Merge pull request #1032 from ScilifelabDataCentre/develop

Make latest changes live

content/english/about/_index.md

@@ -1,13 +1,13 @@
 ---
 title: About the Swedish Pathogens Portal
 menu:
-    navbar_top:
-        name: About
-        weight: 10
-        identifier: about
-    footer_about:
-        name: About the portal
-        weight: 10
+  navbar_top:
+    name: About
+    weight: 10
+    identifier: about
+  footer_about:
+    name: About the portal
+    weight: 10
 ---
 
 <div class="mb-4">
@@ -29,7 +29,7 @@ menu:
 
 #### Introduction
 
-The *Swedish Pathogens Portal* provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university.
+The _Swedish Pathogens Portal_ provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university.
 
 The Portal is operated by the [SciLifeLab Data Centre](https://scilifelab.se/data/) and [partners](partner_organisations). We welcome community contributions to the Portal and provide information on the different ways that the community can contribute, for more details see [contribute](/contribute/) page. In addition to running the Portal, the team can also either provide support on data-related questions surrounding pandemic preparedness research or help find suitable support services. For more general data support, please see our related research data management service([RDM Guidelines](https://data-guidelines.scilifelab.se/)).
 
@@ -57,7 +57,7 @@ The team are happy to help with using the Portal, to take suggestions regarding
       <div><span class="text-muted">Project leader</span></div>
     </div>
     <div class="col-md-2 pt-2">
-      <div><img src="/img/people/kos.jpeg" width="150" class="img-thumbnail"/></div>
+      <div><img src="/img/people/kos2.jpg" width="150" class="img-thumbnail"/></div>
       <div><b>Katarina Öjefors Stark</b></div>
       <div><span class="text-muted">Data steward</span></div>
     </div>

