ScilifelabDataCentre · Ziip-dev · Jul 2, 2024 · Jun 14, 2024 · Jun 14, 2024 · Jun 17, 2024
diff --git a/content/english/citation.md b/content/english/citation.md
@@ -1,10 +1,9 @@
 ---
 title: How to cite the Portal
 menu:
-  top_actions:
+  navbar_top:
     name: Cite us
-    weight: 80
-    pre: <i class="bi bi-patch-exclamation-fill me-2"></i>
+    weight: 50
   footer_about:
     name: Cite us
     weight: 30

diff --git a/content/english/contribute.md b/content/english/contribute.md
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 ---
 title: Contribute
 menu:
-  top_actions:
+  navbar_top:
     name: Contribute
-    weight: 40
-    pre: <i class="bi bi-plus-circle-fill me-2"></i>
+    weight: 30
 ---
 
 The _Swedish Pathogens Portal_ was built to serve the community of researchers working on relevant topics and we welcome any contributions from the community or suggestions on how the Portal can help the community. Whenever there is anything that you would like to share with your colleagues, do not hesistate to share it through the Portal. We welcome suggestions for new information or edits in all sections as well as ideas for new sections that could be launched.

diff --git a/content/english/dashboards/serology-statistics.md b/content/english/dashboards/serology-statistics.md
@@ -14,6 +14,7 @@ menu:
 aliases:
   - /data_types/health_data/serology-statistics/
 dashboards_topics: [COVID-19, Infectious diseases]
+plotly: true
 ---
 
 <div class="alert alert-info">
@@ -29,20 +30,6 @@ Serology tests involve testing bodily fluids for the presence of antibodies or o
 
 <div class="alert alert-info">Data last updated: {{% serology_date_modified %}}.</div>
 
-<!-- ## Number of serology tests completed
-
-The below plot shows the total number (sum total) of serology tests related to SARS-CoV-2 completed by the SciLifeLab Autoimmunity and Serology Profiling unit since the beginning of the pandemic.
-
-<br>
-
-<div class="d-lg-none alert alert-info">
-  Scroll the plot sideways to view all of the data.
-</div>
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-<div class="plot_wrapper">
-  <div class="w-100" id="total-number"></div>
-</div> -->
-
 ## Weekly serology tests
 
 The number of SARS-CoV-2 serology tests completed by the SciLifeLab Autoimmunity and Serology Profiling unit each week, divided according to whether tests were positive, negative, or research & development (R&D).
@@ -51,10 +38,14 @@ The number of SARS-CoV-2 serology tests completed by the SciLifeLab Autoimmunity
   Scroll the plot sideways to view all of the data.
 </div>
 
-<div class="plot_wrapper">
-  <div class="w-100" id="bar-chart"></div>
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weekly_serology_tests.json" height="550px" >}}</div>
 </div>
 
+<!-- **Download the data:** [The number of R&D, negative, and positive tests done per week](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->
+
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/weekly-serology-tests.py).
+
 ## Cumulative serology tests
 
 The cumulative number of positive, negative, and research & development (R&D) SARS-CoV-2 serology tests completed over time at the SciLifeLab Autoimmunity and Serology Profiling unit.
@@ -63,22 +54,18 @@ The cumulative number of positive, negative, and research & development (R&D) SA
   Scroll the plot sideways to view all of the data.
 </div>
 
-<div class="plot_wrapper">
-  <div class="w-100" id="cumulative-plot"></div>
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/cumulative_serology_tests.json" height="550px" >}}</div>
 </div>
 
+<!-- **Download the data:** [The number of R&D, negative, and positive tests done per week](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->
+
+**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/cumulative-serology-tests.py).
+
 #### About serology testing at the Autoimmunity and Serology Profiling unit
 
 Early in the COVID-19 pandemic, work was initiated to [develop a serological assay](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/other-scilifelab-efforts/serology/) for large scale testing of plasma and serum samples for antibodies against SARS-CoV-2. The work was undertaken by three research groups at [the Department of Protein Science, KTH Royal Institute of Technology (KTH)](https://www.kth.se/pro) and the [Autoimmunity and Serology Profiling unit](https://www.scilifelab.se/facilities/autoimmunity-profiling/) at [SciLifeLab](https://www.scilifelab.se).
 
