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Merge pull request #1036 from ScilifelabDataCentre/develop
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LianeHughes authored Oct 3, 2023
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9 changes: 9 additions & 0 deletions config.yaml
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highlights_topic: highlights_topics
highlights_voc: highlights_vocs
dashboards_topic: dashboards_topics

permalinks:
highlights_topics: "/highlights/topics/:slug/"
highlights_vocs: "/highlights/vocs/:slug/"
dashboards_topics: "/dashboards/topics/:slug/"

related:
includeNewer: false
indices:
- name: tags
weight: 100
threshold: 80
toLower: false
33 changes: 10 additions & 23 deletions content/english/about/_index.md
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footer_about:
name: About the portal
weight: 10
navbar_about:
name: "Overview<br><br>"
weight: 10
layout: about_navbar
---

<div class="mb-4">
<ul class="nav nav-tabs nav-justified">
<li class="nav-item active">
<a class="nav-link active" href="#"><b>Overview<br><br></b></a>
</li>
<li class="nav-item">
<a class="nav-link" href="organisations_and_programs">Programs & organisations<br>behind the portal</a>
</li>
<li class="nav-item">
<a class="nav-link" href="editorial_committee">Editorial committee<br><br></a>
</li>
<li class="nav-item">
<a class="nav-link" href="partner_organisations">Partner organisations<br><br></a>
</li>
</ul>
</div>

#### 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.
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The team are happy to help with using the Portal, to take suggestions regarding new and existing sections, and to answer any questions that you may have. Please just get in touch using for [contact](/contact/) form.

<div class="container mb-3">
<div class="row">
<div class="col-md-2 pt-2">
<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.png" 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-md-2 pt-2">
<div class="col pt-2">
<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>
<div class="col-md-2 pt-2">
<div class="col pt-2">
<div><img src="/img/people/sp.jpeg" 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-md-2 pt-2">
<div class="col pt-2">
<div><img src="/img/people/hk.jpg" 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-md-2 pt-2">
<div class="col pt-2">
<div><img src="/img/people/jr.jpg" width="150" class="img-thumbnail"/></div>
<div><b>Johan Rung</b></div>
<div><span class="text-muted">Head of SciLifeLab Data Centre</span></div>
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22 changes: 5 additions & 17 deletions content/english/about/editorial_committee.md
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---
title: Editorial committee
menu:
navbar_about:
name: "Editorial committee<br><br>"
weight: 30
layout: about_navbar
---

<div class="mb-4">
<ul class="nav nav-tabs nav-justified">
<li class="nav-item">
<a class="nav-link" href="../">Overview<br><br></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../organisations_and_programs/">Programs & organisations<br>behind the portal</a>
</li>
<li class="nav-item">
<a class="nav-link active" href="#"><b>Editorial committee<br><br></b></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../partner_organisations/">Partner organisations<br><br></a>
</li>
</ul>
</div>

Below are the six editorial committee members for 2023, alongside their affiliation and area of expertise. The editorial committee enable a more direct link between the Portal and the wider research community. They collaborate with the Portal team to create content and advise on resources that would be beneficial to researchers in their area of expertise.

{{< editorial_committee_cards >}}
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40 changes: 15 additions & 25 deletions content/english/about/organisations_and_programs.md
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@@ -1,31 +1,19 @@
---
title: Programs and organisations behind the portal
menu:
navbar_about:
name: "Programs & organisations<br>behind the portal"
weight: 20
layout: about_navbar
---

<div class="mb-4">
<ul class="nav nav-tabs nav-justified">
<li class="nav-item">
<a class="nav-link" href="../">Overview<br><br></a>
</li>
<li class="nav-item">
<a class="nav-link active" href="#"><b>Programs & organisations<br>behind the portal</b></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../editorial_committee">Editorial committee<br><br></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../partner_organisations/">Partner organisations<br><br></a>
</li>
</ul>
</div>

<div class="row">
<div class="col-sm-12 col-md-12 col-lg-3">
<div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
<figure class="figure mt-3">
<img width="250" height="130" alt="PLP logo" src="/img/plp_default2.png">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 col-lg-9">
<h6>Pandemic Laboratory Preparedness (PLP) Program</h6>
<p>SciLifeLab (Science for Life Laboratory) was <a href="https://www.regeringen.se/rattsliga-dokument/proposition/2020/12/forskning-frihet-framtid--kunskap-och-innovation-for-sverige/">commissioned by the Swedish govenment</a> to prepare resources and capabilities that can be used to deal with future pandemics. The assignment broadly involved supporting research related to infectious diseases (e.g. in diagnostics, analysis of infection, immunity, and the development of resistance to therapies in pathogens), and building competence and developing technologies related to pandemic research (e.g. in sequencing, genetic analysis, immunology, and big data).</p>
<p>The <a href="https://www.scilifelab.se/capabilities/pandemic-laboratory-preparedness/">Pandemic Laboratory Preparedness (PLP) program</a> was established as a result of the commission from the government in December 2020. The services, tools, and resources (termed ‘capabilities’) established through the PLP program are intended to complement those established elsewhere in society (e.g. authorities, municipalities and regions) when tackling future pandemics. As such, the PLP program will work closely with governmental agencies, e.g. <a href="https://www.folkhalsomyndigheten.se">Swedish Public Health Agency (FoHM)</a>.</p>
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<hr class="faded" />

