Merge pull request #1153 from ScilifelabDataCentre/develop

send latest changes to live

content/english/about/_index.md

@@ -39,27 +39,27 @@ The team are happy to help with using the Portal, to take suggestions regarding
 <div class="container mb-3">
   <div class="row row-cols-2 row-cols-md-3 row-cols-lg-6">
     <div class="col pt-2">
-      <div><img src="/img/people/lh.jpg" width="150" class="img-thumbnail"/></div>
+      <div><img src="/img/people/lh.jpg" alt="Picute of Liane H" width="150" class="img-thumbnail"/></div>
       <div><b>Liane Hughes</b></div>
       <div><span class="text-muted">Project leader</span></div>
     </div>
     <div class="col pt-2">
-      <div><img src="/img/people/kos.jpg" width="150" class="img-thumbnail"/></div>
+      <div><img src="/img/people/kos.jpg" alt="Picute of Katarina ÖS" width="150" class="img-thumbnail"/></div>
       <div><b>Katarina Öjefors Stark</b></div>
       <div><span class="text-muted">Data steward</span></div>
     </div>
     <div class="col pt-2">
-      <div><img src="/img/people/sp.jpg" width="150" class="img-thumbnail"/></div>
+      <div><img src="/img/people/sp.jpg" alt="Picute of Senthilkumar P" width="150" class="img-thumbnail"/></div>
       <div><b>Senthilkumar Panneerselvam</b></div>
       <div><span class="text-muted">Systems developer</span></div>
     </div>
     <div class="col pt-2">
-      <div><img src="/img/people/hk.jpg" width="150" class="img-thumbnail"/></div>
+      <div><img src="/img/people/hk.jpg" alt="Picute of Hanna K" width="150" class="img-thumbnail"/></div>
       <div><b>Hanna Kultima</b></div>
       <div><span class="text-muted">Vice head of SciLifeLab Data Centre</span></div>
     </div>
     <div class="col pt-2">
-      <div><img src="/img/people/jr.jpg" width="150" class="img-thumbnail"/></div>
+      <div><img src="/img/people/jr.jpg" alt="Picute of Johan R" width="150" class="img-thumbnail"/></div>
       <div><b>Johan Rung</b></div>
       <div><span class="text-muted">Head of SciLifeLab Data Centre</span></div>
     </div>

content/english/about/organisations_and_programs.md

@@ -25,7 +25,7 @@ layout: about_navbar
 <div class="row mt-4">
   <div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
     <figure class="figure">
-      <img width="250" src="/img/logos/scilifelab_kaw_logo.png">
+      <img width="250" alt="KAW logo" src="/img/logos/scilifelab_kaw_logo.png">
     </figure>
   </div>
   <div class="col-12 col-md-8 col-lg-9">
@@ -38,7 +38,7 @@ layout: about_navbar
 <div class="row mt-4">
   <div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
     <figure class="figure">
-      <img width="250" src="/img/logos/scilifelab-logo.svg">
+      <img width="250" alt="Scilifelab logo" src="/img/logos/scilifelab-logo.svg">
     </figure>
   </div>
   <div class="col-12 col-md-8 col-lg-9">

content/english/about/partner_organisations.md

@@ -10,7 +10,7 @@ layout: about_navbar
 <div class="row">
   <div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
     <figure class="figure">
-      <img height="50" alt="The European COVID-19 Data Platform logo" src="/img/site_logo/eml_pathogens_logo.svg">
+      <img height="50" alt="The European pathogens portal logo" src="/img/site_logo/eml_pathogens_logo.svg">
     </figure>
   </div>
   <div class="col-12 col-md-8 col-lg-9">

content/english/dashboards/npc-statistics.md

@@ -4,12 +4,13 @@ description: The national Pandemic Centre (NPC) conducted testing related to SAR
 banner: /dashboard_thumbs/NPC_logo.png
 banner_border: true
 menu:
-     dashboard_menu:
-        identifier: npc-statistics
-        name: "National Pandemic Centre (Historic)"
+  dashboard_menu:
+    identifier: npc-statistics
+    name: "SARS-CoV-2 tests at National Pandemic Centre"
 toc: false
+plotly: true
 aliases:
-    - /data_types/health_data/npc-statistics/
+  - /data_types/health_data/npc-statistics/
 dashboards_topics: [COVID-19, Infectious diseases]
 ---
 
@@ -19,131 +20,94 @@ dashboards_topics: [COVID-19, Infectious diseases]
   <a class="dark-blue" href="https://nyheter.ki.se/covid-19-tester-ki-atergar-till-ordinarie-laboratorieverksamhet-men-har-fortsatt-beredskap">KI Press Release</a>
 </div>
 
-The dataset visualised in the graphs on this page is available [here](https://datagraphics.dc.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418).  The numbers reported here were compiled automatically and, as such, might not correspond to
-the numbers reported through other sources for different reasons.
+The dataset visualised in the graphs on this page is available [on SciLifeLab's Blobserver](https://blobserver.dc.scilifelab.se/blob/NPC-statistics-data-set.csv). The numbers reported here were compiled automatically and, as such, might not correspond to the numbers reported through other sources for different reasons.
 
