Merge pull request #1116 from ScilifelabDataCentre/develop

Deployment to production

CITATION.cff

@@ -1,41 +1,39 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
+cff-version: 1.2.1
+message: "If you use or reuse this software, please cite it using the following metadata."
 authors:
 - family-names: "Hughes"
   given-names: "Liane"
+  orcid: 0000-0002-4784-5436
 - family-names: "Stark"
   given-names: "Katarina Öjefors"
+  orcid: 0000-0001-7970-7778
 - family-names: "Kochari"
   given-names: "Arnold"
+  orcid: 0000-0003-1373-5121
 - family-names: "Panneerselvam"
   given-names: "Senthilkumar"
 - family-names: "Ewels"
   given-names: "Phil"
-- family-names: "Ostberg"
+  orcid: 0000-0003-4101-2502
+- family-names: "Östberg"
   given-names: "Linus"
 - family-names: "Kraulis"
   given-names: "Per"
-- family-names: "Rung"
-  given-names: "Johan"
+  orcid: 0000-0003-0560-974X
 - family-names: "Lorenz"
   given-names: "Jan"
 - family-names: "Asklof"
   given-names: "Anna"
 - family-names: "Kallberg"
   given-names: "Yvonne"
+  orcid: 0000-0002-3977-9600
 - family-names: "Islam"
   given-names: "Kazi Jahurul"
-- family-names: "Ouyang"
-  given-names: "Wei"
-- family-names: "Kronander"
-  given-names: "Elin"
 - family-names: "Tewatia"
   given-names: "Parul"
-- family-names: "Englund"
-  given-names: "Markus"
-- family-names: "Hammaren"
-  given-names: "Rickard"
-- family-names: "Xu"
-  given-names: "Hao"
+  orcid: 0000-0002-3096-1318
+- family-names: "Rung"
+  given-names: "Johan"
+  orcid: 0000-0001-5875-8429
 title: "Swedish Pathogens Portal"
 url: "https://github.com/ScilifelabDataCentre/pathogens-portal"

CONTRIBUTING/running_a_local_copy.md

@@ -1,16 +1,15 @@
 # Running a local copy of the portal
 
-The portal is built using [Hugo](https://gohugo.io/), a static site generator. This makes it relatively easy to run a full version of the portal on your computer (i.e. locally). This means that you can see how the changes that you're making would look on the site.
-
+The portal is built using [Hugo](https://gohugo.io/), a static site generator. This makes it relatively easy to run a full version of the portal on your computer (i.e. locally). This means that you can change the code and see exactly how those changes would look on the site before you deploy the changes to the site.
 #### Clone a copy of the portal code
 
-All of the code behind the portal is stored in [this GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal). There are multiple ways to clone a GitHub repository so that you have your own copy on your computer. Please view the information in [the GitHub documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) in order to do this.
+All of the code behind the portal is stored in [this GitHub repository](https://github.com/ScilifelabDataCentre/pathogens-portal). There are multiple ways to clone a GitHub repository so that you have your own copy on your computer. Please see [the GitHub documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) for information on how to do this.
 
 #### Using Hugo
 
-In order to run a local copy, you first need to install Hugo on your computer. Instructions for how to do this are available on the Hugo website: [https://gohugo.io/](https://gohugo.io/).
+In order to run a local copy, you first need to install Hugo on your computer. Detailed instructions for how to do this are available on the Hugo website: [https://gohugo.io/](https://gohugo.io/).
 
