diff --git a/Dockerfiles/Dockerfile b/Dockerfiles/Dockerfile index 68599625..84cc1f6e 100644 --- a/Dockerfiles/Dockerfile +++ b/Dockerfiles/Dockerfile @@ -16,6 +16,7 @@ RUN wget --quiet "https://github.com/gohugoio/hugo/releases/download/v${HUGO_VER # Serve the generated html using nginx FROM nginxinc/nginx-unprivileged:alpine RUN sed -i '3 a\ absolute_redirect off;' /etc/nginx/conf.d/default.conf && \ + sed -i '4 a\ add_header X-Frame-Options DENY always;' /etc/nginx/conf.d/default.conf && \ sed -i 's/#error_page 404/error_page 404/' /etc/nginx/conf.d/default.conf COPY --from=build /target /usr/share/nginx/html diff --git a/content/news/2020-10-20.md b/content/news/2020-10-20.md index 700affec..ce02bb96 100644 --- a/content/news/2020-10-20.md +++ b/content/news/2020-10-20.md @@ -1,6 +1,9 @@ --- title: Wallenberg National Program on Data-Driven Life Science (DDLS) announced date: 2020-10-20 +thumbnail: "/img/news/kaw.png" +caption: "The Knut and Alice Wallenberg logo" +images: ["/img/news/kaw.png"] --- The Knut and Alice Wallenberg foundation has [announced the Data-Driven Life Science (DDLS) program](https://kaw.wallenberg.org/en/press/sek-37-billion-funding-life-science-knut-and-alice-wallenberg-foundation-launches-new). 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. diff --git a/content/news/2021-03-10.md b/content/news/2021-03-10.md index 8f5b88f6..5024a113 100644 --- a/content/news/2021-03-10.md +++ b/content/news/2021-03-10.md @@ -1,6 +1,9 @@ --- title: SciLifeLab Data Centre to lead work on databases and data support for DDLS date: 2021-03-10 +thumbnail: "/img/news/ddls_fund.png" +caption: "Representation of DDLS generated using AI." +images: ["/img/news/ddls_fund.png"] --- In a recent [meeting](https://www.scilifelab.se/wp-content/uploads/2021/03/SciLifeLab-board-minutes-no-50-210310-final.pdf), 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)](https://www.scilifelab.se/data-driven). 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. \ No newline at end of file diff --git a/content/news/2022-06-02.md b/content/news/2022-06-02.md index d4f03aa9..d89d71ba 100644 --- a/content/news/2022-06-02.md +++ b/content/news/2022-06-02.md @@ -2,6 +2,9 @@ title: SciLifeLab Data Platform website launched publishDate: 2022-05-18 date: 2022-06-02 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- Today marks the official launch of the SciLifeLab Data Platform website, which can be found at [data.scilifelab.se](https://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. diff --git a/content/news/2022-06-17.md b/content/news/2022-06-17.md index 95a017eb..35b6b94d 100644 --- a/content/news/2022-06-17.md +++ b/content/news/2022-06-17.md @@ -1,8 +1,11 @@ --- title: New section on calls/jobs/projects related to data-driven life science in Sweden date: 2022-06-17 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- -A new section has been added to the SciLifeLab Data Platform. In our new ['Calls & Jobs section'](/funding), 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. +A new section has been added to the SciLifeLab Data Platform. In our new ['Calls & Jobs section'](/funding_calls), 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**](https://data.scilifelab.se/contact/) with us to make suggestions for how to improve the page, or to tell us about opportunties that you think should be listed. \ No newline at end of file +**_See something we've missed?_** Feel free to [**get in touch**](https://data.scilifelab.se/contact/) with us to make suggestions for how to improve the page, or to tell us about opportunties that you think should be listed. diff --git a/content/news/2022-06-21.md b/content/news/2022-06-21.md index 899c7928..761eb007 100644 --- a/content/news/2022-06-21.md +++ b/content/news/2022-06-21.md @@ -1,9 +1,13 @@ --- title: New data highlight 'A deep learning framework to estimate species diversity' added date: 2022-06-21 +thumbnail: "/img/news/deep_learning_framework_estimate_biodiv_small.jpeg" +caption: "The data preparation workflow implemented in Andermann et al. 2022 (Fig. 2 in original article)." +show_thumbnail_on_page: True +images: ["/img/news/deep_learning_framework_estimate_biodiv_small.jpeg"] --- -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'](https://data.scilifelab.se/highlights/deep_learning_framework_estimate_biodiversity/) considers a recent publication by [Andermann *et al.* (2022)](https://www.frontiersin.org/articles/10.3389/fpls.2022.839407/full). The study explores whether deep learning frameworks can be used to accurately estimate biodiversity, and thus to target conservation efforts. +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'](https://data.scilifelab.se/highlights/deep_learning_framework_estimate_biodiversity/) considers a recent publication by [Andermann _et al._ (2022)](https://www.frontiersin.org/articles/10.3389/fpls.2022.839407/full). 