New DDLS Strategy launched

The strategy for the SciLifeLab and Wallenberg Netional Program for Data-Driven Life Science (DDLS) has been updated. The corresponding strategy document is now publicly available.

It is clear that the future of science is becoming increasingly data driven, with the quantity and complexity of data seemingly ever-increasing. To meet the new challenges arising from this, the scientific community must gain more data analysis expertise and develop new capabilities. The DDLS encapsulates this in it’s vision ‘The future is data-driven’, and aims to equip the life science community of Sweden with the necessary skills and capabilities to enable them to thrive in this new scientific age.

The DDLS program was funded in late 2020 by the Knut and Alice Wallenberg Foundation (KAW), and is hosted primarily by SciLifeLab. It is a 12 year, 3.1 Billion SEK program. The program will recruit 39 DDLS fellows, 250 PhD students, and around 200 Postdocs.

This new long-term strategy reflects the plans for the next 10 years of the program. It was developed by the DDLS steering group, the eleven participating organisations (ten universities, Chalmers, GU, KI, KTH, LiU, LU, NRM, SLU, SU, UmU and UU, and the Swedish Museum of Natural History, NRM), as well as the SciLifeLab Board, SciLifeLab International Advisory Board (IAB), SciLifeLab Management Group, SciLifeLab Operations Office, SciLifeLab Data Centre, NBIS, and in communication with other KAW-funded research programs. Please see the official news release from Scilifelab for more.

Get your work featured!

It is now easier than ever to get your work featured on the SciLifeLab Data Platform. All you have to do is get in touch to tell us about what you’d like to share/have hosted, so that we can begin the review process.

We offer hosting for services related to data-driven life science in Sweden, and are happy to include services hosted elsewhere in our Service catalogue. We also publish short, data-focused articles (data highlights) to promote research that shares data and/or code in accordance with the principles of FAIR and open data sharing.

We update jobs, calls, and events/training opportunities on the site weekly, and are happy to hear about opportunities that you’d like promoted within the Swedish data-driven life science community.

New highlight on study revealing sex determination genes in a malaria parasite that are essential in disease transmission

We have published a new data highlight, entitled ‘Discovery of sex determination genes in a malaria parasite that are essential for mosquito transmission’, which is based on Russell et al. (2023)

Malaria remains a major threat to public health. Understanding how malaria is transmitted via mosquitoes is crucial in tackling the spread of the disease, because it could enable scientists to devise new methods of preventing the spread. In a recent publication resulting from an international collaboration, reserachers studied how sex is determined in Plasmodium berghei, and how this affects transmission of malaria. Plasmodium berghei is a causative agent of malaria in rodents, and can be used as a model to study malaria in humans. The researchers combined functional screens of barcoded mutants and single cell transcriptomics to understand the biology of this highly divergent and poorly tractable eukaryote. Raw data, as well as mass spectrometry data and code were shared openly.

Do you have some data-driven life science research that you’d like to highlight, or even present as a service, on the SciLifeLab Data Platform? If so, please fill out the forms on the appropriate pages or get in touch.

Making it easier to find job/funding/project opportunities in data-driven life science.

You may have become familiar with our ‘Calls & Jobs’ section over the last few months. The section included funding calls, jobs, postdoc positions, PhD positions, and project opportunities related to data-driven life science. We’re now making it easier for you to find exactly what you’re looking for!

We’ve split ‘Calls & Jobs’ into two sections; ‘Jobs’ and ‘Funding calls’. In the Jobs section, you’ll find postdoc positions, BSc/MSc project opportunities, and other jobs in data-driven life science. Anyone that wants to promote a relevant position on the page is welcome to use the form on that page to get in touch (alternatively, you can email data-platform@scilifelab.se or datacentre@scilifelab.se). In the Funding calls section, you’ll find direct links to funding opportunties from SciLifeLab, and potential other sources of funding for data-driven life science projects.

We’ve also added filtering to the Jobs section. This allows you to search for a given type of position (job/postdoc position/PhD position/project opportunity), and/or for positions with a given employer.

