Merging new changes to main W37

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
 

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.

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.

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.

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.
+**_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.

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?
 

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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/).

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)

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.

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.

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)