 #### Total NPC test numbers
 
 The total number of SARS-CoV-2 (COVID-19) tests conducted at the national Pandemic Centre (NPC) since the start of the pandemic, separated according to whether the results were positive, negative, or invalid/inconclusive.
 
-Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1).
-
-<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="w-100" id="total-numbers-chart"></div>
+ <div class="plot_wrapper mb-3">
+    <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_total_tests.json" height="200px">}}</div>
 </div>
 
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_total_tests.py).
+
 #### NPC test numbers
 
 The number of SARS-CoV-2 (COVID-19) tests ran daily or weekly, divided according to whether results were positive, negative, or invalid/inconclusive.
 
-Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below.
-
-  <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_stacked_bar_chart" aria-expanded="true" aria-controls="#daily_stacked_bar_chart">
-    Daily
-  </button>
-  </div>
-<div class="collapse show" id="daily_stacked_bar_chart">
-  <div class="d-lg-none alert alert-info">
-    Scroll the plot sideways to view all data.
-  </div>
-  <div class="plot_wrapper">
-    <div class="w-100" id="stacked-bar-chart"></div>
-  </div>
+##### Daily
+
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
 </div>
-<div id="dwbuttons">
-<button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#weekly_stacked_bar_chart" aria-expanded="true" aria-controls="weekly_stacked_bar_chart">
-  Weekly
-</button></div>
-<div class="collapse show" id="weekly_stacked_bar_chart">
-  <div class="d-lg-none alert alert-info">
-    Scroll the plot sideways to view all data.
-  </div>
-  <div class="plot_wrapper">
-    <div class="w-100" id="stacked-bar-chart-weekly"></div>
-  </div>
+
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_tests_daily.json" height="350px">}}</div>
 </div>
 
-#### NPC tests positive fraction
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_tests_daily.py).
 
-The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that were positive,
-as percentage of all tests conducted (excluding invalid/inconclusive).
-
-Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db) graphs below.
-
-<div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_positive_bar_chart" aria-expanded="true" aria-controls="#daily_positive_bar_chart">
-  Daily
-</button></div>
-<div class="collapse show" id="daily_positive_bar_chart">
-    <div class="d-lg-none alert alert-info">
-      Scroll the plot sideways to view all data.
-    </div>
-    <div class="plot_wrapper">
-      <div class="w-100" id="positive-bar-chart"></div>
-    </div>
-    <p class="small"><i>*Note that as the number of reported analyses vary, some days may have a low number of samples, affecting the statistics a lot for that day, e.g. August 24th where only seven samples were reported, all positive.</i></p>
+##### Weekly
+
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
 </div>
-<div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#weekly_positive_bar_chart" aria-expanded="true" aria-controls="weekly_positive_bar_chart">
-  Weekly
-</button></div>
-<div class="collapse show" id="weekly_positive_bar_chart">
-  <div class="d-lg-none alert alert-info">
-    Scroll the plot sideways to view all data.
-  </div>
-  <div class="plot_wrapper">
-    <div class="w-100" id="positive-bar-chart-weekly"></div>
-  </div>
+
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_tests_weekly.json" height="350px">}}</div>
 </div>
 
-#### Cumulative NPC test numbers
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_tests_weekly.py).
 
-The sum of all SARS-CoV-2 (COVID-19) virus tests conducted at NPC since the
-start of the pandemic, as a function of date, and divided according to whether results were positive, negative, or invalid/inconclusive.
+#### NPC tests positive fraction
 
-Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6).
+The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that were positive,
+as percentage of all tests conducted **(excluding invalid/inconclusive)**.
+
+##### Daily
+
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
 
-<div class="d-lg-none alert alert-info">
-  Scroll the plot sideways to view all data.
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_positiveTests_fraction_daily.json" height="350px">}}</div>
 </div>
 
-<div class="plot_wrapper">
-  <div class="w-100" id="cumulative-plot"></div>
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_positiveTests_fraction_daily.py).
+
+##### Weekly
+
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
 </div>
 
-The National Pandemic Centre (NPC) was a facility for
-[SARS-CoV-2 (COVID-19) testing](https://ki.se/mtc/ctmr-and-covid-19)
-established within the
-[Centre for Translational Microbiome Research (CTMR)](https://ki.se/en/research/centre-for-translational-microbiome-research-ctmr)
-at
-[Karolinska Institutet (KI)](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/).
-At the end of March 2020, the large-scale microbiome research lab was
-quickly converted into a centre to assist Sweden with analysing
-SARS-CoV-2 tests. This was made possible by a donation from the
-[Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en) and a previously established collaboration with
-[MGI Tech](https://en.mgitech.cn/) in Shenzen, China. The NPC initially helped to expand the RNA-extraction capacity at Karolinska
-Universitets laboratoriet. However, it quickly expanded into a facility that increased the testing capacity across all regions of Sweden.
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_positiveTests_fraction_weekly.json" height="350px">}}</div>
+</div>
 
-The final capacity of the National Pandemic Centre at KI/SciLifeLab
-was approximately 10,000 tests per day. The results were typically
-returned within 24 hours of the sample arriving to the lab. NPC
-exclusively performed PCR-based analyses, not serological
-(antibody-based) analyses.
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_positiveTests_fraction_weekly.py).
 