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](/highlights/). Why not check out our other highlights too? diff --git a/content/news/2022-07-07.md b/content/news/2022-07-07.md index b80f05d6..24790bd1 100644 --- a/content/news/2022-07-07.md +++ b/content/news/2022-07-07.md @@ -1,6 +1,10 @@ --- title: New data highlight 'Unravelling the assembly of the mitoribosome' added date: 2022-07-07 +thumbnail: "/img/news/mitoribosome_assembly_small.jpeg" +caption: "Small mitoribosomal subunit (Credit; Verena Resch)." +show_thumbnail_on_page: True +images: ["/img/news/mitoribosome_assembly_small.jpeg"] --- Check out the latest [data highlight](/highlights/) added to the SciLifeLab Data Platform. This highlight, entitled ['Unravelling the assembly of the mitoribosome'](/highlights/unravelling_mitoribosome_assembly/), relates to a recent publication by [Itoh *et al.* (2022)](https://www.nature.com/articles/s41586-022-04795-x). The study uses cryo-electron microscopy to understand the mechanisms underlying mitoribosomal assembly. diff --git a/content/news/2022-08-12.md b/content/news/2022-08-12.md index d1c79c10..2b3154a8 100644 --- a/content/news/2022-08-12.md +++ b/content/news/2022-08-12.md @@ -1,6 +1,10 @@ --- title: New data highlight 'DNA methylation inherited across generations in water fleas may influence freshwater ecosystems' added. date: 2022-08-12 +thumbnail: "/img/news/daphnia_banner.jpeg" +caption: "The graphical abstract from Feiner et al. (2022)" +show_thumbnail_on_page: True +images: ["/img/news/daphnia_banner.jpeg"] --- We're starting off the post-summer season on the SciLifeLab Data Platform with a new [data highlight](/highlights/). This [latest highlight](/highlights/daphnia_dna_methylation/), summarises a recent paper by [Feiner *et al.* (2022)](https://www.cell.com/iscience/fulltext/S2589-0042(22)00573-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004222005739%3Fshowall%3Dtrue). 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. diff --git a/content/news/2022-09-02.md b/content/news/2022-09-02.md index e332e378..365a7fd0 100644 --- a/content/news/2022-09-02.md +++ b/content/news/2022-09-02.md @@ -1,6 +1,9 @@ --- title: New feature added - Recent apps deployed on SciLifeLab Serve displayed on homepage date: 2022-09-02 +thumbnail: "/img/news/Scilifelab_serve.png" +caption: "Screenshot from Scilifelab Serve site" +images: ["/img/news/Scilifelab_serve.png"] --- We have added a new feature that is related to one of our services; [SciLifeLab Serve](https://serve.scilifelab.se). 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. diff --git a/content/news/2022-09-29.md b/content/news/2022-09-29.md index 3cd17c79..8918ca80 100644 --- a/content/news/2022-09-29.md +++ b/content/news/2022-09-29.md @@ -1,6 +1,9 @@ --- title: New service related to the management of life science research data in Sweden date: 2022-09-29 +thumbnail: "/img/news/rdm.jpg" +caption: "Illustration for RDM" +images: ["/img/news/rdm.jpg"] --- We are pleased to announce the launch of [SciLifeLab RDM (research data management) guidelines](https://data-guidelines.scilifelab.se). This new resource, developed and maintained in collaboration with [NBIS](https://nbis.se), 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](https://data-guidelines.scilifelab.se/contact/) with any feedback that you might have on this new service. diff --git a/content/news/2022-10-03.md b/content/news/2022-10-03.md index 30a98751..b62f03ed 100644 --- a/content/news/2022-10-03.md +++ b/content/news/2022-10-03.md @@ -1,6 +1,10 @@ --- title: New service related to the subcellular localisation of proteins and the outcomes of the SubCellBarCode project. date: 2022-10-03 +thumbnail: "/img/news/subcell.jpg" +caption: "SubCellBarCode Logo" +show_thumbnail_on_page: True +images: ["/img/news/subcell.jpg"] --- Today, we have launched a new [service page](/services/) related to the SubCellBarCode project. The [SubCellBarCode service page](/subcellbarcode/) 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. diff --git a/content/news/2022-10-06.md b/content/news/2022-10-06.md index 52b62512..3b604285 100644 --- a/content/news/2022-10-06.md +++ b/content/news/2022-10-06.md @@ -1,6 +1,9 @@ --- title: New data highlight 'Bayesian deep learning model finds clues about the evolution of open habitats' added. date: 2022-10-06 +thumbnail: "/img/news/still_transition_model.png" +caption: "Snapshot of vegetation over time. Courtesy Tobias Andermann, Uppsala University" +images: ["/img/news/still_transition_model.png"] --- Our latest [data highlight](/highlights/) is now live on the SciLifeLab Data Platform. This [latest highlight](/highlights/bayesian_open_habitat/), summarises a recent paper by [Andermann *et al.* (2022)](https://www.nature.com/articles/s41467-022-32300-5). 