-On Mac OSX, it is recommended to use [Homebrew](https://brew.sh/) to install Hugo. Once Hugo is set up, you can run the following command in a terminal window to install Hugo:
+On Mac OSX, it is recommended to use [Homebrew](https://brew.sh/) to install Hugo. Once Homebrew is set up, you can run the following command in a terminal window to install Hugo:
 
 ```bash
 brew install hugo

Dockerfiles/Dockerfile

@@ -1,8 +1,21 @@
-FROM klakegg/hugo:0.104.3-ubuntu-onbuild AS build
+# Use alpine Linux, download desired version of HUGO and build html files
+FROM alpine:3.19.1 AS build
+RUN apk add --no-cache wget=1.21.4-r0
+ARG HUGO_VERSION="0.123.7"
+RUN wget --quiet "https://github.com/gohugoio/hugo/releases/download/v${HUGO_VERSION}/hugo_${HUGO_VERSION}_Linux-64bit.tar.gz" && \
+    tar xzf hugo_${HUGO_VERSION}_Linux-64bit.tar.gz && \
+    rm -r hugo_${HUGO_VERSION}_Linux-64bit.tar.gz && \
+    mv hugo /usr/bin && \
+    chmod 755 /usr/bin/hugo
+WORKDIR /src
+COPY ./ /src
+RUN mkdir /target && \
+    hugo -d /target
 
+# 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
-RUN sed -i 's/#error_page  404/error_page  404/' /etc/nginx/conf.d/default.conf
+RUN sed -i '3 a\    absolute_redirect off;' /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
 
 EXPOSE 8080

README.md

@@ -26,6 +26,8 @@ It uses the [Bootstrap](https://getbootstrap.com/) framework. In addition, it us
 
 <a href="https://zenodo.org/doi/10.5281/zenodo.10629602"><img src="https://zenodo.org/badge/256458920.svg" alt="DOI"></a>
 
+Click on 'Cite this repository' near the top right of this repository to see how to formally cite this repository.
+
 ## Development and contributions
 
 ### Adding and editing information in different sections
@@ -55,16 +57,3 @@ If you have any questions regarding any of the code or content associated with t
 ## Credits
 
 The website was built and is maintained by [SciLifeLab Data Centre](https://www.scilifelab.se/data/). We are grateful to many collaborators, both from the Data Centre and elsewhere, for their contributions.
-
-The primary contributors have been:
-
-- [@SonjaAits](https://github.com/SonjaAits)
-- [@ewels](https://github.com/ewels)
-- [@talavis](https://github.com/talavis)
-- [@pekrau](http://github.com/pekrau/)
-- [@akochari](http://github.com/akochari/)
-- [@LianeHughes](https://github.com/LianeHughes)
-- [@KatarinaOjeforsStark](https://github.com/KatarinaOjeforsStark)
-- [@senthil10](https://github.com/senthil10)
-- [@HannaKultima](https://github.com/HannaKultima)
-- [@johanrung](https://github.com/johanrung)

config.yaml

@@ -35,8 +35,8 @@ params:
       twitter_link: Twitter
       linkedin_link: LinkedIn
     sv:
-      home_title: "Patogens Portal Sverige: stöd för pandemiberedskap"
-      enquire_email_footer_dc: "Kontakta den Svenska Patogens Portalen"
+      home_title: "Pathogens Portal Sverige: stöd för pandemiberedskap"
+      enquire_email_footer_dc: "Kontakta Pathogens Portal Sverige"
       support_feedback: Support och Feedback
       privacy: Integritetspolicy
       github_link: Webbplatskod på GitHub
@@ -68,7 +68,7 @@ languages:
     languageName: Svenska
     contentDir: content/svenska
     weight: 2
-    description: "Den Patogens Portal Sverige tillhandahåller information, riktlinjer, verktyg och tjänster för att stödja forskare vid svenska lärosäten verksamma inom forskningsfältet pandemisk beredskap med datarelaterade frågor."
+    description: "Pathogens Portal Sverige tillhandahåller information, riktlinjer, verktyg och tjänster för att stödja forskare vid svenska lärosäten verksamma inom forskningsfältet pandemisk beredskap med datarelaterade frågor."
 
 markup:
   goldmark:

content/english/dashboards/wastewater/influenza_quantification/_index.md

@@ -68,7 +68,7 @@ The group provide reports to summarise their latest findings. The latest report
 
 **Contact:** <[email protected]> and <[email protected]>
 
-**Download the data:** [Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file](https://raw.githubusercontent.com/ScilifelabDataCentre/pathogens-portal/develop/static/ww_data_temp/SLU_wastewater_data.csv). Data are available for Influenza A from week 42 of 2022 and for Influenza B from week 12 of 2023; updated weekly.
+**Download the data:** [Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file](https://blobserver.dc.scilifelab.se/blob/SLU_wastewater_data.csv). Data are available for Influenza A from week 42 of 2022 and for Influenza B from week 12 of 2023; updated weekly.
 
 **How to cite the dataset:**
 

content/english/editorials/microbioterrorism.md

@@ -0,0 +1,66 @@
+---
+title: "(Micro)bioterrorism: leveraging genomic data to improve anthrax surveillance"
+date: 2024-04-05
+summary: A perspective on Bacillus anthracis, a pathogen known as a biological threat, and how WGS data and surveillance can help researchers respond to cases and threats.