These sections are updated weekly (usually on Fridays), so it’s worth checking back regularly for new opportunities!

If you have any suggestions for improvements that can be made to any element of the SciLifeLab Data Platform, or recommendations for new sections/services that could be added, please get in touch.

New data highlight related to the use of a long-read sequencing method in cancer diagnostics

We have published a new data highlight, entitled ‘Novel long-read sequencing workflow developed for use in routine cancer diagnostics’, which is based on Schaal et al. (2022).

Some patients develop resitance to drugs used to treat Chronic Myeloid Leukemia (CML). Sanger sequencing is routinely used in clinical settings to identify mutations related to this drug resistance. Sanger sequencing has known limitations, but is used as routine due to difficulties in establishing newer methods in a clinical setting. Schaal et al. (2022) developed a workflow/pipeline that makes use of long-read sequencing, which was recently named Method of the Year 2022 by Nature Methods, to detect and identify mutations related to drug resistance in Chronic Myeloid Leukemia (CML) treatment. The showed that this pipeline was both more senstive than Sanger sequencing, and relatively simple to establish in clinical settings.

Do you have some data-driven life science research that you’d like to highlight on the SciLifeLab Data Platform? Or perhaps you have events/jobs/projects in your group that you’d like to advertise on the SciLifeLab data platform? If so, please fill out the forms on the appropriate pages (e.g. in the data highlights section), or email us at datacentre@scilifelab.se.

Happy holidays to all (see you in the new year)!

We on the SciLifeLab Data Platform would like to take this opportunity to to wish you all ‘God jul och gott nytt år!’. We’d also like to thank the data-driven life science community in Sweden for their support in our very first year! We’ve developed some great collaborations with the community this year, and look forward to continuing those (and building even more!) next year.

The team are also getting into the spirit, and support levels will be lower during the holiday period. We’ll be back to normal levels of support from 9th January 2023.

In the meantime, please feel free to get in touch with us, and we’ll get back to you as quickly as you can! We’re always really happy to hear about any jobs, funding, or project opportunities, potential data highlights, or events that could be of interest to the data-driven life science community.

New data highlight related to the study of enteroviruses

We have published a new data highlight, entitled ‘Cryo-electron tomography allows new knowledge about poliovirus replication and assembly sites in situ’, which is based on Dahmane et al. (2022). The study used cryo-electron tomography to examine how enteroviruses are assembled and packaged into autophagosomes. Enteroviruses cause many diseases, some of which can have devastating effects on society, such as polio. The data and code related to the study are openly shared to support the reproduction of the results of the present study, as well as future studies in this area. This highlight is also published on the COVID-19 and Pandemic Preparedness Portal, as it relates to pandemic preparedness work.

Do you have some data-driven life science research that you’d like to highlight on the SciLifeLab Data Platform? Or perhaps you have events/jobs/projects in your group that you’d like to advertise on the SciLifeLab data platform? If so, please fill out the forms on the appropriate pages (e.g. in the data highlights section), or email us at datacentre@scilifelab.se.

Improving user experience and Data Science Node (DSN) jobs

We’ve made multiple changes to the Data Platform aimed at improving user experience. In particular, we’ve made changes to the homepage layout, adjusted the colour and size of some elements (e.g. services cards, hyperlinks) to make them clearer, and made it possible to link directly to different data higlights and services by clicking on the images associated with them. We’d be interested to hear any feedback that you might have for further improvements that we should consider.

Today, we are also releasing our largest single update of jobs to date. Many of the jobs in this update are related to the establishment of Data Science Nodes (DSNs) that are being established as part of the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS). Our jobs page is updated weekly, so we encourage those looking for positions in the area of Data-Driven Life Science to check back regularly! Those advertising a position in this area are invited to inform us of it by filling in the form on our jobs page.

We will continue to add new events, data highlights, and services as they become available. Please get in touch if you’re interested in advertising an event on the Data Platform, or if you’re interested in having your research become the subject of a data highlight.