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. diff --git a/content/news/2022-10-13.md b/content/news/2022-10-13.md index a61c1806..d4714346 100644 --- a/content/news/2022-10-13.md +++ b/content/news/2022-10-13.md @@ -1,6 +1,10 @@ --- title: New data highlight 'GenErode pipeline can compare patterns of genomic erosion using genomic data from historical, ancient and modern samples' added. date: 2022-10-13 +thumbnail: "/img/news/GenErode.png" +caption: "Image courtesy of David Díez-del-Molino." +show_thumbnail_on_page: True +images: ["/img/news/GenErode.png"] --- Today, we have published a new [data highlight](/highlights/) on the SciLifeLab Data Platform. This [latest highlight](/highlights/generode/), details work on the GenErode pipeline as described in a recent paper by [Kutschera *et al.* (2022)](https://doi.org/10.1186/s12859-022-04757-0). 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. diff --git a/content/news/2022-10-21.md b/content/news/2022-10-21.md index 75218001..6547e5f2 100644 --- a/content/news/2022-10-21.md +++ b/content/news/2022-10-21.md @@ -1,6 +1,10 @@ --- title: New data highlight added, and other updates date: 2022-10-21 +thumbnail: "/img/news/diversity_of_life_thumbnail.png" +caption: "Cropped figure 1 from Jamy et al. (2022), Global eukaryotic 18S–28S phylogeny from environmental samples and the distribution of habitats." +show_thumbnail_on_page: True +images: ["/img/news/diversity_of_life_thumbnail.png"] --- Our latest [data highlight](/highlights/), entitled ['New study shows crossing the salt barrier has shaped the diversity of life'](/highlights/diversity_of_life/) is based on [Jamy *et al.* (2022)](https://doi.org/10.1038/s41559-022-01838-4). 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. diff --git a/content/news/2022-12-09.md b/content/news/2022-12-09.md index 07dea867..0afec210 100644 --- a/content/news/2022-12-09.md +++ b/content/news/2022-12-09.md @@ -1,6 +1,9 @@ --- title: Improving user experience and Data Science Node (DSN) jobs date: 2022-12-09 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- 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](/contact/) that you might have for further improvements that we should consider. diff --git a/content/news/2022-12-19.md b/content/news/2022-12-19.md index b4d64bfe..ee044e45 100644 --- a/content/news/2022-12-19.md +++ b/content/news/2022-12-19.md @@ -1,6 +1,10 @@ --- title: New data highlight related to the study of enteroviruses date: 2022-12-19 +thumbnail: "/img/news/segmentation_highReso.jpeg" +caption: "Cropped cryo-electron tomogram gives a 3D view of a poliovirus-infected." +show_thumbnail_on_page: True +images: ["/img/news/segmentation_highReso.jpeg"] --- We have published a new [data highlight](/highlights/), entitled ['Cryo-electron tomography allows new knowledge about poliovirus replication and assembly sites in situ'](/highlights/poliovirus_replication/), which is based on [Dahmane *et al.* (2022)](https://doi.org/10.1038/s41467-022-33483-7). 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](https://www.covid19dataportal.se/), as it relates to pandemic preparedness work. diff --git a/content/news/2022-12-22.md b/content/news/2022-12-22.md index c9817b3c..06eaee90 100644 --- a/content/news/2022-12-22.md +++ b/content/news/2022-12-22.md @@ -1,6 +1,10 @@ --- title: Happy holidays to all (see you in the new year)! date: 2022-12-22 +thumbnail: "/img/news/christmas.jpeg" +caption: "Representation of Christmas using free licensed image from [unsplash.com](https://unsplash.com/)." +show_thumbnail_on_page: True +images: ["/img/news/christmas.jpeg"] --- 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. diff --git a/content/news/2023-01-20a.md b/content/news/2023-01-20a.md index a59e219b..756fc3cf 100644 --- a/content/news/2023-01-20a.md +++ b/content/news/2023-01-20a.md @@ -1,6 +1,10 @@ --- title: New data highlight related to the use of a long-read sequencing method in cancer diagnostics date: 2023-01-20 +thumbnail: "/img/news/long_read_seq_pipeline.jpg" +caption: "Figure 5 from Schaal et al. (2022) comparing long-read and Sanger sequencing." +show_thumbnail_on_page: True +images: ["/img/news/long_read_seq_pipeline.jpg"] --- We have published a new [data highlight](/highlights/), entitled ['Novel long-read sequencing workflow developed for use in routine cancer diagnostics'](/highlights/long_read_seq_workflow/), which is based on [Schaal *et al.* (2022)](https://doi.org/10.1177/11769351221110872). diff --git a/content/news/2023-01-20b.md b/content/news/2023-01-20b.md index 584311b9..112ac7b7 100644 --- a/content/news/2023-01-20b.md +++ b/content/news/2023-01-20b.md @@ -1,6 +1,9 @@ --- -title: Making it easier to find job/funding/project opportunities in data-driven life science. +title: Making it easier to find job/funding/project opportunities in data-driven life science. date: 2023-01-20 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- 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! @@ -9,6 +12,6 @@ We've split 'Calls & Jobs' into two sections; ['Jobs'](/jobs/) and 'Funding call We've also added filtering to the [Jobs](/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! +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](/contact/). diff --git a/content/news/2023-02-24.md b/content/news/2023-02-24.md index 453e0291..0da22561 100644 --- a/content/news/2023-02-24.md +++ b/content/news/2023-02-24.md @@ -1,6 +1,10 @@ --- title: New highlight on study revealing sex determination genes in a malaria parasite that are essential in disease transmission date: 2023-02-24 +thumbnail: "/img/news/mosquito_transmission_small.jpeg" +caption: "Small mitoribosomal subunit intermediates complexed with auxiliary factors, revealing a sequential mechanism of assembly (Credit; Verena Resch)." +show_thumbnail_on_page: True +images: ["/img/news/mosquito_transmission_small.jpeg"] --- We have published a new data highlight, entitled ['Discovery of sex determination genes in a malaria parasite that are essential for mosquito transmission'](/highlights/sex_determination_malaria/), which is based on [Russell *et al.* (2023)](https://doi.org/10.1016/j.chom.2022.12.011) diff --git a/content/news/2023-03-03.md b/content/news/2023-03-03.md index c1f931ab..67105d8e 100644 --- a/content/news/2023-03-03.md +++ b/content/news/2023-03-03.md @@ -1,6 +1,9 @@ --- title: Get your work featured! date: 2023-03-03 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- 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](/contact/) to tell us about what you'd like to share/have hosted, so that we can begin the review process. diff --git a/content/news/2023-03-24.md b/content/news/2023-03-24.md index 5f21f3a0..55cfa910 100644 --- a/content/news/2023-03-24.md +++ b/content/news/2023-03-24.md @@ -1,6 +1,9 @@ --- title: New DDLS Strategy launched date: 2023-03-24 +thumbnail: "/img/news/ddls_fund.png" +caption: "Representation of DDLS generated using AI." +images: ["/img/news/ddls_fund.png"] --- The strategy for the SciLifeLab and Wallenberg Netional Program for Data-Driven Life Science (DDLS) has been updated. The corresponding [strategy document](https://www.scilifelab.se/data-driven/ddls-strategy) is now publicly available. diff --git a/content/news/2023-04-18.md b/content/news/2023-04-18.md index 51fd987c..797e3434 100644 --- a/content/news/2023-04-18.md +++ b/content/news/2023-04-18.md @@ -1,6 +1,10 @@ --- title: New highlight defining a new concept in antibiotic resistance - antibiotic perseverance date: 2023-04-18 +thumbnail: "/img/news/antibiotic_resistance_development_small.jpg" +caption: "Artistic illustration over perseverance courtesy Elf lab / Johan Elf, Irmeli Barkefors." +show_thumbnail_on_page: True +images: ["/img/news/antibiotic_resistance_development_small.jpg"] --- We have published a new data highlight, entitled ['New study shows that perserverance can be the reason for antibiotic resistance development'](/highlights/antibiotic_resistance_development/), which is based on [Brandis *et al.* (2023)](https://doi.org/10.1073/pnas.2216216120) diff --git a/content/news/2023-04-18a.md b/content/news/2023-04-18a.md index 52a135a1..7e7cd26d 100644 --- a/content/news/2023-04-18a.md +++ b/content/news/2023-04-18a.md @@ -1,6 +1,9 @@ --- title: Launch of the SciLifeLab Data Platform date: 2023-04-18 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- Please join us for the [official launch of the Platform - May 26th at 11am via Zoom](https://www.scilifelab.se/event/scilifelab-data-platform-launch/)! diff --git a/content/news/2023-04-28.md b/content/news/2023-04-28.md index 9804a0c1..2e531ec3 100644 --- a/content/news/2023-04-28.md +++ b/content/news/2023-04-28.md @@ -1,6 +1,10 @@ --- title: New services launched related to compute resources date: 2023-04-28 +thumbnail: "/img/news/compute.jpg" +caption: "Representaion of compute resources generated by AI" +show_thumbnail_on_page: True +images: ["/img/news/compute.jpg"] --- We have added two new [services](/services/) pages that are designed to aid researchers, research groups, and research infrastructure to make use of compute resources (otherwise known as e-infrastructure). diff --git a/content/news/2023-05-05.md b/content/news/2023-05-05.md index 7fac2c60..a22fa710 100644 --- a/content/news/2023-05-05.md +++ b/content/news/2023-05-05.md @@ -1,6 +1,10 @@ --- title: New highlight shows variability in IGH antibody genes influences the response to SARS-CoV-2. date: 2023-05-05 +thumbnail: "/img/news/igh_antibody_genes_small.jpg" +caption: "Graphical abstract (Image courtesy Pushparaj et al. 2023)" +show_thumbnail_on_page: True +images: ["/img/news/igh_antibody_genes_small.jpg"] --- We have published a new data highlight, entitled: [Variability in IGH antibody genes influences the response to SARS-CoV-2](/highlights/igh_antibody_genes/), which is based on [Pushparaj et al. (2023)](https://doi.org/10.1016/j.immuni.2022.12.005). diff --git a/content/news/2023-06-01.md b/content/news/2023-06-01.md index fc99ee5a..f566b0f3 100644 --- a/content/news/2023-06-01.md +++ b/content/news/2023-06-01.md @@ -1,6 +1,10 @@ --- title: New highlight shows how changes in METTL3 localisation could hold the key to new antiviral strategies against