Zoom
Greg Vladimer

Vice President, Translational Research at Exscientia

Greg Vladimer, VP, Translational Research joined Exscientia through the acquisition of Allcyte, a pioneer in the field of AI-first functional precision oncology and translational cancer research, where he was a Scientific Co-Founder and the Chief Scientific Officer. At Allcyte, he and his team pushed the boundaries of translational cancer research through the use of disease relevant primary human cancer samples, high content imaging, custom AI-powered computer vision, and scalable cloud computing. Greg has a PhD from University of Massachusetts Medical School in Immunology, after which he moved to Vienna as an EMBO-supported Postdoctoral Fellow at CeMM where he and a colleague invented the first-generation platform used for the translational work, and spearheaded the first ever prospective interventional clinical trial showing that drugs prioritised using a functional precision medicine tool had clinical benefit for late stage blood cancer patients.

register to receive zoom link

Moderator: Päivi Östling, SciLifeLab

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.

Functional analysis of human protein phosphorylation sites
2022-12-15 16:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Matthias Selbach

Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. I will present three different ways to characterise the function of human phosphorylation sites. First, I will show how data from in vitro kinase assays can be used to predict kinase activity in phosphoproteomic datasets. Second, I will show quantitative affinity purification experiments with synthetic phosphopeptides can help to assess their cellular function. Finally, I will outline how quantitative RNA-interactome capture (qRIC) can quantify the fraction of cellular RNA-binding proteins that are pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allows us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of RBPs. Using qRIC, we identify over hundred phosphorylation sites with regulatory potential, including known regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localisation, association with cytosolic RNA granules and alternative splicing.

Selected publications

Vieira-Vieira, CH, Dauksaite, V., Sporbert, A., Gotthardt, M. and Selbach M. (2022) Proteome-wide quantitative RNA-interactome capture identifies phosphorylation sites with regulatory potential in RBM20. Mol Cell 82, 2069-2083.

Meyer, K., Kirchner, M., Uyar, B., Cheng, J.Y., Russo, G., …, and Selbach, M. (2018). Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs. Cell 175, 239-253.

Imami, K., Milek, M., Bogdanow, B., Yasuda, T., Kastelic, N., …, and Selbach, M. (2018). Mol Cell. Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis. Mol Cell 72,

Zauber, H., Kirchner, M., and Selbach, M. (2018). Picky: a simple online PRM and SRM method designer for targeted proteomics. Nat Methods 15, 156-157.

McShane, E., Sin, C., Zauber, H, Wells JN, Donnelly N, …, and Selbach M. (2016). Kinetic analysis of protein stability reveals age-dependent degradation. Cell 167, 803-815.

Schwanhausser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., and Selbach, M. (2011). Global quantification of mammalian gene expression control. Nature 473, 337-342.

Campus Solna Seminar Series: Bruno Urien and Kalliroi Sdougkou
2022-12-15 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:

Bruno Urien

Bennie Lemmens – alpha 5

Study of Nuclear DNA Replication using Structured Illumination Microscopy.

Kalliroi Sdougkou

Jonathan Martin – gamma 5

Sample preparation workflows for enhanced chemical exposomics in human plasma.

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

Chemical Biology Seminar Series
2022-12-14 15:30 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
“TARGETING RIBOSOME BIOGENESIS IN CANCER”

Dimitris KanellisDept. of Medical Biochemistry and Biophysics, Karolinska Institutet“SYNTHETIC SWITCHES FOR DNA REPAIR – CONTROLLING ENZYMATIC FUNCTIONS AT WILL”Maurice MichelDept. of Oncology-Pathology, Karolinska Institutet

Date: Wednesday December 14

Time: 3.30 pm

Location: Air & Fire, SciLifeLab

The seminars are also available on Zoom.

https://ki-se.zoom.us/j/66622023014

Web-editing Workshop for Unit Website Editors
2022-12-14 09:00 - 11:00 | 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

Cancelled: SciLifeLab Metabolomics platform - Metabolomics for the masses
2022-12-13 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
SciLifeLab Metabolomics platform – Metabolomics for the masses

Otto Savolainen

This event is cancelled

Metabolites 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 resaerchers interested in metabolomics.