 By comparing and combining a large number of variants of SARS-CoV-2 proteins as antigens, a [highly sensitive and specific multiplex bead-based assay](https://doi.org/10.1002/cti2.1312) was established. The high-throughput assay can be used to process up to 8000 samples per week. The vast majority of samples analysed to date originated from healthcare personnel, population-based studies, personnel in the pharmaceutical and biotechnology industry, and from within multiple research collaborations. Collaborators and sample providers include the community study at Danderyd University Hospital ([see news involving a follow-up study at Danderyd University Hospital](https://www.scilifelab.se/news/four-out-of-five-still-have-antibodies-against-sars-cov-2)), Karolinska University Hospital, Uppsala University Hospital, Skåne University Hospital, Örebro University Hospital, Sophiahemmet Hospital, Public Health Agency of Sweden, RISE (Research Institutes of Sweden), AstraZeneca, Cytiva, SVPH, Karolinska Institutet, KTH, Uppsala University, and Lund University.
 
 Check out the [Autoimmunity and Serology Profiling unit page](https://www.scilifelab.se/units/autoimmunity-profiling/) on the SciLifeLab website to find out more about the unit itself. Publications produced by studies making use of the unit are available in the [SciLifeLab Infrastructure Publications database](https://publications.scilifelab.se/label/Autoimmunity%20and%20Serology%20Profiling).
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diff --git a/content/english/dashboards/variants_region_uppsala.md b/content/english/dashboards/variants_region_uppsala.md
@@ -79,6 +79,8 @@ Use the **’Deselect all lineages’ button** to clear data from all lineages f
 
 ## Publications
 
+Cumlin, T., Karlsson, I., Haars, J., Rosengren, M., Lennerstrand, J., Pimushyna, M., Feuk, L., Ladenvall, C., Kaden, R. (2024). SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance. _Int. J. Mol. Sci._, **25**, 6645. DOI: [10.3390/ijms25126645](https://doi.org/10.3390/ijms25126645).
+
 Haars, J., Palanisamy, N., Wallin, F., Mölling, P., Lindh, J., Sundqvist, M., Ellström, P., Kaden, R., Lennerstrand, J. (2023). Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023. _Microorganisms_, **11**, 2417. DOI: [10.3390/microorganisms11102417](https://doi.org/10.3390/microorganisms11102417).
 
 Mannsverk, S., Bergholm, J., Palanisamy, N., Ellström, P., Kaden, R., Lindh, J., Lennerstrand, J. (2022). SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. _Virology Journal_, **19**, 164. DOI: [10.1186/s12985-022-01896-x](https://doi.org/10.1186/s12985-022-01896-x).

diff --git a/content/english/data-sources.md b/content/english/data-sources.md
@@ -0,0 +1,11 @@
+---
+Title: Data sources & repositories
+---
+
+This page includes displays **Data Sources** and **Repositories** relevant to the scope of the Swedish Pathogens Portal (i.e. infectious disease and pandemic preparedness in Sweden). **Data sources** are defined as resources where at least some users can access (but not submit) data. **Repositories**, by contrast, are resources in which at least some users can both access and submit data.
+
+Use the **Search** function to locate data sources/repositries by name/keywords (often more granular than other filters). It is also possible to filter data sources according to **Data Type**.
+
+[Get in touch](/contact/) about adding further data sources.
+
+{{< data_sources >}}
diff --git a/content/english/events/_index.md b/content/english/events/_index.md
@@ -2,6 +2,10 @@
 title: Events & Training
 description: Community-sourced collection of events and training opportunities.
 recaptcha: true
+menu:
+    navbar_top:
+        name: Events & Training
+        weight: 40
 ---
 
 This section includes a list of upcoming conferences, webinars, workshops, and training opportunities related to pandemic preparedness and infectious disease. This includes events related to the management of data for these topics. We also welcome suggestions for events related to research data management in general. Such events will instead be listed on the [SciLifeLab Data Platform](https://data.scilifelab.se/events/). We highly encourage users to explore those events.

