Merge pull request #1060 from ScilifelabDataCentre/develop

send temporary additions live

content/english/biobanks/_index.md

@@ -1,22 +1,22 @@
 ---
 title: Swedish COVID-19 Sample Collection Database
 menu:
-  homepage_biobanks:
-  name: Sample Collection Database
-  identifier: biobanks
-  post: Registry of Swedish biobanks and sample collections for COVID-19 research. <a href="/biobanks/">About the database <i class="bi bi-arrow-right-circle-fill"></i></a>
+ homepage_biobanks:
+ name: Sample Collection Database
+ identifier: biobanks
+ post: Registry of Swedish biobanks and sample collections for COVID-19 research. <a href="/biobanks/">About the database <i class="bi bi-arrow-right-circle-fill"></i></a>
 toc: false
 ---
 
 ### About the Swedish COVID-19 Sample Collection Database
 
-The [Swedish COVID-19 Sample Collection Database](https://biobanks.covid19dataportal.se/) is a tool for researchers wishing to make use of samples and data stored in various biobanks across Sweden in their research. The database allows to find sample collections matching their needs using various filters. The filter searches include: sample collection name, keywords, diagnosis, available sample types (e.g., nasal swabs, DNA, saliva, whole blood, RNA, etc.), sample collection type (healthcare sample collections or research sample collections) and data types (e.g., data about biological material and medical records). For each collection, a short description, donor information, sample information as well as contact information for sample requests are provided.
+The [Swedish COVID-19 Sample Collection Database](https://biobanks.pathogens.se/) is a tool for researchers wishing to make use of samples and data stored in various biobanks across Sweden in their research. The database allows to find sample collections matching their needs using various filters. The filter searches include: sample collection name, keywords, diagnosis, available sample types (e.g., nasal swabs, DNA, saliva, whole blood, RNA, etc.), sample collection type (healthcare sample collections or research sample collections) and data types (e.g., data about biological material and medical records). For each collection, a short description, donor information, sample information as well as contact information for sample requests are provided.
 
-Both the so-called *healthcare sample collections* and *research sample collections* are listed in the database. Healthcare sample collections are intended for diagnostics, treatment, and healthcare use but can be made available if a corresponding ethical approval from the Swedish Ethical Review Authority has been obtained. In case of the research sample collections, the responsible researcher has the right of disposal to the sample collection, and requests should be made directly to collection head (the new research study needs to either fall under the original ethics research approval or a new one will need to be obtained).
+Both the so-called _healthcare sample collections_ and _research sample collections_ are listed in the database. Healthcare sample collections are intended for diagnostics, treatment, and healthcare use but can be made available if a corresponding ethical approval from the Swedish Ethical Review Authority has been obtained. In case of the research sample collections, the responsible researcher has the right of disposal to the sample collection, and requests should be made directly to collection head (the new research study needs to either fall under the original ethics research approval or a new one will need to be obtained).
 
 As of May 2023, the Sample Collection Database contains information about **36 sample collections** from **18 different biobanks, as well as one national collection**. The database is gradually expanded as information about new sample collections and biobanks is submitted.
 
-<span style="font-size:1.3em;"><b><a href="https://biobanks.covid19dataportal.se/">Search in the COVID-19 Sample Collection Database <i class="bi bi-arrow-right-circle-fill"></i> </a></b></span>
+<span style="font-size:1.3em;"><b><a href="https://biobanks.pathogens.se/">Search in the COVID-19 Sample Collection Database <i class="bi bi-arrow-right-circle-fill"></i> </a></b></span>
 
 ### Submit information about sample collections
 
@@ -28,8 +28,8 @@ The Swedish COVID-19 Sample Collection Database is operated in collaboration wit
 
 <div class="row">
  <div class="col">
- <img class="mr-4" src="https://covid19dataportal.se/img/logos/scilifelab-logo.svg" alt="SciLifeLab" height="40">
- <img class="mr-4" src="https://covid19dataportal.se/img/logos/biobanksverige_logo.jpg" alt="Biobank Sverige" height="40">
+ <img class="mr-4" src="https://pathogens.se/img/logos/scilifelab-logo.svg" alt="SciLifeLab" height="40">
+ <img class="mr-4" src="https://pathogens.se/img/logos/biobanksverige_logo.jpg" alt="Biobank Sverige" height="40">
  </div>
 </div>
 

content/english/dashboards/RECOVAC.md

@@ -25,7 +25,8 @@ EPN Nr 2020-01800, 2020-05829, 2021-00267, 2021-00829, 2021-02106, 2021-04098, 2
 