SciLifeLab 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

Data-Driven Precision Medicine and Diagnostics Research Area Symposium
2022-12-12 10:00 - 18:30 | Sune Bergström Aula, BioClinicum, New Karolinska University Hospital, Solnavägen 30, Stockholm, 17164, Sweden
Welcome to the first in-person symposium in data-driven precision medicine and diagnostics (PMD) research area. Listen to the Data Driven Life Science (DDLS) fellows recruited in this research area and expand your network with international and national colleagues.

The data-driven precision medicine and diagnostics symposium on December 12, 2022, is the first in-person symposium in the research area of precision medicine and diagnostics of the DDLS program. This meeting brings together the community in precision medicine and diagnostics and researchers who implemented artificial intelligence and machine learning applications in their research in PMD to improve human health and diagnostics, introduces newly appointed DDLS fellows in the PMD research area, and provides opportunities for networking across the research community and the SciLifeLab infrastructures. We are excited to host three international keynote speakers and welcome the community to join us. Hopefully, this event will inspire you on the potentials of data-driven precision medicine and diagnostics in Sweden.

Target group: We welcome all researchers interested in the DDLS program and data-driven precision medicine and diagnostics.

Venue: Sune Bergström Aula, BioClinicum, New Karolinska University Hospital, Solnavägen 30, Stockholm

Organizer: SciLifeLab, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science.

Deadline for registration extended to December 12th 9 am (earlier 2nd of December).

Agenda & speaker bios

Register here

AGENDA

TimeSession/Title of the presentationPresenter10.00Registration10:15Welcome and Introduction to Precision Medicine and Diagnostics Research AreaJanne Lehtiö10:30Scientific presentations – Precision Medicine Chair: Fulya Taylan Opening Keynote: FinnGen: a public-private partnership improving human health through genetic researchMervi Aavikko Genomic Medicine Sweden: Lessons learned and future possibilities within the Swedish health data spacePer Sikora Implementation of an academic clinical decision support system for precision oncology: the Molecular Tumor Board Portal (Digital)David Tamborero11:40Lunch 12:45Scientific presentations – Imaging and AI for Precision Medicine Chair: Magnus Boman AIDA – supporting AI research in diagnostic imagingClaes Lundström AI-based precision pathology – scalable solutions for cancer patient stratification and phenotypingMattias Rantalainen Deep learning for PET image analysisIda Häggström 13:40Scientific presentations – Digital Twins in Healthcare Chair: Päivi Östling Building an ecosystem for digital twins in healthcareLiesbet Geris M4-health and digital twins: bring a digital copy of yourself with you throughout your health journeyGunnar Cedersund Towards precision prevention of rheumatoid arthritis; novel tools and novel resultsLars Klareskog14:35Coffee break 15:00SciLifeLab and DDLS Precision Medicine and Diagnostics Chair: Janne Lehtiö Introduction to SciLifeLab and DDLS ProgramOlli Kallioniemi SciLifeLab’s Data Center and Precision Medicine & Diagnostics Data Science NodeJohan Rung Bioinformatics support for Precision Medicine and DiagnosticsPär Engström Q&A sessionJanne Lehtiö16:00DDLS Fellows Chair: Åsa Johansson Deep lipidomics profiling provides potential biomarkers for precision nutrition approaches in cardiometabolic disease preventionClemens Wittenbecher Integrative multi-omics for precision medicineWen Zhong Harnessing the promise of next-generation plasma profiling for pan-cancer diagnosticsFredrik Edfors 17:00Closing Keynote Chair: Janne Lehtiö The need to model OMICs and routine (para)clinical data together – CLL as an example (Digital)Carsten Utoft Niemann17:30 – 18:30Networking with drinks

SciLifeLab Integrated Structural Biology Platform Symposium
2022-12-12 09:00 - 16:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
SciLifeLab Integrated Structural Biology invites you to the ISB annual users meeting to be held in Solna on December 12, 9-16.

The program will contain an overview of infrastructures in Sweden that can support your structural biology project, from gene to final 3D structure. We will also hear examples of projects that were supported by the SciLifeLab infrastructures during 2022, comprising Cryo-EM, Structural Proteomics and NMR.

We welcome you to join in person in the SciLIfeLab building (Tomtebodavägen 23, 171 65 Solna) but also understand if you prefer to join in by zoom. The meeting will be a hybrid meeting.