+banner: /editorials/topic_infectious_disease.jpg
+banner_caption: "Splenic tissue from a monkey with inhalation anthrax, showing a red blood cell (red) and rod-shaped bacilli (yellow). (Credit: Arthur Friedlander)"
+tags:
+  [
+    pathogens,
+    Bacillus anthracis,
+    WGS data,
+    Whole genome sequencing,
+    preparedness,
+    health threat,
+    Infectious disease,
+  ]
+editorials_topics: [Infectious diseases]
+editorials_authors: [Laura Carroll]
+images: [/editorials/topic_infectious_disease.jpg]
+---
+
+### What is anthrax?
+
+Anthrax is a serious, life-threatening infectious disease, which is caused by a rod-shaped bacterium called *Bacillus anthracis* ([CDC, 2024a](https://www.cdc.gov/anthrax/basics/index.html)).
+_B. anthracis_ is arguably most well-known for its previous use as a biological weapon and bioterrorism agent ([CDC, 2024b](https://www.cdc.gov/anthrax/bioterrorism/threat.html); [Wagar, 2015](https://journals.asm.org/doi/10.1128/cmr.00033-15)).
+However, in some parts of the world, _B. anthracis_ naturally resides in soil, where it can form highly resilient spores capable of withstanding harsh environmental conditions ([CDC, 2024a](https://www.cdc.gov/anthrax/basics/index.html); [Mock and Fouet, 2001](https://www.annualreviews.org/doi/10.1146/annurev.micro.55.1.647)).
+Wild and domestic animals (livestock that graze, in particular; e.g., cattle, goats, sheep) can become infected by ingesting or inhaling _B. anthracis_ spores present in soil, water, and other natural environments ([CDC, 2024a](https://www.cdc.gov/anthrax/basics/index.html); [FDA, 2024](https://www.fda.gov/vaccines-blood-biologics/vaccines/anthrax)).
+Anthrax cases among humans can occur when _B. anthracis_ spores enter the body (e.g., by inhaling or ingesting spores, or when spores come in contact with a cut or lesion), as such, people who interact with infected animals or animal products have an increased risk of exposure ([CDC, 2024a](https://www.cdc.gov/anthrax/basics/index.html); [CDC, 2024c](https://www.cdc.gov/anthrax/transmission/index.html); [FDA, 2024](https://www.fda.gov/vaccines-blood-biologics/vaccines/anthrax)).
+
+### Bacillus anthracis: the original anthrax-causing pathogen
+
+For over a century, _B. anthracis_ has been known to be a causative agent of anthrax.
+In 1876, scientist Robert Koch demonstrated that _B. anthracis_, when injected into animals, caused disease ([CDC 2024d](https://www.cdc.gov/anthrax/basics/anthrax-history.html); [Blevins and Bronze, 2010](https://www.sciencedirect.com/science/article/pii/S1201971210023143); [Koch, 1876](https://edoc.rki.de/handle/176904/5139)).
+Not only did his studies provide insight into _B. anthracis_ biology, but they were the first to link a specific bacterium to a specific disease ([Blevins and Bronze, 2010](https://www.sciencedirect.com/science/article/pii/S1201971210023143)).
+Further, Koch's work with *B. anthracis* led to the publication of what are now famously known as Koch's Postulates, which serve as formal criteria for establishing a causal relationship between a microbe and a disease ([CDC 2024d](https://www.cdc.gov/anthrax/basics/anthrax-history.html)).
+
+Since Koch's discoveries in the late 1800s, research into _B. anthracis_ biology and pathogenesis has led to numerous breakthroughs in anthrax prevention and treatment ([CDC 2024d](https://www.cdc.gov/anthrax/basics/anthrax-history.html)).
+Several anthrax vaccines have been developed for both humans and animals, and improvements in anthrax treatment (e.g., antibiotics, anthrax antitoxins) have led to better patient outcomes ([CDC 2024d](https://www.cdc.gov/anthrax/basics/anthrax-history.html); [Person, et al., 2022](https://academic.oup.com/cid/article/75/Supplement_3/S392/6762174)).
+However, these breakthroughs are often overshadowed by the use of _B. anthracis_ as a bioweapon, with the first documented case occurring during World War I ([CDC 2024d](https://www.cdc.gov/anthrax/basics/anthrax-history.html)).
+
+### "Bacillus cereus" biovar Anthracis: a new type of anthrax
+
+Over 100 years after Koch linked _B. anthracis_ to anthrax, researchers at the U.S.
+Centers for Disease Control and Prevention (CDC) discovered a novel pathogen capable of causing anthrax-like illness ([Hoffmaster, et al., 2004](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC420414/)).
+Later termed "_Bacillus cereus_" biovar Anthracis ([Antonation, et al., 2016](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015827/); [Carroll, et al., 2020](https://journals.asm.org/doi/full/10.1128/mbio.00034-20); [Klee, et al., 2006](https://journals.asm.org/doi/full/10.1128/jb.00303-06)), this novel pathogen resembled a completely different species, "_Bacillus cereus_", but was able to cause anthrax-like disease like *B. anthracis* ([Hoffmaster, et al., 2004](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC420414/); [Klee, et al., 2006](https://journals.asm.org/doi/full/10.1128/jb.00303-06)).