<div class="row mt-4">
<div class="col-sm-12 col-md-12 col-lg-3">
<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">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 col-lg-9">
<h6>SciLifeLab & Wallenberg National Program for Data-Driven Life Science</h6>
<p>Life science research is becoming increasingly data-driven. The amount and complexity of data is also growing exponentially. Data is the most valuable product of research, and it is therefore crucially important that we ensure it is managed appropriately throughout its lifecycle. To this end, SciLifeLab and The Knut and Alice Wallenberg Foundation have established the Data-Driven Life Science (DDLS) program in Sweden. The mission of the DDLS program is to recruit and train the next generation of life scientists, and to create strong data science capabilities for life science in Sweden that are internationally competitive. The DDLS program has been funded by The Knut and Alice Wallenberg foundation for 12 years. SciLifeLab, as a national infrastructure for life science, coordinates this program in close collaboration with ten Swedish universities and the Swedish Museum of Natural History. You can read more about the DDLS program <a href="https://www.scilifelab.se/data-driven/">here</a>.</p>
</div>
</div>
<hr class="faded" />

<div class="row mt-4">
<div class="col-sm-12 col-md-12 col-lg-3">
<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">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 col-lg-9">
<h6 class="d-md-none">Science for Life Laboratory</h6>
<p>SciLifeLab (Science for Life Laboratory) is an institution for the advancement of molecular biosciences in Sweden. We are funded as a national research infrastructure by the Swedish government. Our organisation leverages the unique strengths of individual researchers across Sweden into a focused resource for the life science community. Thousands of researchers rely on us to provide access to the cutting-edge instrumentation and deep scientific expertise needed to produce internationally competitive bioscience research. These technologies are supported and developed by our research community, which includes internationally recognised experts in life science and technology. Our facilities and expertise create a unique environment for carrying out health and environmental research at the highest level.</p>
<p>SciLifeLab began in 2010 as a joint effort between four Swedish universities (<a href="https://www.ki.se/">Karolinska Institutet</a>, <a href="https://www.kth.se/">KTH Royal Institute of Technology</a>, <a href="https://www.su.se/">Stockholm University</a> and <a href="https://www.uu.se/">Uppsala University</a>). However, today we have expanded far beyond this, and support research activities at all major Swedish universities.</p>
</div>
</div>
<hr class="faded" />

<div class="row mt-4">
<div class="col-sm-12 col-md-12 col-lg-3">
<div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
<figure class="figure">
<img height="95" alt="SciLifeLab Data Centre logo" src="/img/logos/dc_branding_light_bg.svg">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 col-lg-9">
<h6 class="d-md-none">Scilifelab Data Centre</h6>
<p>Life science research is increasingly becoming data-driven, rather than primarily technology-driven. SciLifeLab coordinates and supports activities throughout the data life cycle, from project planning and data production, right through to data publishing and reuse, where researchers are dependent on advanced data analysis and e-infrastructures.</p>
<p>At SciLifeLab, we see data as one of the most valuable and long-lasting products of our operations. We strive to ensure our data adheres to the principles of <a href="https://www.force11.org/group/fairgroup/fairprinciples">FAIR</a> and Open Science. We also put considerable effort into maximising the long-term value of our data to the scientific community.</p>
</div>
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---
title: Partner organisations
menu:
navbar_about:
name: "Partner organisations<br><br>"
weight: 40
layout: about_navbar
---

<div class="mb-4">
<ul class="nav nav-tabs nav-justified">
<li class="nav-item">
<a class="nav-link" href="../">Overview<br><br></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../organisations_and_programs/">Programs & organisations<br>behind the portal</a>
</li>
<li class="nav-item">
<a class="nav-link" href="../editorial_committee">Editorial committee<br><br></a>
</li>
<li class="nav-item">
<a class="nav-link active" href="#"><b>Partner organisations<br><br></b></a>
</li>
</ul>
</div>

<div class="row">
<div class="col-sm-12 col-md-12 col-lg-3">
<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">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 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">
<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/logos/european_covid19dataportal.svg">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 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/" 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>
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<hr class="faded" />

<div class="row mt-4">
<div class="col-sm-12 col-md-12 col-lg-3">
<div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
<figure class="figure mt-3">
<img height="40" alt="BY-COVID logo" src="/img/logos/by-covid-logo.svg">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 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/" 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>
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<hr class="faded" />

<div class="row mt-4">
<div class="col-sm-12 col-md-12 col-lg-3 mt-3">
<div class="col-12 col-md-4 col-lg-3 d-none d-md-block">
<figure class="figure me-3">
<img height="65" alt="National Bioinformatics Infrastructure (NBIS) logo" src="/img/logos/nbislogo-orange-txt.svg">
</figure>
<figure class="figure">
<img height="65" alt="ELIXIR logo" src="/img/logos/elixir-se-logo.png">
</figure>
</div>
<div class="col-sm-12 col-md-12 col-lg-9">
<div class="col-12 col-md-8 col-lg-9">
<h6>NBIS and ELIXIR Sweden</h6>
<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>
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<figure class="figure">
<img height="65" alt="Global Alliance for Genomics & Health logo" src="/img/logos/ga4gh_logo.png">
</figure>
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weight: 20
identifier: contact
footer_about:
name: Contact form
weight: 20
name: Support & Feedback
weight: 30
aliases:
- /suggestions/
recaptcha: true
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</div>
</div>

<div class="d-md-none alert alert-info">
Rotating your phone may improve graph layout
</div>

<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>
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</div>
</div>

<div class="d-md-none alert alert-info">
Rotating your phone may improve graph layout
</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>
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