content/english/about/partner_organisations.md

@@ -19,6 +19,19 @@ title: Partner organisations
   </ul>
 </div>
 
+<div class="row">
+  <div class="col-sm-12 col-md-12 col-lg-3">
+    <figure class="figure">
+      <img height="50" alt="The European COVID-19 Data Platform logo" src="/img/site_logo/eml_pathogens_logo.svg">
+    </figure>
+  </div>
+  <div class="col-sm-12 col-md-12 col-lg-9">
+  <h6>Pathogens Portal</h6>
+    <p>The <a href="https://www.pathogensportal.org/" target="_blank">Pathogens Portal</a>, maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (<a href="https://www.ebi.ac.uk/" target="_blank">EMBL-EBI</a>) and partners, was launched in July 2023. The Pathogens Portal is a resource for e.g. researchers, clinicians, and policymakers. Its aim is  to facilitate access to the latest and most comprehensive datasets on pathogens. The COVID-19 pandemic put a  spotlight on the importance of data sharing and for focused access to relevant datasets. Therefore, the Pathogens Portal was developed as a centralised platform for  data sharing and accessing data on key pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. Bringing together data from a number of sources, and linking data contributes to a better understand Pathogen ́s Biology. Funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: <a href="https://recodid.eu/" target="_blank">RECODID</a>, <a href="https://www.veo-europe.eu/" target="_blank">VEO</a>, <a href="https://www.eosc-life.eu/" target="_blank">EOSC-Life</a>, <a href="https://elixir-europe.org/about-us/how-funded/eu-projects/converge" target="_blank">CONVERGE</a> and <a href="https://by-covid.org/" target="_blank">BY-COVID</a>. Moving forward, national nodes of the Pathogens Portal will be added, the Swedish Pathogens Portal is the first to launch in Sept 2023. </p>
+  </div>
+</div>
+<hr class="faded" />
+
 <div class="row">
   <div class="col-sm-12 col-md-12 col-lg-3">
     <figure class="figure">
@@ -27,7 +40,7 @@ title: Partner organisations
   </div>
   <div class="col-sm-12 col-md-12 col-lg-9">
   <h6>European COVID-19 Data Platform</h6>
-    <p>The Swedish Pathogens Portal was originally launched as the ‘Swedish COVID-19 Data Portal’ and it was a national node of the <a href="https://www.covid19dataportal.org/">European COVID-19 Data Platform</a>. The European COVID-19 Data Platform is operated by the <a href="https://ebi.ac.uk">European Bioinformatics Institute</a> (a part of the <a href="https://www.embl.org/">European Molecular Biology Laboratory</a> (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes <a href="/partners/">can be found here</a>.</p>
+    <p>The Swedish Pathogens Portal was originally launched as the ‘Swedish COVID-19 Data Portal’ and it was a national node of the <a href="https://www.covid19dataportal.org/" target="_blank">European COVID-19 Data Platform</a>. The European COVID-19 Data Platform is operated by the <a href="https://ebi.ac.uk" target="_blank">European Bioinformatics Institute</a> (a part of the <a href="https://www.embl.org/" target="_blank">European Molecular Biology Laboratory</a> (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes <a href="/partners/">can be found here</a>.</p>
     <p>The European COVID-19 Data Platform aims to facilitate data sharing and analysis in order to accelerate coronavirus research. It enables researchers to upload, access and analyse reference data and specialist datasets related to COVID-19. It is synchronised with COVID-19-related data and scientific literature held in EMBL-EBI's data resources, including ENA, UniProt, PDBe, EMDB, Expression Atlas and Europe PMC. The data continues to grow in diversity and volume, but include sequences, structures, expression data, compound screens, biochemistries and scientific publications.</p>
   </div>
 </div>
@@ -41,9 +54,9 @@ title: Partner organisations
   </div>
   <div class="col-sm-12 col-md-12 col-lg-9">
       <h6>BY-COVID consortium</h6>
-    <p>The Swedish Pathogens Portal is one of the partners in the <a href="https://by-covid.org/">BY-COVID consortium</a>. BY-COVID is a Horizon project <a href="https://by-covid.org/news-events/by-covid-launch/">funded by the European Comission</a> and brings together <a href="https://by-covid.org/about">53 partners from 19 countries</a>. Stakeholders include individuals and organisation from multiple areas, including the biomedical field, hospitals, public health, social sciences and humanities.</p>