Registration

Program

Program – December 12

ISB2022_221212Download

Science & SciLifeLab Prize Symposium
2022-12-08 09:30 - 12:30 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
Welcome to the Scientific Symposium presenting the winners of the 2022 Science & SciLifeLab Prize for Young Scientists.

You can still register to join on Zoom and onsite if seats are available. For onsite registration, we can not consider special food requirements after November 30.

registration

Science, the American Association for the Advancement of Science (AAAS), and SciLifeLab joined forces in 2013, creating the Science & SciLifeLab Prize for Young Scientists to recognize excellence amongst young researchers from around the world. A global Prize aimed at rewarding scientists at an early stage of their careers.

The Prize was launched with the vision of recognizing that global economic health depends on a vibrant research community. A vision that will only come true if we encourage our best and brightest to continue in their chosen fields of research.

Considering the difficult economic environment for budding scientists, it is crucial that we provide them with extra encouragement as they begin their scientific careers.

The international Prize is awarded annually to four young scientists for outstanding life science research based on a doctoral degree earned in the previous two years. Each year, a Grand Prize winner is selected from the applicants to receive 30,000 USD in prize money, and the three other category winners are awarded 10,000 USD each for their accomplishments. The grand prize-winning essay will be published in Science, and essays from the three category winners will be published online.

All four winners of the Science & SciLifeLab Prize for Young Scientists are invited to Sweden December 6-11 to participate in a unique week filled with events in honor of science. They will have the opportunity to meet with leading scientists in their field of research and create life-long connections to support their careers.

Program

09:00Breakfast is served outside the Lecture Hall09:30Welcome words:Olli Kallioniemi, SciLifeLab Director Valda Vinson, Science AAAS09:45The winners present their research (15’+5′)Moderators: Alexandra Teleki & Mikael Sellin, SciLifeLab FellowsEndosomes, Receptors and Viruses: Deciphering the Mechanisms of Infection at the Host-Pathogen Interface James Daly, Cell & Molecular Biology Category Prize WinnerUncovering the Degrader of D-type Cyclins Daniele Simoneschi, Molecular Medicine Category Prize WinnerCoffee break How do bacteria cope with a changing world? Stefany Moreno-Gámez, Ecology and Environment Category Prize WinnerThe autobiography of a gut bacterium Florian Schmidt, Proteomics and Systems Biology Approaches, Grand Prize Winner11:35Interview with the WinnersModerators: Alexandra Teleki & Mikael Sellin, SciLifeLab Fellows11:55Keynote lecture: Rediscover Your Why – Don’t Lose Sight of Why You Pursued Scientific InquiryGilda A. Barabino, President of the American Association for the Advancement of Science (Bio below)12:25Closing words:Mia Phillipson, SciLifeLab Co-Director12:30Lunch is served

Booklet

Gilda A. Barabino – Bio

Please contact events@scilifelab.se if you have any questions.

Data-driven Epidemiology and biology of infections Research Area Symposium
2022-12-07 13:00 - 2022-12-08 13:00 | Europasalen, Konferenscentrum Wallenberg, Gothenburg, Medicinaregatan 20, Göteborg, 413 90, Sweden
Welcome to a symposia with the new DDLS Fellows and national as well as international researchers within the area of data-driven epidemiology and biology of infections.

We encourage personal participation to network with the new DDLS Fellows and other experts of the field however online participation is possible.

Deadline for registration November 29th

Register here

Program Wednesday, 7 December

12:00 LUNCH will be served

13:00- 13:20 Welcomes and Introductions

Siv Andersson, Head of Basic Research at Knut and Alice Wallenberg Foundation, Uppsala University,

Olli Kallioniemi, Director SciLifeLab and DDLS Director, Karolinska Institutet

Maria Smedh Site Coordinator, SciLifeLab Göteborg

13:20 DDLS in Epidemiology and Biology of Infection

Oliver Billker, DDLS Research Area Lead, Umeå University

13:30 Keynote: Using genomic surveillance data to understand bacterial epidemiology

Nicholas J Croucher, Imperial College London

14:10 DDLS Fellow talk: Predicting the disease threats of the future

Johan Bengtsson-Palme, DDLS Fellow at Chalmers University of Technology

14:50 Keynote (virtual) Data and decisions in an imperfect world

Bill Hanage, Associate Professor, Harvard, School of Public Health

15:30 COFFEE

16:00 DDLS Fellow talk: A global perspective on antimicrobial resistance in animals raised for food