 ## Data visualisations
 
-<div class="alert alert-info">All data last updated: {{% RECOVAC_date_modified %}}</div>
+<!-- <div class="alert alert-info">All data last updated: {{% RECOVAC_date_modified %}}</div> -->
+<div class="alert alert-info">All data last updated: 08-11-2023</div>
 
 _All code used to produce the visualisations on this page is available on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/RECOVAC). The particular scripts used in each case are linked below the plots._
 
@@ -93,8 +94,11 @@ When hovering over the plot with the cursor, additional grey icons appear in the
  Rotating your phone may improve graph layout
 </div>
 
-<div class="plot_wrapper mb-3">
+<!-- <div class="plot_wrapper mb-3">
  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}</div>
+</div> -->
+<div class="plot_wrapper mb-3">
+ <div class="table-responsive">{{< plotly json="/img/swedishpop_subplot_button.json" height="800px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py).
@@ -148,7 +152,8 @@ When hovering over the plot with the cursor, additional grey icons appear in the
 </div>
 
 <div class="plot_wrapper mb-3">
- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div>
+ <div class="table-responsive">{{< plotly json="/img/comorbs_subplot_button.json" height="800px" >}}</div>
+ <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div> -->
 </div>
 
 **Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py).

content/english/dashboards/variants_region_uppsala.md

@@ -21,7 +21,7 @@ This dashboard includes two visualisations of the data from the section for Clin
 
 ## SARS-CoV-2 Sequence Visualisations
 
-<div class="alert alert-info">Last updated: <span id="last_modified_uuclinmicro"></span></div>
+<div class="alert alert-info">Last updated: 2023-11-06 <span id="last_modified_uuclinmicro"></span></div>
 
 The sequences are presented according to their [World Health Organisation (WHO) label](https://www.who.int/activities/tracking-SARS-CoV-2-variants) (a greek letter) and/or their Pango lineage. The Pango lineage is determined using [Pangolin](https://cov-lineages.org/resources/pangolin.html), [Nextclade](https://clades.nextstrain.org/), and an in-house annotation-based mutation analysis workflow.
 
@@ -36,7 +36,8 @@ Use the **‘Last 16 weeks’ button** to see data only from the last 16 weeks,
 </div>
 
 <div class="plot_wrapper mb-3">
- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}</div>
+ <div class="table-responsive">{{< plotly json="/img/lineage_four_recent.json" height="600px" >}}</div>
+ <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_four_recent.json" height="600px" >}}</div> -->
 </div>
 
 **Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_four_recent.py).
@@ -52,7 +53,8 @@ Use the **’Deselect all lineages’ button** to clear data from all lineages f
 </div>
 
 <div class="plot_wrapper mb-3">
- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_one_wholetime.json" height="600px" >}}</div>
+ <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/lineage_one_wholetime.json" height="600px" >}}</div> -->
+ <div class="table-responsive">{{< plotly json="/img/lineage_one_wholetime.json" height="600px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Graph and data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/ClinMicro/lineage_one_plot.py).

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

@@ -22,7 +22,7 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p
 
 ## Visualisations
 
-<div class="alert alert-info">Last updated: <span id="last_modified_gu"></span></div>
+<div class="alert alert-info">Last updated: 2023-11-08<span id="last_modified_gu"></span></div>
 
 _The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023)._
 
@@ -60,14 +60,15 @@ _The blue block on the graph indicates the period where sample collection was no
 </div>
 
  <div class="plot_wrapper mb-3">
- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}</div>
+ <div class="table-responsive">{{< plotly json="/img/wastewater_gothenburg.json" height="550px" >}}</div>
+ <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}</div> -->
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/gothenburg_covid.py).
 
 ## Commentary from the research group
 
-<div><b>Date:</b> <span id="gu_comment_date"></span><br><b>Commentary:</b> <span id="gu_comment"></span></div>
+<div><b>Date: 2023-11-08</b> <span id="gu_comment_date"></span><br><b>Commentary:</b> There are still low amounts of SARS-CoV-2 in Gothenburg's wastewater. However, there was a small increase in weeks 41, 42, and 43 but there are still low levels. <span id="gu_comment"></span></div>
 
 {{< ww_dynamic_content >}}
 

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

@@ -20,17 +20,17 @@ The data presented on this page is generated in the SLU (Swedish University of A
 
 The data and visualisation on this page are usually updated weekly, typically on Fridays. Please note that the scores provided in the dataset and depicted in plot below are preliminary, so corrections and changes may occur. Data and information about the group on this dashboard are updated frequently, so please check back regularly to stay up to date.
 