+    <p>The Swedish Pathogens Portal is one of the partners in the <a href="https://by-covid.org/" target="_blank">BY-COVID consortium</a>. BY-COVID is a Horizon project <a href="https://by-covid.org/news-events/by-covid-launch/" target="_blank">funded by the European Comission</a> and brings together <a href="https://by-covid.org/about" target="_blank">53 partners from 19 countries</a>. Stakeholders include individuals and organisation from multiple areas, including the biomedical field, hospitals, public health, social sciences and humanities.</p>
     <p>The BeYond-COVID (BY-COVID) project aims to make COVID-19 data accessible to anyone that can use it, including medical staff in hospitals, researchers in labs, and government officials. The project will provide a framework for making data from other infectious diseases open and accessible to everyone. The project will integrate established national and European infrastructures with ELIXIR, BBMRI, ECRIN, PHIRI and CESSDA. It will build on existing efforts, such as the COVID-19 Data Platform and the Versatile Emerging infectious disease Observatory project (VEO), in order to maximise efficiency. It will also develop synergies with the European Health Data Space.</p>
-    <p>Members of the Portal team are involved in the development of the <a href="https://www.infectious-diseases-toolkit.org">Infectious Disease Toolkit</a>, a major deliverable of the BY-COVID project.</p>
+    <p>Members of the Portal team are involved in the development of the <a href="https://www.infectious-diseases-toolkit.org" target="_blank">Infectious Disease Toolkit</a>, a major deliverable of the BY-COVID project.</p>
   </div>
 </div>
 <hr class="faded" />
@@ -59,7 +72,7 @@ title: Partner organisations
   </div>
   <div class="col-sm-12 col-md-12 col-lg-9">
   <h6>NBIS and ELIXIR Sweden</h6>
-    <p><a href="https://nbis.se">NBIS (National Bioinformatics Infrastructure Sweden)</a> is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities, and the Knut and Alice Wallenberg Foundation. It provides state-of-the-art bioinformatics to the life science research community in Sweden. NBIS is also the Swedish contact point to the European infrastructure for biological information, <a href="https://www.elixir-europe.org/">ELIXIR Europe</a>.</p>
+    <p><a href="https://nbis.se" target="_blank">NBIS (National Bioinformatics Infrastructure Sweden)</a> is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities, and the Knut and Alice Wallenberg Foundation. It provides state-of-the-art bioinformatics to the life science research community in Sweden. NBIS is also the Swedish contact point to the European infrastructure for biological information, <a href="https://www.elixir-europe.org/" target="_blank">ELIXIR Europe</a>.</p>
   </div>
 </div>
 <hr class="faded" />
@@ -72,7 +85,7 @@ title: Partner organisations
   </div>
   <div class="col-sm-12 col-md-12 col-lg-9">
       <h6>GA4GH</h6>
-    <p>The Swedish COVID-19 & Pandemic Preparedness Data Portal is one of the many partners of the <a href="https://www.ga4gh.org/">Global Alliance for Genomics and Health (GA4GH)</a> and part of their <a href="https://www.ga4gh.org/what-we-do/communities-of-interest/">Infectious Disease Community</a>.</p>
+    <p>The Swedish COVID-19 & Pandemic Preparedness Data Portal is one of the many partners of the <a href="https://www.ga4gh.org/" target="_blank">Global Alliance for Genomics and Health (GA4GH)</a> and part of their <a href="https://www.ga4gh.org/what-we-do/communities-of-interest/" target="_blank">Infectious Disease Community</a>.</p>
     <p>GA4GH is an international, non-profit organisation focused on advancing the responsible and effective sharing of genomic and health-related data. GA4GH aims to establish harmonised frameworks and standards in order to promote data interoperability and collaboration in genomics research and healthcare. At the same time, the alliance focuses on fully protecting the human rights of people who share their data. GA4GH brings together experts from various sectors, including academia, industry, and government, to address the ethical, legal, and technical challenges associated with genomic data sharing.</p>
     <p>The Infectious Disease Community, a vital component of the GA4GH, plays a crucial role in bridging the realms of pathogen and host genomics. This community brings together international groups dedicated to standardising the use of genomic data for improved diagnosis and treatment of infectious diseases. International groups within the community collaborate to identify opportunities for sharing datasets, workflows, and processes, enabling them to address complex and previously insurmountable questions. Through these collective activities, the Infectious Disease Community facilitates the advancement of genomic research, ultimately leading to improved diagnostic and treatment approaches for infectious diseases.
     </p>