Thomas van Boeckel, ETH Zurich and future DDLS Fellow at Gothenburg University

16:40 Pandemic preparedness – The SciLifeLab perspective

Staffan Svärd, SciLifeLab Scientific Director, Uppsala University

17:10 Discussion and conclusion of the first day

17:30 Snacks and mingle in Restaurant Nordic

18:30 SYMPOSIUM DINNER in Restaurant Nordic

Program Thursday, 8 December

8:30 DDLS Fellow Talk: Strength in numbers: leveraging publicly available (meta)genomic data to gain insight into the epidemiology and virulence potential of bacterial pathogens

Laura Michelle Carroll, Umeå University

9:10 Keynote: Data-driven dynamic disease surveillance and studies for mapping systemic effects of the human gut microbiome

Tove Fall, Uppsala University

9:50 COFFEE

10:20 DDLS Fellow Talk: Intimately microbial: symbioses in OB-GYN,

Luisa Warchavchik Hugerth, DDLS Fellow Uppsala University

11:00 National services for data and bioinformatics within DDLS and SciLifeLab

Sara El-Gebali, SciLifeLab Data Centre,

Björn Nystedt, National Bioinformatics Infrastructure

Short presentations followed by a discussion to determine needs for computational support for infections research in Sweden.

12:00 Discussion: DDLS initiative and Data-Driven Epidemiology and Biology of Infection: where next?

12:30 LUNCH will be served

Cancelled: OligoNova Hub - National resource for development of oligonucleotide therapies
2022-12-06 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
OligoNova Hub – National resource for development of oligonucleotide therapies

Pär Matsson

We will present OligoNova Hub and the capabilities we provide for academic researchers to transform their scientific discoveries into new oligonucleotide therapies.

SciLifeLab 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

This event has been cancelled.

SciLifeLab Uppsala PhD&Postdoc Online Seminar Series – Cancer Theme
2022-12-06 11:00 - 12:00 | Online event via Zoom
Welcome back to the SciLifeLab Uppsala PhD&Postdoc seminar series!
This seminar will take place on Tuesday December 6 from 11h to 11:50h on Zoom (https://uu-se.zoom.us/j/66489618700)
For this occasion the speakers will be:
1. Xiaonan Zhang, Postdoc at Tobias Sjöblom’s Lab (Cancer Precision Medicine), Dept. of Immunology, Genetics and Pathology, Uppsala University

Title: Exploiting allelic loss in cancer therapy: Identification of NAT2 and CYP2D6 as potential targets

Summary:
Loss of heterozygosity (LOH) is observed in >90% of human cancers and results in the loss of allelic variation in thousands of genes. LOH thus creates genetic differences between tumor and normal cells, particularly at gene loci where the individual is heterozygous for a wildtype and a loss-of-function (LoF) allele. We have sought to identify genes with common LoF polymorphisms where tumor cells that have lost the gene activity can be targeted by low-molecular-weight drugs or other means. We previously reported that recurring LOH at the NAT2 locus at 8p22 in colorectal cancers (CRCs), and the ensuing loss of NAT2 enzyme activity, could be exploited for anticancer therapy. Recently, we discovered a group of ATPase inhibitors that exhibited specific toxicity to CRC cells with high NAT2 activity. In parallel, we investigated the CYP2D6 locus as the CYP2D6 enzyme metabolizes ~25% of clinically used drugs and frequently undergoes LOH in several tumor types. We have established liver cancer cell models and demonstrated that the activity of three anti-cancer compounds, used in clinic or in clinical trials, is dependent on CYP2D6. We anticipate that a subset of CRC and liver cancer patients with LOH events in NAT2 or CYP2D6 will benefit from this research.

