Merge pull request #1145 from ScilifelabDataCentre/develop

content/english/dashboards/wastewater/covid_quantification/historic_stockholm.md

@@ -1,37 +1,30 @@
 ---
 title: "Historic data for Stockholm"
+plotly: true
 aliases:
-    - /data_types/environment/wastewater/historic_stockholm/
-    - /dashboards/wastewater/historic_stockholm/
+  - /data_types/environment/wastewater/historic_stockholm/
+  - /dashboards/wastewater/historic_stockholm/
 ---
 
-This page displays data on the amount of SARS-CoV-2 in Stockholm between April 2020 and August 2021 calculated as Gene copy number/week (raw wastewater) with bovine + PMMoV factor. From September 2021 onwards, the method was changed. Please [see this page for the most recent data](./).
+This page displays data on the amount of SARS-CoV-2 in the wastewater in Stockholm between April 2020 and August 2021. The amount of SARS-CoV-2 in wastewater was calculated as the number of gene copies per week (raw wastewater) with bovine + PMMoV factor. From September 2021 onwards, the method was changed. Please [see this page for the most recent data](/dashboards/wastewater/covid_quantification/covid_quant_kth/).
 
-This project, led by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology; <[email protected]>), is a collaboration between the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and the [SEED](https://www.kth.se/en/seed) and [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association. The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000; 860,000 and 500,000, respectively. Please consult [this map for the exact catchment area of the wastewater collection channels in Käppala](/wastewater/map_Kappala.pdf) and [this map for the exact catchment area of the wastewater collection channels in Bromma and Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf).
+This project was led by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology: <[email protected]>). The project was a collaboration between the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19), the [Sustainable Development, Environmental Science and Engineering (SEED)](https://www.kth.se/en/seed) and [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) departments at the KTH Royal Institute of Technology (KTH), as well as Stockholm Vatten och Avfall and the Käppala Association. The sampling of wastewater began in mid-April 2020, from the Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000, 860,000, and 500,000 people, respectively. Please see the catchment maps for [Käppala](/wastewater/map_Kappala.pdf) and [Bromma and Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf) to understand where the wastewater originated from in each case.
 
-After concentration, filtering, and preparation, the samples are analyzed using qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema and colleagues (2020)](https://doi.org/10.1016/j.scitotenv.2020.142939)). In some cases, the raw wastewater has been frozen at –20 degrees, and  concentrated wastewater or purified RNA have been stored at -80 C before the next analysis step was carried out. The concentration method used by prof. Zeynep Cetecioglu Gurol and her colleagues is based on their published study ([Jafferali and colleagues, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)) comparing four different concentration methods. The study concluded that the double ultrafiltration method adapted by KTH has a significantly higher efficiency compared to single filtration and adsorption methods. For detailed information about the concentration method, see the publication.
+After concentration, filtering, and preparation, the samples are analysed using qPCR to test for SARS-CoV-2 RNA. Primers of the nucleocapsid (N) gene (previously used and verified by [Medema _et al._ (2020)](https://doi.org/10.1016/j.scitotenv.2020.142939)) were used to detect SARS-COV-2. In some cases, samples of raw wastewater were frozen at –20<sup>o</sup>C, and concentrated wastewater or purified RNA were stored at -80<sup>o</sup>C before the next analysis step was carried out. The concentration method used by prof. Gurol and colleagues was based on their published study ([Jafferali _et al._, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)), in which they compared four different concentration methods. The study concluded that the double ultrafiltration method adapted by KTH was significantly more efficient than single filtration and adsorption methods. Please see [Jafferali _et al._ (2021)](https://doi.org/10.1016/j.scitotenv.2020.142939) for more information on the methods. More information about [data summaries and preliminary conclusions are also available](https://www.kth.se/water/research/covid-1.979048).
 
-See also [the page of the research group where summaries of data and preliminary conclusions are presented](https://www.kth.se/water/research/covid-1.979048).
-
-**Download the data:** [Gene copy number/week (raw wastewater) with bovine + PMMoV factor; Excel file.](https://blobserver.dc.scilifelab.se/blob/wastewater_data_Stockholm.xlsx) Numbers for Stockholm overall and divided by Inlet Henriksdal, Sickla, Hässelby, Järva, Riksby, and Käppala are available. Results are available (partially) starting from week 16 of 2020 and until week 34 of 2021.
+**Download the data:** [Gene copy number/week (raw wastewater) with bovine + PMMoV factor; Excel file.](https://blobserver.dc.scilifelab.se/blob/wastewater_data_Stockholm.xlsx). The numbers for Stockholm overall, and for the Henriksdal, Sickla, Hässelby, Järva, Riksby, and Käppala inlets are provided. At least partial data are available between week 16 of 2020 and week 34 of 2021.
 