SARS-CoV-2. date: 2023-06-01 +thumbnail: "/img/news/mettl3_localisation_small.png" +caption: "Graphical abstract (Image courtesy Vaid and Mendez et al. (2023))." +show_thumbnail_on_page: True +images: ["/img/news/mettl3_localisation_small.png"] --- We have published a new data highlight, entitled: [METTL3 localisation during SARS-CoV-2 infection could highlight new novel antiviral strategy](/highlights/mettl3_localisation/), which is based on [Vaid and Mendez _et al._ (2023)](https://doi.org/10.1101/gr.276407.121). diff --git a/content/news/2023-06-01a.md b/content/news/2023-06-01a.md index b2652660..e157de84 100644 --- a/content/news/2023-06-01a.md +++ b/content/news/2023-06-01a.md @@ -1,6 +1,10 @@ --- title: New services and SciLifeLab Data Platform Launch materials now available date: 2023-06-01 +thumbnail: "/img/news/services_section.png" +show_thumbnail_on_page: True +caption: "Screenshot of the Data Platform's services section." +images: ["/img/news/services_section.png"] --- Thank you to all of those that were able to join us for the official launch of the SciLifeLab Data Platform on 26th May. For those who missed it, the recording is now available via the SciLifeLab Data Repository (one of the services on the SciLifeLab Data Platform). You can access it at: [DOI: 10.17044/scilifelab.23266088](https://doi.org/10.17044/scilifelab.23266088). diff --git a/content/news/2023-07-04.md b/content/news/2023-07-04.md index c33c5943..9228b5a5 100644 --- a/content/news/2023-07-04.md +++ b/content/news/2023-07-04.md @@ -1,6 +1,9 @@ --- title: Glad sommar! date: 2023-07-04 +thumbnail: "/img/news/summer.jpeg" +caption: "Representation of summer using free licensed image from [unsplash.com](https://unsplash.com/)." +images: ["/img/news/summer.jpeg"] --- The team behind the SciLifeLab Data Platform wish you all a wonderful summer break. There will be limited support for the Platform throughout July, but if you [get in touch](/contact/), we will reply to you ASAP! diff --git a/content/news/2023-08-08.md b/content/news/2023-08-08.md index 9272e5fb..a899585e 100644 --- a/content/news/2023-08-08.md +++ b/content/news/2023-08-08.md @@ -1,6 +1,9 @@ --- title: Launch of resources section date: 2023-08-08 +thumbnail: "/img/news/sll_dp_social_media.png" +caption: "Scilifelab Data platform Logo" +images: ["/img/news/sll_dp_social_media.png"] --- We are delighted to announce the launch of our new [resources section](/resources/). The aim of this section is to provide general information that could be of use for those working in data-driven life sciences in Sweden. This section currently includes introductory information about [computing resources available in Sweden](/resources/e-infrastructure/). In the coming months, we will also add information about storage resources available in Sweden, and how researchers can maximise their Altmetrics score. If you have any suggestions for other information that could be useful for data-driven life science in Sweden, please [get in touch](/contact/). diff --git a/content/news/2023-09-07.md b/content/news/2023-09-07.md index 2f25a6d7..2e147bf1 100644 --- a/content/news/2023-09-07.md +++ b/content/news/2023-09-07.md @@ -1,6 +1,10 @@ --- title: Information about accessing storage resources added date: 2023-09-07 +thumbnail: "/img/news/storage.jpg" +caption: "Representation of storage resources generated using AI." +show_thumbnail_on_page: True +images: ["/img/news/storage.jpg"] --- We have now added a second resource to our new [resources section](/resources/). This resource details the [storage resources](/resources/storage/) available in Sweden and how to access them. These resources can be used to store data and potentially other types of resources. This latest page is considered a compliment to our [compute resources page](/resources/e-infrastructure/), which provides information about resources related to analysis and hosting. diff --git a/content/news/2023-09-20.md b/content/news/2023-09-20.md index 5c839ce0..92de42bf 100644 --- a/content/news/2023-09-20.md +++ b/content/news/2023-09-20.md @@ -1,6 +1,10 @@ --- title: New highlight details a large study investigating the initiation of replication in E. coli. date: 2023-09-20 +thumbnail: "/img/news/ELF_banner.png" +caption: "Image courtesy Johan Elf lab." +show_thumbnail_on_page: True +images: ["/img/news/ELF_banner.png"] --- Our latest [data highlight](/highlights/), entitled: [Large effort study to elucidate replication initiation in bacteria](/highlights/bacterial_replication/), is based on [Knöppel _et al._ (2023)](https://www.pnas.org/doi/10.1073/pnas.2213795120). diff --git a/content/news/2023-09-29.md b/content/news/2023-09-29.md index 58f92e6a..fdeca853 100644 --- a/content/news/2023-09-29.md +++ b/content/news/2023-09-29.md @@ -1,6 +1,10 @@ --- title: New resource on using alternative metrics date: 2023-09-29 +thumbnail: "/img/news/plumx_cloud.png" +caption: "Word cloud created using [wordart.com](https://wordart.com/)." +show_thumbnail_on_page: True +images: ["/img/news/plumx_cloud.png"] --- We have now launched our third [resource](/resources/), which is focused on how to use alternative metrics. In particular, the resource describes what altmetrics are, why they're important for researchers, how to use them, and how to maximise your score. The resources have now been made accessible directly on the front page of the platform. As you'll see, the other resources detail the [compute](/resources/e-infrastructure/) and [storage](/resources/storage/) resources in Sweden, and how to access them. diff --git a/content/news/2023-11-15.md b/content/news/2023-11-15.md index 6720170c..8f54d984 100644 --- a/content/news/2023-11-15.md +++ b/content/news/2023-11-15.md @@ -1,6 +1,10 @@ --- title: SciLifeLab FAIR Storage date: 2023-11-15 +thumbnail: "/img/news/fairstorage.jpg" +caption: "Representation of FAIR Storage generated using AI." +show_thumbnail_on_page: True +images: ["/img/news/fairstorage.jpg"] --- [SciLifeLab FAIR Storage](/services/fairstorage) has now been added as our latest [service](/services/). SciLifeLab FAIR Storage is a service providing storage resources to enable FAIR data sharing within Swedish data-driven life science. The applications and allocation of resources will be managed by SciLifeLab Data Centre. diff --git a/content/news/2023-12-20.md b/content/news/2023-12-20.md index 4fb17a08..344cd14f 100644 --- a/content/news/2023-12-20.md +++ b/content/news/2023-12-20.md @@ -1,6 +1,10 @@ --- title: New highlight details a workflow that could aid in future drug development date: 2023-12-20 +thumbnail: "/img/news/Schwenk_gpcr.jpeg" +caption: "Visual representation of the methods used in the laboratory. Figure 1A of Dahl et al 2023." +show_thumbnail_on_page: True +images: ["/img/news/Schwenk_gpcr.jpeg"] --- Our latest [data highlight](/highlights/), entitled ['research into the immunogenicity of GPCR epitopes to enhance future drug development'](/highlights/gpcr_epitomes_drug_development/), is based on [Dahl _et al._ (2023)](https://www.science.org/doi/10.1126/sciadv.adf9297). diff --git a/content/news/2024-01-11.md b/content/news/2024-01-11.md index 6a7d1231..e6127ea5 100644 --- a/content/news/2024-01-11.md +++ b/content/news/2024-01-11.md @@ -1,6 +1,10 @@ --- title: Multiple open source services added date: 2024-01-11 +thumbnail: "/img/news/services_section.png" +show_thumbnail_on_page: True +caption: "Screenshot of the Data Platform's services section." +images: ["/img/news/services_section.png"] --- We have recently added multiple open source tools to our [services list](/services/). We define services as tools, databases, and support services (e.g. hosting and compute services) that can be used in data-driven life science research. Whilst we list services associated with SciLifeLab, the services can be used anywhere in the world, free of charge, unless otherwise stated. diff --git a/content/news/2024-01-19.md b/content/news/2024-01-19.md index 70fff9a2..dd8454fb 100644 --- a/content/news/2024-01-19.md +++ b/content/news/2024-01-19.md @@ -1,6 +1,10 @@ --- title: New highlight explores expansion of Bantu-speaking populations date: 2024-01-19 +thumbnail: "/img/news/BSP_banner_small.png" +caption: "Image courtesy Fortes-Lima et al 2023." +show_thumbnail_on_page: True +images: ["/img/news/BSP_banner_small.png"] --- One of two [data highlights](/highlights/) published today explores the expansion of Bantu-speaking populations. It is entitled ['New DNA research into Bantu-speaking populations' expansion provides a resource for future studies'](/highlights/bantu_expansion/). It is based on work recently published in Nature, please see [Fortes-Lima _et al._ (2023)](https://www.nature.com/articles/s41586-023-06770-6) for the original open-access article. diff --git a/content/news/2024-01-19b.md b/content/news/2024-01-19b.md index 85565375..19245014 100644 --- a/content/news/2024-01-19b.md +++ b/content/news/2024-01-19b.md @@ -1,6 +1,10 @@ --- title: New data highlight exploring alterations to the serum proteome caused by COVID-19 date: 2024-01-19 +thumbnail: "/img/news/covimapp_logo.png" +caption: "CoViMAPP logo." +show_thumbnail_on_page: True +images: ["/img/news/covimapp_logo.png"] --- One of two [data highlights](/highlights/) published today details a meta-analysis of alterations in the soluble blood proteome caused by COVID-19. It is entitled ['CoViMAPP – analysing changes in the soluble blood proteome due to COVID-19'](/highlights/covimapp/). It is based on work recently published in Nature. Please see [Babačić _et al._ (2023)](https://doi.org/10.1038/s41467-023-41159-z) for the original open-access article. diff --git a/content/news/2024-04-15.md b/content/news/2024-04-15.md index fd01d105..682a845f 100644 --- a/content/news/2024-04-15.md +++ b/content/news/2024-04-15.md @@ -1,6 +1,9 @@ --- title: List of data sources available for researchers date: 2024-04-15 +thumbnail: "/img/news/data_sources.jpg" +caption: "Representation