2. Kehuan Wang, PhD Student at Carl-Henrik Heldin’s Lab (Cancer), Dept. of Medical Biochemistry and Microbiology, Uppsala University

Title: The Proteasomal, Lysosomal and Autophagosomal Degradation Pathways of PDGFRβ

Summary:

Platelet-derived growth factor (PDGF)-induced signaling via PDGF receptor β (PDGFRβ) leads to activation of downstream signaling pathways which regulate multiple cellular responses, such cell migration, proliferation and survival. Signaling via PDGFRβ is dependent on subcellular location of signaling molecules and hence the internalization of the receptor. It is not clear exactly how PDGFRβ is degraded, both endosomal/lysosomal and proteasomal degradation has been suggested. In this study, we have characterized the proteolytic cleavage of ligand-induced PDGFRβ and found that proteolytic cleavage of PDGFRβ resulted in two fragments. This cleavage is dependent on the internalization of PDGFRβ, which can be blocked by the treatment with bortezomib. Treatment with bortezomib resulted in increased phosphorylation of PDGFRβ and the down-stream signaling molecules PLCγ and STAT3, while phosphorylation of Erk1/2 MAPK was reduced and Akt was unaffected. We also investigated the possibility that PDGFRβ is degraded by selective autophagy in response to starvation or ligand-induced downregulation of receptor from the cell surface. We found that PDGFRβ accumulated in cells treated with bafilomycin A1 upon serum starvation which could be reversed by inhibition of protein synthesis with cycloheximide. Overexpression of LC3A, but not LC3B, promoted the formation of a complex between PDGFRβ and p62. Additionally, PDGFRβ interacted with LC3A and other members of LC3-like family, i.e. GABARAP and GABARAPL1. In conclusion, we speculate that the step-wise proteolytic cleavage of PDGFRβ may have functional consequences for signaling. Macroautophagy may not play a major role in ligand-induced downregulation of PDGFRβ but it could be involved in downregulation of PDGFRβ during starvation via targeting by p62 to non-conventional autophagic or proteasomal pathways that include LC3A and GABARAPs. The functional involvement of these pathways in the control of PDGFRβ levels remains to be further investigated.

SciLifeLab Optical Clearing and Expansion symposium
2022-12-06 09:00 - 18:45 | Eva & Georg Klein, Solnavägen 9, Stockholm, 17165, Sweden
The Advanced Light Microscopy unit at Science for Life laboratory cordially welcomes you to a symposium on developments and applications of clearing and expansion methods from world leading experts.

Registration

Registration form

Program

12:45Whole-body/organ imaging with single-cell resolution by CUBICHiroki Ueda – University Tokyo/Riken BDR, Japan13:15DISCO clearing approaches paired with spatial molecular mappingHarsharan Bhatia, Helmholtz Munich, Germany13:45Volumetric imaging of cleared samplesJacques Paysan – ZEISS14:15Coffee break14:40Expansion Microscopy: Development, Application, and Future DirectionsJinyoung Kang – MIT, USA15:10Pan-ExM-t for molecular ultrastructural visualization of brain tissueOns M’Saad – Yale University, USA15:40Coffee break16:05Cryo-ExM: coupling cryo-fixation with expansion microscopyVirginie Hamel – University of Geneva, Switzerland16:35Visualizing cellular and tissue ultrastructure using TRExHugo Damstra – Utrecht University, The Netherlands17:15-18:45POSTER session with snacks/beverages

Contact

hans.blom@scilifelab.se

Workshop on Advanced Correlative Light and Electron Microscopy (CLEM) methods
2022-12-05 08:00 - 2022-12-08 17:00 | Kemiskt Biologiskt Centrum, Umeå University, Linnaeus väg 6, Umeå, 90736
This 4-day workshop aims to highlight the advanced correlative light and electron microscopy (CLEM) techniques. Participants will learn the latest workflows on how to correlate fluorescence microscopy images with high resolution EM images obtained from state-of-the-art equipment.

Read more

Workshop Content:The workshop includes both theory lectures and practical sessions on In-resin preserved florescence for CLEM, Tokuyasu ultramicrotome sectioning combined with staining techniques on sections, Cryo-CLEM and cryo-FIB milling, as well as opportunities to discuss specific research projects and receive practical advice. Technical challenges and new ideas will be discussed, and the participants are welcome to contribute with their experiences.

Target Audience:This workshop is supported by the Nordic EMBL partnership for Molecular Medicine and welcomes applications from its members and other institutions. Participants are required to have practical experience in both light and electron microscopy. Due to limited number of places, registration is based on a selection process. Selected lectures will be open to a larger range of participants and can be registered for under a ‘lecture only’ registration.Certificate/Credits:A course certificate will be provided to successful participants and a recommendation for 1,5 ECTS.