diff --git a/content/english/share-data.md b/content/english/share-data.md
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 title: Share data
 toc: true
-menu:
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 aliases:
   - /data_types/genomics_transcriptomics/guidelines/
   - /data_types/compound_and_target_data/guidelines/

diff --git a/content/english/support.md b/content/english/support.md
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 title: Get support
 toc: false
-menu:
-  top_actions:
-    name: Get support
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 aliases:
   - /support_services/bioinformatics/
 ---

diff --git a/content/svenska/citation.md b/content/svenska/citation.md
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 ---
 title: Citera data, information och resurser från portalen
 menu:
-  top_actions:
+  navbar_top:
     name: Citera oss
-    weight: 80
-    pre: <i class="bi bi-patch-exclamation-fill me-2"></i>
+    weight: 40
   footer_about:
     name: Citera oss
     weight: 30

diff --git a/content/svenska/contribute.md b/content/svenska/contribute.md
@@ -2,10 +2,9 @@
 title: Bidra till Portalen
 toc: false
 menu:
-  top_actions:
+  navbar_top:
     name: Bidra till Portalen
-    weight: 40
-    pre: <i class="bi bi-plus-circle-fill me-2"></i>
+    weight: 30
 ---
 
 Pathogens Portal Sverige har som syfte att stödja forskare som arbetar inom de forskningsområden som Portalen specifikt är inriktade på. Vi välkomnar både förslag på och bidrag till Portalens innehåll och förslag på hur Portalen kan utvecklas för att bättre stödja forskningen. Som forskare uppmanar vi dig att interagera med Portalen, exempelvis genom att dela data eller information genom Portalen. Vi tar även gärna emot förslag på nytt innehåll, nya sektioner samt förslag på hur nuvarande sektioner kan utvecklas och förnyas.

diff --git a/content/svenska/dashboards/post_covid.md b/content/svenska/dashboards/post_covid.md
@@ -205,12 +205,3 @@ I vetenskapliga publikationer och medias rapportering används flera olika begre
 ### Aktuell forskning
 
 Ett stort antal vetenskapliga artiklar, fallrapporter och reviews med fokus på postcovid har publicerats under det senaste året (jmfr. [[Dani _et al._ (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre _et al._ (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil _et al._ (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin _et al._ (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). De flesta vetenskapliga artiklar har haft som syfte att identifiera riskfaktorer och faktorer som kan användas för att prediktera individer som kan utveckla postcovid efter den akuta covid-19 infektionen. En nyligen publicerad studie av [Sudre och kollegor](https://doi.org/10.1038/s41591-021-01292-y) har lagt fram en modell för att prediktera individer som riskerar utveckla postcovid utifrån data från [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/). I denna studie självrapporterar deltagarna sina symtom i en app på sin mobiltelefon. Resultaten indikerade att individer som upplevde fler än fem symtom under den första sjukdomsveckan hade högre risk att utveckla kvarstående symptom efter covid-19 (oddskvot = 3,53 (2,76–4,50)). Dessutom visade studien att postcovid var mer sannolikt hos kvinnor och att risken också ökade med ökande ålder och högre BMI. Forskarna bakom studien föreslår att deras prediktionsmodell kan användas för att identifiera individer som riskerar att utveckla postcovid. Dessa resultat kan användas för förebyggande vård och för att utveckla behandlingsmetoder och stöd vid planering av utbildning och rehabilitering.
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diff --git a/content/svenska/dashboards/serology-statistics.md b/content/svenska/dashboards/serology-statistics.md
@@ -9,6 +9,7 @@ menu:
     name: SARS-CoV-2 antikoppstester som utförts av SciLifeLab
 aliases:
   - /sv/data_types/health_data/serology-statistics/
+plotly: true
 ---
 
 <div class="alert alert-info">
@@ -24,20 +25,6 @@ Serologiska tester innebär att kroppsvätskor testas för förekomst av antikro
 
 <div class="alert alert-info">Senaste uppdatering: {{% serology_date_modified %}}.</div>
 
-<!-- ## Number of serology tests completed
-
-The below plot shows the total number (sum total) of serology tests related to SARS-CoV-2 completed by the SciLifeLab Autoimmunity and Serology Profiling unit since the beginning of the pandemic.
-
-<br>
-
-<div class="d-lg-none alert alert-info">
-  Scroll the plot sideways to view all of the data.
-</div>
-
-<div class="plot_wrapper">
-  <div class="w-100" id="total-number"></div>
-</div> -->
-
 ## Serologiska tester per vecka
 