-<script src="https://cdn.jsdelivr.net/npm/vega@5.12.1"></script>
-<script src="https://cdn.jsdelivr.net/npm/vega-lite@4.12.2"></script>
-<script src="https://cdn.jsdelivr.net/npm/vega-embed@6.8.0"></script>
+#### Cumulative NPC test numbers
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1.js?id=total-numbers-chart"></script>
+The sum of all SARS-CoV-2 (COVID-19) virus tests conducted at NPC since the
+start of the pandemic, as a function of date, and divided according to whether results were positive, negative, or invalid/inconclusive.
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc.js?id=stacked-bar-chart"></script>
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf.js?id=stacked-bar-chart-weekly"></script>
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_cumulative_tests.json" height="550px">}}</div>
+</div>
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65.js?id=positive-bar-chart"></script>
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_cumulative_tests.py).
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6.js?id=cumulative-plot"></script>
+The National Pandemic Centre (NPC) was a facility for [SARS-CoV-2 (COVID-19) testing](https://ki.se/mtc/ctmr-and-covid-19) established within the [Centre for Translational Microbiome Research (CTMR)](https://ki.se/en/research/centre-for-translational-microbiome-research-ctmr) at [Karolinska Institutet (KI)](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/). At the end of March 2020, the large-scale microbiome research lab was quickly converted into a centre to assist Sweden with analysing SARS-CoV-2 tests. This was made possible by a donation from the [Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en) and a previously established collaboration with [MGI Tech](https://en.mgitech.cn/) in Shenzen, China. The NPC initially helped to expand the RNA-extraction capacity at Karolinska Universitets laboratoriet. However, it quickly expanded into a facility that increased the testing capacity across all regions of Sweden.
 
-<script src="https://datagraphics.dc.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db.js?id=positive-bar-chart-weekly"></script>
+The final capacity of the National Pandemic Centre at KI/SciLifeLab was approximately 10,000 tests per day. The results were typically returned within 24 hours of the sample arriving to the lab. NPC exclusively performed PCR-based analyses, not serological (antibody-based) analyses.

content/english/data-management.md

@@ -14,11 +14,11 @@ On this page, you will find information about where to access direct, one-on-one
 
 ### Swedish Pathogens Portal
 
-Whilst the portal contains many general guidelines for RDM e.g. how to [share data](/share-data/), we also offer direct support for individual projects. To access this, please send an email to <a href="mailto:pathogens@scilifelab.se">pathogens@scilifelab.se</a> or send a messsage via the [contact form](/contact/). You can typically expect a response within one working day.
+Whilst the portal contains many general guidelines for RDM e.g. how to [share data](/share-data/), we also offer direct support for individual projects. To access this, please send an email to [pathogens@scilifelab.se](mailto:pathogens@scilifelab.se) or send a messsage via the [contact form](/contact/). You can typically expect a response within one working day.
 
 ### SciLifeLab Data Management Helpdesk
 
-The SciLifeLab Data Management Helpdesk is operated by experts in RDM from the SciLifeLab Data Centre and National Bioinformatics Infrastructure Sweden (NBIS). The purpose of the helpdesk is to provide direct, customised RDM support for those working in life science research in Sweden. To get in touch, send an email to <a href="mailto:data-management@scilifelab.se">data-management@scilifelab.se</a>. Alternatively, you can go to the [SciLifeLab Research Data Management Guidelines](https://data-guidelines.scilifelab.se) and submit questions via the contact form.
+The SciLifeLab Data Management Helpdesk is operated by experts in RDM from the SciLifeLab Data Centre and National Bioinformatics Infrastructure Sweden (NBIS). The purpose of the helpdesk is to provide direct, customised RDM support for those working in life science research in Sweden. To get in touch, send an email to [data-management@scilifelab.se](mailto:data-management@scilifelab.se). Alternatively, you can go to the [SciLifeLab Research Data Management Guidelines](https://data-guidelines.scilifelab.se) and submit questions via the contact form.
 
 ## Resources for infectious disease data
 

content/english/highlights/antibiotic_resistance_development.md

@@ -7,7 +7,7 @@ banner_large: /highlights/banners/antibiotic_resistance_development.jpg
 banner_caption: Artistic illustration of perseverance courtesy Elf lab / Johan Elf, Irmeli Barkefors
 highlights_topics: [Antibiotic resistance]
 tags: [Antibiotic resistance, Bacteria, Escherichia coli, Perseverance, Time-lapse microscopy]
-announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/antibiotic_resistance_development/), as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the [Data Platform](https://data.scilifelab.se/) for more."
+announcement: "This data highlight was also <a class='dark-blue' target='_blank' href='https://data.scilifelab.se/highlights/antibiotic_resistance_development/'>published on the SciLifeLab Data Platform</a>, as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the <a class='dark-blue' target='_blank' href='https://data.scilifelab.se/'>Data Platform</a> for more."
 images: [/highlights/banners/antibiotic_resistance_development_small.jpg]
 ---