[Clinical Talks] Recording biology to the genome itself
2022-12-01 17:30 - 18:00 | Online event via Zoom
Jay Shendure

Professor of Genome Sciences at the University of Washington

Jay Shendure is a Investigator of the Howard Hughes Medical Institute, Professor of Genome Sciences at the University of Washington, Director of the Allen Discovery Center for Cell Lineage Tracing, and Scientific Director of the Brotman Baty Institute for Precision Medicine.

His 2005 doctoral thesis with George Church included one of the first successful reductions to practice of next generation DNA sequencing. Dr. Shendure’s research group in Seattle pioneered exome sequencing and its earliest applications to gene discovery for Mendelian disorders and autism; cell-free DNA diagnostics for cancer and reproductive medicine; massively parallel reporter assays, saturation genome editing; whole organism lineage tracing, and massively parallel molecular profiling of single cells.Dr. Shendure is the recipient of the Curt Stern Award from the American Society of Human Genetics (2012), the Richard Lounsbery Award from the National Academy of Sciences (2019) and the Mendel Award from the European Society of Human Genetics (2022) and is an elected member of the American Association for the Advancement of Science (AAAS) and the National Academy of Sciences (NAS). He serves or has previously served as an advisor to the NIH Director, the US Precision Medicine Initiative, the National Human Genome Research Institute, the Chan-Zuckerberg Initiative and the Allen Institutes for Cell Science and Immunology. He received his MD and PhD degrees from Harvard Medical School in 2007.

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: Pontus Höjer and Guido Baselli
2022-12-01 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:

Pontus Höjer

Afshin Ahmadian – alpha 3

Omics exploration with Droplet Barcode Sequencing (DBS).

Guido Baselli

Vicent Pelechano – gamma 5

Identification of novel factors regulating non genetic cell plasticity in Chronic Myeloid Leukemia.

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

FAIRPoints-Introducing Community Guidelines for Sharing Dataset Quality Information
2022-11-30 17:00 - 18:00 | Online event via Zoom
Location: Online via Zoom

See Event in your Time Zone

Speaker: Dr.Ge Peng

Knowledge about the quality of data and associated metadata, software, workflows and computing environment is important to establish the trustworthiness of individual datasets, support informed decisions on their (re)use, and is an essential part of the diverse data and information distribution ecosystem that supports open-source science. However, quality information, being difficult to curate and often context-specific, is currently not readily available for sharing within and across disciplines.

To help address this challenge, and to promote the creation and (re)use of freely and openly shared dataset quality information, members of multiple, international groups collaborating with domain experts have undertaken the development of community guidelines with practical recommendations for the Earth science community. The guidelines follow the guiding principles of being findable, accessible, interoperable, and reusable (FAIR).

The FAIR dataset quality information guidelines are intended to help stakeholders, such as scientific data centers, digital data repositories, and producers, publishers, stewards and managers of data, to achieve the following: i) capture, describe, and represent quality information of their datasets in a manner that is consistent with the FAIR guiding principles; ii) allow for the maximum discovery, trust, sharing, and reuse of their datasets; and iii) enable international access to and integration of dataset quality information.

Bio:

Dr.Ge Peng is currently a Senior principal research scientist from the University of Alabama in Huntsville (UAH), supporting the NASA Interagency Implementation and Advanced Concepts Team (IMPACT) Project. With a Ph.D. in meteorology and a primary research focus on exploring the variability of essential climate variables of Earth atmosphere, ocean, and cryosphere, she has worked with various types of Earth observations and derived data products. She has first-hand experience of the challenges in finding and obtaining data quality information, which led her to find ways to systematically evaluate data quality as well as document and share quality information. Dr. Peng is a strong advocate of promoting scientific data stewardship and open science. She has volunteered for organizations that strive to minimize the barrier to data and information sharing, such as the Earth System Science Data (ESSD) Journal, the World Meteorological Organization (WMO), and the Earth Science Information Partners (ESIP). Dr. Peng is a leading author of several data stewardship assessment models for national and international Earth science organizations and has published a number of peer-reviewed papers on trends and variability of climate data, research data management and stewardship.

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, and SciLifeLab Data Centre.