-## Wastewater collection sites
+<!-- ## Wastewater collection sites
 
 SLU-SEEC collects and analyses samples for SARS-CoV-2 from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). A value of 'null' for the end date indicates that collection is ongoing. An asterisk (\*) next to the number of people indicates that the value is a BOD-7 value (an estimate of the people connected), rather than the number of people physically connected to each WWTP. The information in the below table is [available for download as an excel file](https://blobserver.dc.scilifelab.se/blob/SLU_COVID_collection_sites.xlsx).
 
  <div class="plot_wrapper mb-3">
  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_sluCOVIDsites.json" height="825px" >}}</div>
-</div>
+</div> -->
 
 ## Visualisations
 
-<div class="alert alert-info">Last updated: <span id="last_modified_uppsala"></span></div>
+<div class="alert alert-info">Last updated: 2023-11-08 <span id="last_modified_uppsala"></span></div>
 
 <b>Important note:</b> Historical data for Ekerö, Enköping, Knivsta, Tierp, Vaxholm, Älvkarleby, and Österåker are available in the dataset (linked below). However, they are no longer included in the visualisation.
 
@@ -70,7 +70,8 @@ Please note that although the same methods are used for all cities shown on this
 </div>
 
 <div class="plot_wrapper mb-3">
- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="600px" >}}</div>
+ <div class="table-responsive">{{< plotly json="/img/wastewater_combined_slu_regular.json" height="800px" >}}</div>
+ <!-- <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="600px" >}}</div> -->
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_regular.py).
@@ -89,7 +90,9 @@ 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://blobserver.dc.scilifelab.se/blob/SLU_wastewater_data.csv). Data are available from week 38 of 2020; updated weekly.
+**Download the data:** [Respiratory virus gene copy numbers normalised per PMMoV gene copy number.CSV file.](/ww_data_temp/SLU_wastewater_data.csv). Data are available from week 38 of 2020; updated weekly.
+
+<!-- https://blobserver.dc.scilifelab.se/blob/SLU_wastewater_data.csv -->
 
 **How to cite the dataset:**
 
@@ -105,7 +108,7 @@ For most cities represented on this page, raw, untreated wastewater samples that
 
 The freshly collected samples are processed according to standard methodologies. For samples collected up to and including week 18 of 2021, viral particles were concentrated using the electronegative filtration method ([Ahmed _et al._, 2020](https://www.sciencedirect.com/science/article/pii/S004896972033480X)). Since week 19 of 2021, the viral genomic material has instead been concentrated and extracted by the direct capture method, using the Maxwell RSC Enviro TNA kit (Promega).
 
-Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes was performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.fda.gov/media/134922/download). From week 32 of 2023 quantification is performed using the Flu SC2 Multiplex Assay (CDC). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39).
+Absolute quantification of the copy numbers of the SARS-CoV-2 genome is performed using One-Step RT-qPCR. Until week 31 of 2023 the quantification of the viral genomes was performed using the [SARS-CoV-2 specific N1 assay from the Centers for Disease Control and Prevention (CDC)](https://www.fda.gov/media/134922/download). From week 32 of 2023 quantification is performed using the Flu SC2 Multiplex Assay (CDC). To correct for variations in population size and wastewater flow, the pepper mild mottle virus (PMMoV) is quantified using a modified version of the assay of [Zhang _et al._ (2006)](https://doi.org/10.1371/journal.pbio.0040003). PMMoV is an abundant RNA virus in human faeces and serves as an estimator of human faecal content ([Symonds _et al._, 2019](https://doi.org/10.1371/journal.ppat.1007639)). For more details about the sample processing method, and the evaluation of the use of the PMMoV normalisation method for Swedish wastewater, please refer to the corresponding publication: [Isaksson _et al._ (2022)](https://www.mdpi.com/2076-3298/9/3/39).
 
 The data in the graph and datafile represent the ratio of the copy numbers measured by the Flu SC2 Multiplex Assay and PMMoV-assays, multiplied by 1000. As the Flu SC2 Multiplex Assay provides a proxy for SARS-CoV-2 virus content in the wastewater and PMMoV is a proxy of the faecal content (which is related to the contributing population), the ratio of the two can be considered to be a proxy for the prevalence of COVID-19 infections in the population of the wastewater catchment area. To align the data generated by the current method with the data generated by methods and quantification assays used earlier, older data has been transformed using conversion factors. The conversion factors are estimated based on common alignment periods when old and new methods are used in parallel.