 **How to cite:**
-Cetecioglu Z G, Williams, C, Khatami, K, Atasoy, M, Nandy, P, Jafferali, M H, Birgersson, M. SARS-CoV-2 Wastewater Data from Stockholm, Sweden. [https://doi.org/10.17044/scilifelab.14315483](https://doi.org/10.17044/scilifelab.14315483) (2021).
+Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali, M. H., Birgersson, M. (2021). SARS-CoV-2 Wastewater Data from Stockholm, Sweden. [https://doi.org/10.17044/scilifelab.14315483](https://doi.org/10.17044/scilifelab.14315483).
 
-<div class="d-lg-none alert alert-info">
-  Scroll the plot sideways to view all data.
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
 </div>
 
-<div class="plot_wrapper">
-  <div class="table-responsive" id="stockholm_combined"></div>
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_data_stockholm.json" height="550px">}}</div>
 </div>
 
-<div class="small text-muted">*NB: All samples until week 21 of 2020 were received by the lab in week 21. Between weeks 21 and 33 of 2020 samples were analyzed biweekly. After week 33 of 2020, samples were analysed weekly.</div>
-
-<div class="small text-muted">**NB: Measurements were taken fortnightly, rather than weekly, between weeks 24 and 32 of 2021.</div>
-
-<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
-<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
-<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
+<div class="small text-muted">All samples up until week 21 of 2020 were received by the lab in week 21. Between weeks 21 and 33 of 2020, samples were analysed biweekly. After week 33 of 2020, samples were typically analysed weekly, although measurements were taken fortnightly, rather than weekly, between weeks 24 and 32 of 2021.</div>
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/956f9390690043b8ae5f62b90d22f84f.js?id=stockholm_combined"></script>
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/historic_stockholm_data.py).

content/svenska/dashboards/wastewater/covid_quantification/historic_stockholm.md

@@ -1,40 +1,30 @@
 ---
 title: "Historiska data för Stockholm"
+plotly: true
 aliases:
-    - /sv/data_types/environment/wastewater/historic_stockholm/
-    - /sv/dashboards/wastewater/historic_stockholm/
+  - /sv/data_types/environment/wastewater/historic_stockholm/
+  - /sv/dashboards/wastewater/historic_stockholm/
 ---
 
-Den här sidan visar data om mängden SARS-CoV-2 i Stockholm mellan april 2020 och augusti 2021 beräknat som genkopienummer/vecka (från avloppsvatten) standardiserat med bovint coronavirus+ PMMoV.  Från september 2021 ändrades metoden. Se [den här sidan för de senaste uppgifterna](../).
+Den här sidan visar data om mängden SARS-CoV-2 i Stockholm mellan april 2020 och augusti 2021 beräknat som genkopienummer/vecka (från avloppsvatten) standardiserat med bovint coronavirus+ PMMoV. Från september 2021 ändrades metoden. Se [den här sidan för de senaste uppgifterna](/dashboards/wastewater/covid_quantification/covid_quant_kth/).
 
 Data som visas här samlades in inom ett forskningsprojekt lett av prof. Zeynep Cetecioglu Gurol och kollegor (KTH) är ett samarbete mellan [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) och avdelningarna [SEED](https://www.kth.se/en/seed) och [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) vid KTH, i nära samarbete med Stockholm Vatten och Avfall och Käppala Association. Provtagningen av avloppsvatten började i mitten av april 2020 från Bromma, Henriksdal och Käppala reningsverk. Dessa reningsverk får avloppsvatten från en befolkning på cirka 360 000; 860 000 respektive 500 000. Se [den här kartan för det exakta avrinningsområdet för insamlingskanalerna i Käppala](/wastewater/map_Kappala.pdf) och [den här kartan för det exakta avrinningsområdet för insamlingskanalerna i Bromma och Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf).
 