Register here

Sign up for future events here

Twitter: @FAIR_Points

Biophysical experiments and biomolecular simulations: A perfect match?
2022-11-30 16:00 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Abstract-BRAINSTRUC__lindorff__Download

A special seminar by Professor Kresten Lindorff-Larsen, University of Copenhagen

DDLS Industry PhD Collaboration Dialogue - online
2022-11-30 09:00 - 11:00 | Online event via Zoom
The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a national 12-year research program that involves 11 partner organizations, collaborators nationally and internationally, the Swedish life science community, industry, healthcare, and other stakeholders in society at large.

During the program, more than 250 PhD students and 200 postdocs in academia and industry will be recruited to facilitate collaborations across sectors and disciplines. The DDLS academic and industrial PhD students and postdocs will all be enrolled in the DDLS Research School promoting acquisition of high competence and skills. This is to meet the future needs within data-driven life sciences, industrial R&D, health care and society. The DDLS Research School will be launched in 2024.

Now, both well established companies, small and medium-sized enterprises, within the data-driven life science sector as well as academia, are invited to partake in this event and contribute to the future of the program.

Aim

The aim of this event is to:

Inform about the program and KAW donation letter that specifies industrial PhDs and Postdocs.

Inform about the DDLS Research School, timeline and recruiting models for industrial PhDs.

Engage industry in the DDLS Program (e.g., being part of the DDLS review committees and involved in decisions and other types of evaluations regarding the DDLS research school).

Discuss how industry would like to contribute to the the DDLS Research School and the program.

Preliminary Agenda

Welcome

Presentation of the DDLS program

Overview of the DDLS Research School

Recruitment Models for DDLS PhD Program – Academia & Industry

Discussion/Dialogue

Registration

Register as soon as possible but no later than November 28th.

Register here

Contact

Mojgan Seraji (contact information below) or DDLS support team: ddls@scilifelab.se

Mojgan SerajiCollaboration ManagerProject leading, SciLifeLab Code of Conduct, DDLS PhD & Postdoc Programs, DDLS Industry CollaborationMojgan.Seraji@scilifelab.uu.se +46 (0) 73 46 97 306

Ancient DNA symposium
2022-11-29 09:00 - 16:30 | Large auditorium, Swedish Museum of Natural History, Frescativägen 40, Stockholm, Sweden
SciLifeLab Ancient DNA. Photo. Mikael Wallerstedt.

The possibility of studying humans, animals, plants, and other forms of life that lived in the past using DNA analysis is providing new insight into history, often with important implications for understanding our contemporary world. Ancient DNA can support investigation of e.g. prehistoric migrations and interactions, cultural practices, and development of agriculture, as well as research into evolution, ecology, and biodiversity.

This symposium is organized to present the forefront and breadth of ancient DNA analysis and its value in context of other information in order to facilitate cross-disciplinary projects.

The event is organized by the Centre for Palaeogenetics at Stockholm University and Swedish Museum of Natural History, in collaboration with SciLifeLab Ancient DNA unit and the National Genomics Infrastructure.

The symposium is free of charge. Deadline for registration is November 18th for on-site participation.

During the coffee breaks, representatives of SciLifeLab Ancient DNA unit, the National Genomics Infrastructure (NGI), and the National Bioinformatics Infrastructure Sweden (NBIS) are available for project discussions.

If you are unable to join the meeting physically, you can take part in all presentations online. Please register below to receive the link.

Registration

Please register for online participation. Registration for on-site participation is closed.

Program and Abstracts

2022-Ancient-DNA-symposium-program-and-abstracts-1Download

The Centre for Cellular Imaging - A research infrastructure for correlated multimodal imaging
2022-11-28 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
The Centre for Cellular Imaging – A research infrastructure for correlated multimodal imaging

Julia Fernandez-Rodriguez

The CCI specializes in 3D correlative imaging, i.e. the sequential combination of two or more imaging techniques to gain knowledge across multiple scales

SciLifeLab 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

Chemical Biology Seminar
2022-11-24 15:00 - 17:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
“DATA-DRIVEN HALLMARKS OF ACUTE MYELOID LEUKEMIA:

BIOLOGICAL, PROGNOSTIC AND THERAPEUTIC IMPLICATIONS”

Tom Erkers

Assistant professor, Dept. of Oncology-Pathology, Karolinska Institutet

“SYNTHETIC SWITCHES FOR DNA REPAIR –

CONTROLLING ENZYMATIC FUNCTIONS AT WILL”