 Antalet SARS-CoV-2 serologitester som SciLifeLab Autoimmunity and Serology Profiling-enheten genomförde varje vecka, uppdelat efter om testerna var positiva, negativa eller inom forskning och utveckling (R&D).
@@ -46,10 +33,14 @@ Antalet SARS-CoV-2 serologitester som SciLifeLab Autoimmunity and Serology Profi
   Att rotera mobiltelefonen kan förbättra grafens layout
 </div>
 
-<div class="plot_wrapper">
-  <div class="w-100" id="bar-chart"></div>
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weekly_serology_tests.json" height="550px" >}}</div>
 </div>
 
+<!-- **Ladda ner data:** [Serology-testing-statistics-dataset-20202021.csv](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->
+
+**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/weekly-serology-tests.py).
+
 ## Kumulativa serologiska tester
 
 Det kumulativa antalet positiva, negativa och forsknings- och utvecklingstester (R&D) av SARS-CoV-2-serologi som slutförts över tid vid SciLifeLab Autoimmunity and Serology Profiling-enheten.
@@ -58,22 +49,18 @@ Det kumulativa antalet positiva, negativa och forsknings- och utvecklingstester
   Att rotera mobiltelefonen kan förbättra grafens layout
 </div>
 
-<div class="plot_wrapper">
-  <div class="w-100" id="cumulative-plot"></div>
+<div class="plot_wrapper mb-3">
+  <div class="table-responsive" style="min-width: 800px">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/cumulative_serology_tests.json" height="550px" >}}</div>
 </div>
 
+<!-- **Ladda ner data:** [Serology-testing-statistics-dataset-20202021.csv](https://blobserver.dc.scilifelab.se/blob/Serology-testing-statistics-dataset-20202021.csv) -->
+
+**Källkod som används för att skapa grafen:** [Källkod](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/serology/cumulative-serology-tests.py).
+
 #### Om serologisk testning vid enheten för Autoimmunity and Serology Profiling
 
 Tidigt under covid-19-pandemin inleddes arbetet med att [utveckla en serologisk analys](https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/pandemic-response/other-scilifelab-efforts/serology/) för storskalig testning av plasma- och serumprover för antikroppar mot SARS-CoV-2. Arbetet utfördes av tre forskargrupper vid [institutionen för proteinvetenskap, Kungliga Tekniska Högskolan (KTH)](https://www.kth.se/sv/pro/protein-science-1.784558) och [enheten för autoimmunitet och serologisk profilering](https://www.scilifelab.se/facilities/autoimmunity-profiling/) vid [SciLifeLab](https://www.scilifelab.se).
 
 Genom att jämföra och kombinera ett stort antal varianter av SARS-CoV-2-proteiner som antigener etablerades en [mycket känslig och specifik så kallad multiplex bead-based assay](https://doi.org/10.1002/cti2.1312). Assayen med hög kapacitet kan användas för att bearbeta upp till 8000 prover per vecka. De allra flesta prover som hittills har analyserats kommer från vårdpersonal, befolkningsbaserade studier, personal inom läkemedels- och bioteknikindustrin samt från flera olika forskningssamarbeten. Samarbetspartners och provleverantörer inkluderar samhällsstudien vid Danderyds universitetssjukhus ([se nyhet om uppföljningsstudie vid Danderyds universitetssjukhus](https://www.scilifelab.se/news/four-out-of-five-still-have-antibodies-against-sars-cov-2)), Karolinska universitetssjukhuset, Akademiska sjukhuset i Uppsala, Skånes universitetssjukhus, Universitetssjukhuset Örebro, Sophiahemmet, Folkhälsomyndigheten, RISE (Research Institutes of Sweden), AstraZeneca, Cytiva, SVPH, Karolinska Institutet, KTH, Uppsala universitet och Lunds universitet.
 
 Kolla in [Autoimmunity and Serology Profiling unit page](https://www.scilifelab.se/units/autoimmunity-profiling/) på SciLifeLabs webbplats för att få reda på mer om själva enheten. Publikationer som producerats av studier som använder enheten finns tillgängliga i databasen [SciLifeLab Infrastructure Publications](https://publications.scilifelab.se/label/Autoimmunity%20and%20Serology%20Profiling).
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