-Efter koncentrering, filtrering och beredning analyserades proverna med RT-qPCR-teknik för SARS CoV-2 RNA. Primers mot nukleokapsidgenen (N) användes för att detektera SARS-COV-2-genen (tidigare använt och verifierat av [Medema et al (2020)](https://doi.org/10.1016/j.scitotenv.2020.142939). I vissa fall har det råa avloppsvattnet frusits ​​vid –20 °C och koncentrerat avloppsvatten eller renat RNA har lagrats vid -80°C innan nästa analyssteg genomfördes. Koncentrationsmetoden som använddes av prof. Zeynep Cetecioglu Gurol och hennes kollegor baseras på forskargruppens publicerade artikel ([Jafferali et al, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)) som jämför fyra olika metoder för att koncentrera avloppsvatten.  Studiens slutsats var att den dubbla ultrafiltreringsmetoden som anpassats av KTH gruppen  har betydligt högre effektivitet jämfört med enstaka filtrerings- och adsorptionsmetoder. För detaljerad information om metoden, se publikationen.
+Efter koncentrering, filtrering och beredning analyserades proverna med RT-qPCR-teknik för SARS CoV-2 RNA. Primers mot nukleokapsidgenen (N) användes för att detektera SARS-COV-2-genen (tidigare använt och verifierat av [Medema _et al._ (2020)](https://doi.org/10.1016/j.scitotenv.2020.142939). I vissa fall har det råa avloppsvattnet frusits ​​vid –20 °C och koncentrerat avloppsvatten eller renat RNA har lagrats vid -80°C innan nästa analyssteg genomfördes. Koncentrationsmetoden som använddes av prof. Zeynep Cetecioglu Gurol och hennes kollegor baseras på forskargruppens publicerade artikel ([Jafferali _et al._, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)) som jämför fyra olika metoder för att koncentrera avloppsvatten. Studiens slutsats var att den dubbla ultrafiltreringsmetoden som anpassats av KTH gruppen har betydligt högre effektivitet jämfört med enstaka filtrerings- och adsorptionsmetoder. För detaljerad information om metoden, se publikationen.
 
 **Ladda ner data:** [Mängd SARS CoV-2 RNA per vecka i råavloppsvatten, med bovin faktor och PPMoV faktor, Excel-fil](https://blobserver.dc.scilifelab.se/blob/wastewater_data_Stockholm.xlsx). Uppgifterna delas av Inlet Henriksdal, Sickla, Hässelby, Järva, Riksby och Käppala. Data tillgänglig (delvis) från och med vecka 16 2020; uppdateras varje vecka.
 
 **Referera till detta dataset:**
-Cetecioglu Z G, Williams, C, Khatami, K, Atasoy, M, Nandy, P, Jafferali, M H, Birgersson, M. SARS-CoV-2 Wastewater Data from Stockholm, Sweden. [https://doi.org/10.17044/scilifelab.14315483](https://doi.org/10.17044/scilifelab.14315483) (2021).
+Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali, M. H., Birgersson, M. (2021). SARS-CoV-2 Wastewater Data from Stockholm, Sweden. [https://doi.org/10.17044/scilifelab.14315483](https://doi.org/10.17044/scilifelab.14315483).
 
-<div class="d-lg-none alert alert-info">
-  Skrolla grafen horisontellt för att se alla data.
+<div class="d-md-none alert alert-info">
+  Att rotera mobiltelefonen kan förbättra grafens layout.
 </div>
 
-<div class="plot_wrapper">
-  <div class="table-responsive" id="stockholm_combined"></div>
+ <div class="plot_wrapper mb-3">
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_data_stockholm.json" height="550px">}}</div>
 </div>
 
-<div class="small text-muted">*NB: Alla prover innan vecka 21 har kommit till labbet vecka 21. Mellan vecka 21 och 33 har prover analyserats varannan vecka. Efter vecka 33 har proverna analyserats varje vecka.</div>
+<div class="small text-muted">Alla prover innan vecka 21 har kommit till labbet vecka 21. Mellan vecka 21 och 33 har prover analyserats varannan vecka. Efter vecka 33 har proverna analyserats varje vecka. Avloppsvattenmätningarna har utförts varannan vecka, inte veckovis, mellan vecka 24 och vecka 32 2021.</div>
 