+
+Since its discovery in 2004, "_B. cereus_" biovar Anthracis has been responsible for several other cases of severe, anthrax-like illness among humans and animals, several of which resulted in fatalities ([Baldwin, 2020](https://www.frontiersin.org/articles/10.3389/fmicb.2020.01731/full)).
+Notably, using whole-genome sequencing (WGS), scientists have revealed that "_B. cereus_" biovar Anthracis strains are incredibly diverse, indicating that different strains--and even species--have acquired the ability to cause anthrax; as a result, novel approaches must be developed to prepare for the emergence of novel anthrax-causing pathogens ([Carroll, et al., 2022](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9413466/)).
+
+### Combating anthrax with genomic data
+
+Due to their severity and bioterrorism potential, anthrax-causing *B. anthracis* and "_B. cereus_" biovar Anthracis represent severe global public health threats.
+To prepare for potential emergencies, scientists are taking proactive, data-driven approaches.
+Specifically, laboratories around the world are routinely using WGS to query the genomes of anthrax-causing bacteria.
+This WGS data is deposited in public databases (e.g. [the National Center for Biotechnology Information (NCBI) databases](https://www.ncbi.nlm.nih.gov/)), often alongside metadata conveying when, where, and how the anthrax-causing strain was isolated ([Ramnath, et al., 2023](https://www.biorxiv.org/content/10.1101/2023.12.20.572685v1.full)).
+
+WGS data and metadata derived from anthrax-causing pathogens have tremendous potential to be utilised within the realms of public health and emergency preparedness.
+Specifically, WGS-based pathogen surveillance tools are allowing scientists to monitor pathogens in close to real-time ([Gardy and Loman, 2018](https://www.nature.com/articles/nrg.2017.88)).
+This (meta)data can be used to identify and resolve outbreaks sooner, leading to better public health outcomes and lower burdens of illness ([Gardy and Loman, 2018](https://www.nature.com/articles/nrg.2017.88); [Ramnath, et al., 2023](https://www.biorxiv.org/content/10.1101/2023.12.20.572685v1.full)).
+We envision that similar methods can be used for anthrax-causing pathogens.
+For example, routine WGS of bacilli can allow public health officials to rapidly identify novel, emerging anthrax-causing pathogens, facilitating faster response times and minimising the number of human illness cases ([Ramnath, et al., 2023](https://www.biorxiv.org/content/10.1101/2023.12.20.572685v1.full)).
+Overall, whether the culprit is _B. anthracis_, "_B. cereus_" biovar Anthracis, or a yet-unknown anthrax-causing pathogen, WGS has the potential to help public health officials and clinicians prepare for and respond to illness cases, outbreaks, and bioterrorism attacks.
+
+#### Cite this editorial
+
+Carroll, L. (2024). Editorial- (Micro)bioterrorism: leveraging genomic data to improve anthrax surveillance. Online resource. DOI: [10.17044/scilifelab.25547476](https://doi.org/10.17044/scilifelab.25547476).

content/english/updates/microbioterrorism.md

@@ -0,0 +1,17 @@
+---
+title: "New Editorial about leveraging genomic data to improve anthrax surveillance"
+date: 2024-04-05
+summary: A perspective on Bacillus anthracis, a pathogen known as a biological threat, and how WGS data and surveillance can help researchers respond to cases and threats.
+banner: /editorials/topic_infectious_disease.jpg
+banner_caption: "Splenic tissue from a monkey with inhalation anthrax, showing a red blood cell (red) and rod-shaped bacilli (yellow). (Credit: Arthur Friedlander)"
+---
+
+We have published a new editorial in our [Editorials section](/editorials/).
+Our editorials are short, opinion-style pieces reflecting the ‘current thinking’ on a topic related to infectious disease and pandemic preparedness.
+
+This latest editorial, entitled [“Micro(bioterrorism) leveraging genomic data to improve anthrax surveillance”](/editorials/microbioterrorism) discusses _Bacillus anthracis_; a pathogen known as the cause of the life-threatening disease anthrax, and a known biological threat. _Bacillus anthracis_ does, however, also naturally occur in soil and can infect lifestock such as cattle, goat, and sheep. The focus of this Editorial is a discussion on how researchers are using surveillance and whole-genome sequencing (WGS) data to proactively study such pathogens.
+
+The editorial was written by Laura Carroll, a DDLS fellow at Umeå University, who is part of the Swedish Pathogens Portal's [editorial committee](/about/editorial_committee/).
+
+If you are interested in writing an editorial for the portal, please [contact the portal team](/contact/).
+We will contact you as soon as possible to discuss your suggestion.