of data sources generated using AI" +images: ["/img/news/data_sources.jpg"] --- A new resource entitled ['Data Sources'](/resources//data_sources/) has been added to the SciLifeLab Data Platform. The resource lists sources of data that can be used by data-driven life science researchers in Sweden. We are looking for feedback from the community about how this resource might be improved in future, and encourage users to [get in touch with us about any suggestions](/contact/). diff --git a/content/news/2024-04-15b.md b/content/news/2024-04-15b.md index 1cfe5fab..2ad98d17 100644 --- a/content/news/2024-04-15b.md +++ b/content/news/2024-04-15b.md @@ -1,6 +1,10 @@ --- title: New data highlight exploring a new metagenomic profiling workflow for ancient DNA date: 2024-04-15 +thumbnail: "/img/news/ameta.png" +caption: "Image courtesy of Pochon et al. 2023." +show_thumbnail_on_page: True +images: ["/img/news/ameta.png"] --- A new [data highlight](/highlights/) entitled ['aMeta: a new metagenomic profiling workflow for ancient DNA'](/highlights/ameta/) explores a new metagenomic profiling workflow for ancient DNA. It is based on work recently published in Genome Biology by [Pochon _et al._ (2023)](https://doi.org/10.1038/s41467-023-41159-z). diff --git a/content/news/2024-08-12b.md b/content/news/2024-08-12b.md index 6eb9c422..7ff80c18 100644 --- a/content/news/2024-08-12b.md +++ b/content/news/2024-08-12b.md @@ -1,6 +1,10 @@ --- title: Addition of multiple services and databases relevant for data-driven life science date: 2024-08-12 +thumbnail: "/img/news/services_section.png" +show_thumbnail_on_page: True +caption: "Screenshot of the Data Platform's services section." +images: ["/img/news/services_section.png"] --- Multiple services have recently been added to our [services list](/services/). This includes multiple open source services, such as [Scout](https://github.com/Clinical-Genomics/scout) (a visualiser for variant call format (VCF) files), and [Tomte](https://github.com/genomic-medicine-sweden/tomte) (a pipeline to analyse RNA-Seq data from rare disease patients) from [Clinical Genomics Stockholm](https://www.scilifelab.se/units/clinical-genomics-stockholm/). Multiple services from the [Sonnhammer Bioinformatics Group](https://sonnhammer.org) were also added, including [InParanoiDB](https://inparanoidb.sbc.su.se/) (a protein ortholog database for over 640 species), and [PathBIX](https://pathbix.sbc.su.se/) (a web server for novel network-based pathway enrichment analysis). diff --git a/content/news/2024-08-19.md b/content/news/2024-08-19.md index fcf0d53a..c3485820 100644 --- a/content/news/2024-08-19.md +++ b/content/news/2024-08-19.md @@ -1,6 +1,10 @@ --- title: New data highlight exploring a new analysis pipeline for mRNA-Seq and ATAC-Seq data date: 2024-08-19 +thumbnail: "/img/news/cactus.png" +caption: "Image courtesy Salignon et al. (2024)" +show_thumbnail_on_page: True +images: ["/img/news/cactus.png"] --- The latest [data highlight](/highlights/) is entitled ['New pipeline for mRNA-Seq and ATAC-Seq analysis allows for biological insights without in-depth bioinformatics skills'](/highlights/cactus/), and is based on recent research by [Salignon _et al._ (2024)](https://doi.org/10.1016/j.ygeno.2024.110858). diff --git a/content/news/2024-08-28.md b/content/news/2024-08-28.md index ae48d216..56994e34 100644 --- a/content/news/2024-08-28.md +++ b/content/news/2024-08-28.md @@ -1,6 +1,10 @@ --- title: Shape national data services in the Evolution and Biodiversity research area date: 2024-08-28 +thumbnail: "/img/news/DSN_EB.png" +show_thumbnail_on_page: True +caption: "Representation of the Evolution and Biodiversity DDLS area." +images: ["/img/news/DSN_EB.png"] --- SciLifeLab collaborates with specific partner organisations to organise work related to data services and bioinformatics support as part of [The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS)](https://www.scilifelab.se/data-driven/). This work takes place at one of four Data Science Nodes. These four nodes, one for each of the scientific focus areas of the DDLS program, are located across Sweden. They comprise staff from the [SciLifeLab Data Centre](https://www.scilifelab.se/data/) and [NBIS (National Bioinformatics Infrastructure Sweden)](https://nbis.se/). The staff are embedded in relevant environments at the hosting organisations, and are also integrated into the Data Platform and bioinformatics support teams, respectively. diff --git a/content/news/2024-08-28a.md b/content/news/2024-08-28a.md index 615523d8..ffc20102 100644 --- a/content/news/2024-08-28a.md +++ b/content/news/2024-08-28a.md @@ -1,6 +1,10 @@ --- title: Advancing precision medicine in Sweden by stregthening competance in the area. date: 2024-08-28 +thumbnail: "/img/news/precision_med.jpeg" +caption: "Representation of advancing precision medicine generated using AI." +show_thumbnail_on_page: True +images: ["/img/news/precision_med.jpeg"] --- SciLifeLab's [Capability