Maurice Michel

Assistant professor, Dept. of Oncology-Pathology, Karolinska Institutet

Nov. 24 at 3.30 pm

Gamma 2 Lunch Room, SciLifeLab Stockholm

And on Zoom

https://ki-se.zoom.us/j/64941340588

Research seminar - Distributing biotechnology and hardware to advance research and health care
2022-11-24 15:00 - 16:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Research seminar with Keith Pardee
Where: Lunch room in Gamma-building floor 2 at SciLifeLab. If you don’t have an access card, wait in the SciLifeLab LobbyWhen: Thursday 24th November, at 3 pm (The early birds will be served some fika, so be there on time)
Keith PardeeAssociate professor, Leslie Dan Faculty of Pharmacy, University of TorontoCanada Research Chair in Synthetic Biology and Human HealthCo-Director, PRiME, Precision Medicine Initiative, Medicine by Design Investigator
Bio
Prof. Keith Pardee is working at the intersection of synthetic biology and human health. His lab is pioneering the development of in vitro devices to host cell-free synthetic gene networks for broad applications in research and human health. Pardee’s research interests include the development of molecular diagnostic tools for communicable diseases like Zika virus, distributed drug manufacturing, and regenerative medicine.
He is also the co-founder of several companies and initiatives including PRiME: A Precision Medicine Initiative, En Carta Diagnostics, Medicine by Design 2.0, LSK Technologies, and Liberum Biotech.
https://www.pardeelab.org/

Campus Solna Seminar Series: Charlotte Stadler and Linnea Påvenius
2022-11-24 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:

Charlotte Stadler

Spatial Proteomics – alpha 2

New multiplexed imaging services and translational research within the Spatial Proteomics Unit.

Linnea Påvenius

Hjalmar Brismar – gamma 3

Mitochondrial dynamics in primary and transformed cells.

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

SciLifeLab Platform Day - Uppsala site
2022-11-24 09:00 - 17:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
This day will be held to promote and introduce an array of SciLifeLab infrastructure platforms based in Uppsala.
Venue: Trippelrummet, and on ZoomTime: 9:00-17:00

REGISTER HERE

SEE THE PROGRAM HERE

Aquatic Microbiome Research Initiative -All-Hands meeting
2022-11-24 08:00 - 2022-11-25 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
This year’s AMRI All-Hands meeting will feature speakers from EMBL, Centro Nacional de Biotecnología, Umeå University, and the LEAF sustainable lab program.

Read more and register

The evening of the 24th we will welcome all AMRI participants on an excursion to the Baltic Sea Science Centre, followed by a dinner.

**A dinner for postdocs and early career researchers is scheduled for the evening of November 23rd, to be followed by a morning workshop designed for postdocs and early careers on November 24th.

AMRI covers the cost of travel and accommodations for those traveling from outside the Stockholm/Uppsala area.

National support with superresolution light microscopy
2022-11-22 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 autumn 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 the schedule for autumn 2022 here.

On November 22nd, 12:00-13:00, you are welcome to participate in the seminar

National support with superresolution light microscopy

by Hans Blom, Royal Institute of Technology (KTH), Head of the Advanced Light Microscopy (ALM) Unit, SciLifeLab

More information about the national SciLifeLab facility Integrated Microscopy Technologies.

About Hans Blom

registration

Registration deadline: Monday, November 21st, 10:00.

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

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

Glycoproteomics - How to analyze the importance of protein glycosylation
2022-11-21 12:00 - 13:00 | Birgit Thilander Lecture Hall, Medicinaregatan 3, Göteborg
Glycoproteomics – How to analyze the importance of protein glycosylation

Carina Sihlbom

Changes in the glycosylation of proteins is one of the first signs of a disease, and advanced mass spectrometry is central for the study of such protein structure.

SciLifeLab 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

NBIS/ELIXIR-SE Tools for Reproducible Research - ONLINE
2022-11-21 09:00 - 2022-11-25 15:30 | Online event via Zoom
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

Apply here

Course webpage

Important dates

Application open: Sep 5, 2022

Application deadline: Oct 21, 2022

Confirmation to accepted participants: Oct 28, 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 outcomes

By 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.