-<div class="small text-muted">**NB: Avloppsvattenmätningarna har utförts varannan vecka, inte veckovis, mellan vecka 24 och vecka 32 2021.</div>
-
-<div class="row ml-0 mt-3"><b>Publikationer:</b></div><div class="row"><div class="col">
-<b><a target="_blank" href="https://doi.org/10.1016/j.scitotenv.2020.142939">Benchmarking virus concentration methods for quantification of SARS-CoV-2 in raw wastewater.</a></b><br>
-                    <span class="text-muted">Jafferali MH, Khatami K, Atasoy M, Birgersson M, Williams C, Cetecioglu Z.</span><br>
-                    <i>Science of The Total Environment</i> 755. DOI: 10.1016/j.scitotenv.2020.142939
-
-<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
-<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
-<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
-
-<script src="https://datagraphics.dc.scilifelab.se/graphic/956f9390690043b8ae5f62b90d22f84f.js?id=stockholm_combined"></script>
+**Källskod som används för att skapa grafen:** [Källskod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/wastewater/historic_stockholm_data.py).

layouts/index.html

@@ -182,7 +182,7 @@ <h5>Biobanks</h5>
     <div class="bg-home-topics mb-4">
       <h4 class="mt-0 mb-1">Pandemic preparedness topics</h4>
       <p class="mb-2 small">Click on one of the <b><a class="dark-blue" href="/topics/">topics</a></b> below to see only the content that is related to that topic.</p>
-      {{ range .Site.Menus.topics_menu }}
+      {{ range where .Site.Menus.topics_menu "Identifier" "ne" "all_topics" }}
         <a href="{{ .Page.RelPermalink }}"><span class="bg-home-topics-btn">{{ .Name }}</span></a>
       {{ end }}
     </div>

layouts/topics/single.html

@@ -1,7 +1,8 @@
 {{ define "main" }}
 
 {{ $page_topic := .Page.Params.topic }}
-{{ $topic_key := $page_topic | urlize }}
+{{ $topic_key := $page_topic | lower }}
+{{ $topic_key_url := $page_topic | urlize }}
 
 <!-- Content from the markdown file -->
 {{ .Content }}
@@ -13,7 +14,7 @@ <h3><i class="bi bi-three-dots-vertical"></i> Data highlights ({{ $n_dh }})</h3>
 <div class="container mt-3 mb-5">
   {{- partial "highlights.html" . -}}
   <div class="mt-2 fw-bold align-content-end">
-    <a href="/highlights/topics/{{ $topic_key }}">See all data highlights on {{ $page_topic }} ({{ $n_dh }}) 
+    <a href="/highlights/topics/{{ $topic_key_url }}">See all data highlights on {{ $page_topic }} ({{ $n_dh }}) 
       <i class="bi bi-arrow-right-circle-fill"></i>
     </a>
   </div>
@@ -27,7 +28,7 @@ <h3><i class="bi bi-three-dots-vertical"></i> Data highlights ({{ $n_dh }})</h3>
 <h3><i class="bi bi-three-dots-vertical"></i> Dashboards ({{ $n_db }})</h3>
 <div class="container mt-3 mb-5">
   {{- partial "dashboards.html" . -}}
-  <div class="mt-2 fw-bold align-content-end"><a href="/dashboards/topics/{{ $topic_key }}">See all dashboards
+  <div class="mt-2 fw-bold align-content-end"><a href="/dashboards/topics/{{ $topic_key_url }}">See all dashboards
     on {{ $page_topic }} ({{ $n_db }}) <i class="bi bi-arrow-right-circle-fill"></i></a></div>
 <hr>
 </div>
@@ -39,7 +40,7 @@ <h3><i class="bi bi-three-dots-vertical"></i> Dashboards ({{ $n_db }})</h3>
 <h3><i class="bi bi-three-dots-vertical"></i> Editorials ({{ $n_ed }})</h3>
 <div class="container mt-3 mb-5">
   {{- partial "editorials.html" . -}}
-  <div class="mt-2 fw-bold align-content-end"><a href="/editorials/topics/{{ $topic_key }}">See all editorials
+  <div class="mt-2 fw-bold align-content-end"><a href="/editorials/topics/{{ $topic_key_url }}">See all editorials
     on {{ $page_topic }} ({{ $n_ed }}) <i class="bi bi-arrow-right-circle-fill"></i></a></div>
 <hr>
 </div>