New data highlight added, and other updates

Our latest data highlight, entitled ‘New study shows crossing the salt barrier has shaped the diversity of life’ is based on Jamy et al. (2022). The study examines the evolution of habitat preference across eukaryotes. Specifically, they considered transitions across the ‘salt-barrier’. Their study showed that such transitions were likely key evolutionary events that were integral to creating the eukaryotic diversity we see today. This data highlight was a contribution direct from the life science community, and was written by first author Mahwash Jamy. As with all of our data highlights, the resources from the project are shared as openly as possible and are directly linked in the highlight to improve findability.

We have also been making regular updates to our jobs and events pages. Please check those out to stay up to date on the latest opportunities relevant to data driven life science.

Do you have some data-driven life science research that you’d like to highlight on the portal? Or perhaps you have events/jobs/projects in your group that you’d like to advertise on the SciLifeLab data platform? If so, please fill out the forms on the appropriate pages (e.g. in the data highlights section), or email us at datacentre@scilifelab.se.

New data highlight 'GenErode pipeline can compare patterns of genomic erosion using genomic data from historical, ancient and modern samples' added.

Today, we have published a new data highlight on the SciLifeLab Data Platform. This latest highlight, details work on the GenErode pipeline as described in a recent paper by Kutschera et al. (2022). The GenErode pipeline is the first bioinformatics pipeline that can process and analyse ancient, historical, and modern sequencing data from the same species with the aim of generating comparable estimates of genomic erosion indices. Experience with coding with not necessary to work with this pipeline, and all bioinformatics steps are well documented, making it very accessible to users.

Have you completed some data-driven life science research and openly shared the data and/or code? Why not get in touch about having it featured as a data highlight? You can contact us by completing the form in our data highlights section, or emailing us at datacentre@scilifelab.se.

New data highlight 'Bayesian deep learning model finds clues about the evolution of open habitats' added.

Our latest data highlight is now live on the SciLifeLab Data Platform. This latest highlight, summarises a recent paper by Andermann et al. (2022). The study explores the evolution and expansion of open grassland habitats. The study uses deep learning models that are trained using information on mammal-plant interactions based on openly available fossil record data.

Have you completed some data-driven life science research and openly shared the data and/or code? Why not get in touch about having it featured as a data highlight? You can contact us by completing the form in our data highlights section, or emailing us at datacentre@scilifelab.se.

New service related to the subcellular localisation of proteins and the outcomes of the SubCellBarCode project.

Today, we have launched a new service page related to the SubCellBarCode project. The SubCellBarCode service page is a collation of all of the resources (including tools, web portal, publications, methodologies, etc.) produced as part of the SubCellBarCode project. This page has been produced in close collaboration with those involved in the project and will be updated with new outcomes over time.

The aim of this service page is to facilitate the use of the tools and resources generated within the SubCellBarCode project. The project has shared a significant amount of data, in-depth explanations regarding the methodologies used, and multiple research tools (e.g. R analysis package, visualisation tools). Each of these elements can be accessed from the SubCellBarCode service page. It is hoped that the collation and promotion of these resources will accelerate efforts related to the subcellular localisation of proteins. Such studies are incredibly important, particularly as they have implications in human disease e.g. in cancer.

If you have a tool/dataset/service/set of resources that you think that we should add to our service catalogue, reach out to let us know!

New service related to the management of life science research data in Sweden

We are pleased to announce the launch of SciLifeLab RDM (research data management) guidelines. This new resource, developed and maintained in collaboration with NBIS, will act as a knowledge hub for the management of life science research data in Sweden. The resource will be updated and expanded over time, with new features and sections already planned. As always, we encourage you to get in touch with any feedback that you might have on this new service.

If you have a tool/dataset/service/set of resources that you think should be added to our service catalogue, please let us know!

New feature added - Recent apps deployed on SciLifeLab Serve displayed on homepage

We have added a new feature that is related to one of our services; SciLifeLab Serve. SciLifeLab Serve is a service for deploying apps (including Shiny and Dash apps) and serving machine learning models (Tensorflow and PyTorch serving). The service is currently in beta testing and is looking for test users.