for Precision Medicine](https://www.scilifelab.se/capabilities/precision-medicine/) and [Training Hub](https://training.scilifelab.se/) are working together to strengthen the competence within precision medicine in Sweden, in order to advance research in this area. diff --git a/content/news/2024-09-05.md b/content/news/2024-09-05.md index ed23a7dc..8bdd5afc 100644 --- a/content/news/2024-09-05.md +++ b/content/news/2024-09-05.md @@ -1,6 +1,10 @@ --- title: Suggest national data services in the Epidemiology and Biology of Infection research area date: 2024-09-05 +thumbnail: "/img/news/DSN_EBI.png" +caption: "Representation of the Epidemiology and Biology Infection DDLS area." +show_thumbnail_on_page: True +images: ["/img/news/DSN_EBI.png"] --- SciLifeLab collaborates with specific partner organisations to organise work related to data services and bioinformatics support as part of [The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS)](https://www.scilifelab.se/data-driven/). This work takes place at one of four Data Science Nodes. These four nodes, one for each of the scientific focus areas of the DDLS program, are located across Sweden. They comprise of staff from [SciLifeLab Data Centre](https://www.scilifelab.se/data/) and [NBIS (National Bioinformatics Infrastructure Sweden)](https://nbis.se/). The staff are embedded in relevant environments at the hosting organisations, and are also integrated in the Data Platform and bioinformatics support teams, respectively. diff --git a/content/news/2024-09-12.md b/content/news/2024-09-12.md new file mode 100644 index 00000000..8ef529a7 --- /dev/null +++ b/content/news/2024-09-12.md @@ -0,0 +1,14 @@ +--- +title: DEADLINE EXTENSION - Shape national data services in Evolution and Biodiversity +date: 2024-09-12 +thumbnail: "/img/news/DSN_EB.png" +show_thumbnail_on_page: True +caption: "Representation of the Evolution and Biodiversity DDLS area." +images: ["/img/news/DSN_EB.png"] +--- + +SciLifeLab collaborates with specific partner organisations to organise work related to data services and bioinformatics support as part of [The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS)](https://www.scilifelab.se/data-driven/). This work takes place at one of four Data Science Nodes. These four nodes, one for each of the scientific focus areas of the DDLS program, are located across Sweden. They comprise staff from the [SciLifeLab Data Centre](https://www.scilifelab.se/data/) and [NBIS (National Bioinformatics Infrastructure Sweden)](https://nbis.se/). The staff are embedded in relevant environments at the hosting organisations, and are also integrated into the Data Platform and bioinformatics support teams, respectively. + +The Data Science Node in Evolution and Biodiversity (DSN-EN), hosted by Uppsala University and the Swedish Museum of Natural History, is reaching out to the data-driven life science community to better understand their needs. In particular, they are seeking proposals for national data services required in the field of evolution and biodiversity. Data services included in the Data Platform will benefit from, among other things, significantly increased visibility, which could lead to greater opportunities for funding and collaboration. + +To find out more about the application process and proposal requirements, please see the [Inventory of National Data Service needs in the Evolution and Biodiversity research area document](/service_requests/Instructions_DSN-EB_needs_inventory_20240823.pdf). **The deadline for submission has now been extended to September 22nd, 2024, at midnight CET**. diff --git a/layouts/index.html b/layouts/index.html index 06765589..ad1702f8 100644 --- a/layouts/index.html +++ b/layouts/index.html @@ -99,7 +99,7 @@

What's new?

{{ .Date | time.Format ":date_long" }}
- {{ .Title }} + {{ .Title }}
{{ if ne $index 3}}
{{ end }} diff --git a/layouts/news/list.html b/layouts/news/list.html index 66d7ec54..772f0016 100644 --- a/layouts/news/list.html +++ b/layouts/news/list.html @@ -1,26 +1,23 @@ {{ define "main" }} -
-
- {{ .Content }} -
-
+{{ .Content }}
-
+
{{ range .RegularPages }}
-
-
- {{ .Date | time.Format ":date_long" }} +
+ +
{{ .Date | time.Format ":date_long" }}
+
-
-
{{ .Title }}
-
-
- {{ .Content }} -
-
{{ end }}
diff --git a/layouts/news/single.html b/layouts/news/single.html new file mode 100644 index 00000000..45dfa316 --- /dev/null +++ b/layouts/news/single.html @@ -0,0 +1,22 @@ +{{ define "main" }} + +

{{ .Title }}

+{{ .Date | time.Format ":date_long" }} + +
+ {{ if .Params.show_thumbnail_on_page }} +
+ news-{{ .Date }} +
+ {{ with .Params.caption }}{{ . | markdownify }}{{ else }}{{ "SciLifeLab Logo" }}{{ end }} +
+
+ {{ end }} + {{ .Content }} +
+ + + +{{ end }} diff --git a/layouts/partials/header.html b/layouts/partials/header.html index fb611deb..c31e7828 100644 --- a/layouts/partials/header.html +++ b/layouts/partials/header.html @@ -16,6 +16,8 @@

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