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

@@ -25,7 +25,7 @@ The data and visualisation on this page are usually updated weekly, typically on
 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_slusites.json" height="825px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_sluCOVIDsites.json" height="825px" >}}</div>
 </div>
 
 ## Visualisations

content/english/highlights/bacterial_replication.md

@@ -0,0 +1,43 @@
+---
+title: Large effort study to elucidate replication initiation in bacteria
+date: 2023-09-20
+summary: This study by Knöppel, Broström et al is a large effort to elucidate replication initiation in bacteria. The authors have openly shared over 3 TB of microscopy imaging data.
+banner: /highlights/banners/ELF_banner.png
+banner_large: /highlights/banners/ELF_large.png
+banner_caption: Image courtesy Johan Elf lab
+highlights_topics: [Infectious Diseases]
+announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/bacterial_replication/), 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."
+---
+
+It is commonly known that all cells must coordinate DNA replication with cell growth; each chromosome should, on average, replicate once per generation. Bacteria, e.g. _Escherichia coli_, have optimised their division speed in order to survive in a very competitive environment. Fast division makes replication coordination extra challenging, especially in cases when the bacterial generation times are shorter than the time it takes to replicate the chromosome. This means that bacteria must have two complete copies of their chromosome ready before cell division, but still keep the ratio between the number of chromosome copies and cell divisions constant.
+
+The research community has, for over 50 years, studied how DNA copying and cell division are coordinated in bacteria. These studies have revealed the importance of a protein known as DNaA in the replication of _E. coli_. DnaA triggers the initiation of chromosome replication when bound to ATP, and there is a negative correlation between cell size at initiation and the intracellular concentration of DnaA. Whilst traditional methods of genetics and molecular biology have been essential for elucidating parts of the _E. coli_ replication processes, advances in microscopy have allowed for more insights into the phenotypic outcome that the interactions between these parts should accomplish. For example, recent studies have used high-throughput microscopy to observe ongoing cell replication in bacteria on a single-cell level. However, a number of key research questions are yet to be addressed, e.g. how the cell decides it’s time to initiate replication. Three main models have been proposed; the inhibitor dilution model, the initiation accumulation model, and the initiator activations/deactivation cycling.
+
+In a recent article in PNAS, researchers from Uppsala University and Science for Life Laboratory (SciLifeLab), Sweden, (First authors: Anna Knöppel and Oscar Broström, Corresponding authors: Johan Elf and David Fange) used high-throughput fluorescence microscopy to study the coordination of replication and division cycles in _E.coli_. By systematically exploring the replication-initiation control, the researchers aimed to find the most likely replication initiation model used in _E. coli_.
+
+In this study, Knöppel, Broström, and colleagues created mutant strains by inserting chromosomal modifications. The replisome can be described as the multiprotein molecular machinery responsible for the replication of DNA. In order to compare how important different parts implicated in replication control are in _E. coli_ replication, the researchers tracked the fluorescently labeled replisomes in individual cells through thousands of division cycles in the wild-type and mutant strains, thereby gaining knowledge of the importance of each regulator.
+
+In one experiment, Knöppel _et al_. used a specific mutant _E. coli_ strain with a sole DnaA gene under the control of an inducible promotor. The results showed that DnaA synthesis is not a requirement for triggering accurate initiation of replication. In addition, initiation size increased marginally as DnaA was diluted by growth after DnaA expression had been turned off. This led the researchers to conclude that the conversion of DnaA between its active ATP-bound state and inactive ADP-bound states is more important for initiation size control than the total free concentration of DnaA.
+
+Further, the researchers studied different pathways known to be important for the DnaA-ATP/ADP conversion. For these experiments, they created mutant _E.coli_ strains with combinations of deletions in the DARS1, DARS2, and datA loci. The results showed that DARS and datA can compensate for each other, e.g. deletion of DARS could be compensated for by deleting datA and, additionally, also by overexpressing DnaA. Among the DnaA-ATP/ADP conversion mechanisms tested, deletion of the regulatory inactivation of DnaA (RIDA) was found to have the most severe impact on replication initiation.
+
+In conclusion, this study is one of the largest efforts to date to elucidate replication initiation in bacteria. It contains over 3 TB of microscopy imaging data. The findings outlined above support the third model suggested for replication initiation: initiator activation/deactivation cycling. However, additional studies into this model are warranted.
+
+#### Data
+
+- Data and all code have been deposited in the [SciLifeLab data repository](https://figshare.scilifelab.se/articles/dataset/Regulatory_elements_coordinating_initiation_of_chromosome_replication_to_the_Escherichia_coli_cell_cycle/22139918/1).
+- Proteomics data have been deposited in PRIDE [(Project PXD036580)](https://www.ebi.ac.uk/pride/archive/projects/PXD036580/).
+
+#### Article
+
+DOI: [10.1073/pnas.2213795120](https://doi.org/10.1073/pnas.2213795120)
+
+Knöppel, A., Broström, O., Gras, K., Elf, J., & Fange, D. (2023). Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle. In: PNAS (Vol. 120, Issue 22, e2213795120).
+
+#### Funding
+
+This work was funded by grants from the European Research Council (advanced grant no. 885360), the Swedish Research Council (grant nos. 2016-06213 and 2018-03958), the Knut and Alice Wallenberg Foundation (grant nos. 2016.0077, 2017.0291, and 2019.0439), and the eSSENCE e-science initiative.
+
+#### Infrastructure
+
+Resources provided by Swedish National Infrastructure for Computing (SNIC) (now known as National Academic Infrastructure for Super­computing in Sweden, NAISS) at UPPMAX enabled data management and computing.