You will find the 8 most recently deployed public apps at the bottom of the homepage on the SciLifeLab Data Platform. You can click on the app title to go directly to a specific app. Alternatively, you can go straight to SciLifeLab Serve itself to explore more public apps and models, as well as find out how to enquire about becoming a test user.

New data highlight 'DNA methylation inherited across generations in water fleas may influence freshwater ecosystems' added.

We’re starting off the post-summer season on the SciLifeLab Data Platform with a new data highlight. This latest highlight, summarises a recent paper by Feiner et al. (2022). The study explored whether epigenetic effects, induced by stressors, could influence freshwater ecosystems long-term. The study focussed in particular on the impact that climate change could have on this threatened ecosystem type.

Have you completed some data-driven life science research and openly shared the data and/or code? Why not get in touch about having it featured as a data highlight? You can contact us by completing the form in our data highlights section, or emailing us at datacentre@scilifelab.se.

New data highlight 'Unravelling the assembly of the mitoribosome' added

Check out the latest data highlight added to the SciLifeLab Data Platform. This highlight, entitled ‘Unravelling the assembly of the mitoribosome’, relates to a recent publication by Itoh et al. (2022). The study uses cryo-electron microscopy to understand the mechanisms underlying mitoribosomal assembly.

It is the first data highlight to be drafted by one of the corresponding authors of the original paper - in this case, senior author Prof. Alexey Amunts. If you’re interested in writing a data highlight to promote data-driven life science research that you’ve been involved in, please complete the form in our data highlights section, or email us at datacentre@scilifelab.se.

New data highlight 'A deep learning framework to estimate species diversity' added

A new data highlight has been added to the SciLifeLab Data Platform. This latest data highlight, entitled ‘A deep learning framework to estimate species diversity’ considers a recent publication by Andermann et al. (2022). The study explores whether deep learning frameworks can be used to accurately estimate biodiversity, and thus to target conservation efforts.

All of our data highlights can be found in our data highlights section. Why not check out our other highlights too?

Want to suggest a study for us to highlight? Get in touch by filling in the form in our data highlights section, or email us at datacentre@scilifelab.se.

New section on calls/jobs/projects related to data-driven life science in Sweden

A new section has been added to the SciLifeLab Data Platform. In our new ‘Calls & Jobs section’, we will show all of the latest funding calls, job listings, and masters thesis opportunities related to data-driven life science in Sweden. You will be able to see the application deadline, location, and basic summary information right on the page. We’ll also provide a link to where you can find out more.

See something we’ve missed? Feel free to get in touch with us to make suggestions for how to improve the page, or to tell us about opportunties that you think should be listed.

SciLifeLab Data Platform website launched

Today marks the official launch of the SciLifeLab Data Platform website, which can be found at data.scilifelab.se. The Platform will act as a hub for data-driven life science in Sweden. It will include work on data-driven life science from all those affiliated with a Swedish research institution, not just SciLifeLab. The Platform will incorporate multiple resources (tools, services, and datasets), and highlight relevant news, data, and events. Much more will be added over time, so watch this space.

We invite the the research community to contribute to all sections of the Platform. We welcome their feedback on the current content, as well as their suggestions on what else they would like to see here.

SciLifeLab Data Centre to lead work on databases and data support for DDLS

In a recent meeting, the SciLifeLab Board assigned SciLifeLab Data Centre to lead work on databases and data support for the Wallenberg National Program on Data-Driven Life Science (DDLS). SciLifeLab Data Centre will report on this work to the DDLS steering group. A budget of 140 MSEK has been allocated for the support of databases and data support during the first three years of the program.

Wallenberg National Program on Data-Driven Life Science (DDLS) announced

The Knut and Alice Wallenberg foundation has announced the Data-Driven Life Science (DDLS) program. Funding for the program comprises 3.1 billion SEK, to be distributed over a period of 12 years. The initiative gives priority to data-driven life science in 4 areas; cellular and molecular biology, evolution and biodiversity, precision medicine and diagnostics, and epidemiology and infection biology.