Initial commit

.gitignore

+public/
+.DS_Store
+.hugo_build.lock
+.idea/
+.vscode/
\ No newline at end of file

.gitmodules

+[submodule "themes/hugo-pathogens-portal"]
+	path = themes/hugo-pathogens-portal
+	url = https://github.com/sib-swiss/hugo-pathogens-portal

content/_index.md

+---
+title: "Swiss Pathogens Portal: supporting researchers for pandemic preparedness and response"
+---
\ No newline at end of file

content/about/_index.md

+---
+title: About the Swiss Pathogens Portal
+menu:
+  navbar_top:
+    name: About
+    weight: 1
+  footer_about:
+    name:  Overview
+    weight: 1
+layout: about_navbar
+---
+
+## Vision
+
+Rapid and open pathogen data sharing is essential to advance research and drive effective surveillance activities. Access to comprehensive data, including genomic sequences, epidemiological information, and clinical data, empowers researchers to track the spread and evolution of pathogens in real-time. This transparency is particularly critical for studying emerging viruses, food-borne pathogens, and antimicrobial-resistant bacteria, which pose significant and complex threats to public health.
+
+A One Health approach, which integrates human, animal, and environmental health perspectives, is crucial in addressing these challenges. By facilitating the sharing of diverse data types across disciplines, this approach promotes a holistic understanding of pathogen dynamics and fosters coordinated research efforts to develop innovative solutions. Rapid and open data sharing not only enhances our ability to respond swiftly to health crises but also accelerates scientific discovery and strengthens global health security and preparedness.
+
+## Aims
+
+The Swiss Pathogens Portal was developed to support researchers in realizing this vision, by notably:
+* Providing a one-stop resource for all Swiss pathogen data and projects.
+* Fostering collaborations and synergies by creating a forum for discussion.
+* Providing documentation and training material on FAIR research data management, especially for pathogen omics data.
+* Showcasing Swiss resources that contribute to pathogen data sharing, access, analysis, and interpretation.
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content/about/partners/_index.md

+---
+title: Programs and Organizations behind the Portal
+menu:
+  footer_about:
+    name:  Partners
+    weight: 3
+layout: about_navbar
+---
+
+{{< organization img="./pathogens_portal_logo.png" name="Pathogens Portal">}}
+The Pathogens Portal, launched in July 2023, is an invaluable resource for researchers, clinicians, and policymakers who need access to the latest and most comprehensive datasets on pathogens. The portal is a collaborative effort between the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and partners. The Pathogens Portal provides a centralised platform for sharing and accessing data on key pathogens, including those that can cause diseases in humans and animals, and on vectors and hosts. By bringing together data from multiple sources, and linking these data where possible, the portal enables researchers to better understand the biology and life cycles of pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. It is funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: RECODID, VEO, EOSC-Life, CONVERGE and BY-COVID.
+
+The national Pathogens Portals provide information, guidelines, tools and services to support researchers in creating and sharing research data on all pathogens and diseases. The purpose of the national portals is to showcase and highlight pathogen research data from each of the participating countries. Similar to the Pathogens Portal, the national portals rely on open and fair access of sequence and other omics data. The national portals are regularly updated with new tools, services and data.
+{{< /organization >}}
+
+{{< organization img="./swe_pathogens_portal_logo.png" name="The Swedish Pathogens Portal">}}
+The Swedish Pathogens Portal provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden.
+
+The Portal is operated by the SciLifeLab Data Centre and partners, who developed an open reference implementation for national data portals using Hugo in combination with Bootstrap for styling, DataTables for tables, and Vega/Vega-Lite and Plotly for interactive graphics. All code used for the Swedish Portal is open source (held under an MIT licence) and is available on GitHub. The Swiss Pathogens Portal reused the code from the Swedish Portal.
+{{< /organization >}}
+
+{{< organization img="./elixir_logo.png" name="ELIXIR">}}
+ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers. Under Web portals (https://elixir-europe.org/what-we-offer/portals) you will find useful portals to support you in making your data and software FAIR. 
+{{< /organization >}}
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content/about/programs-organizations-behind-the-portal/_index.md

+---
+title: Programs and Organizations behind the Portal
+menu:
+  footer_about:
+    name:  Programs and Organizations behind the Portal
+    weight: 2
+layout: about_navbar
+---
+
+{{< organization img="./sib_logo.png" name="SIB Swiss Institute of Bioinformatics - Centre for Pathogen Bioinformatics">}}
+SIB is a leading organization in biological and biomedical data science. It maximizes the impact of, and investments in scientific projects by making data FAIR (Findable, Accessible, Interoperable and Reusable), provides long-term access to leading Swiss biodata resources, and is a high-quality partner enabling innovation in academia, hospitals and industry. It does this through its complementary pillars on coordination, open databases and software tools, and centre of excellence.
+
+The Swiss Pathogens Portal is developed by the SIB Centre for Pathogen Bioinformatics, in collaboration with other SIB groups (e.g. Training).
+{{< /organization >}}
+
+{{< organization img="./bycovid_logo.png" name="BY-COVID">}}
+SIB is one of the partners of the BY-COVID Consortium. The Swiss Pathogens Portal was developed and funded within BY-COVID.
+
+The BeYond-COVID project aims to make COVID-19 data accessible to scientists in laboratories but also to anyone who can use it, such as medical staff in hospitals or government officials.
+
+Going beyond SARS-CoV-2 data, the project will provide a framework for making data from other infectious diseases open and accessible to everyone.
+{{< /organization >}}
\ No newline at end of file

content/access-data/_index.md

+---
+title: Share and Access Data
+toc: false
+menu: 
+  main:
+    name: Share and Access Data
+    identifier: share_access_data
+    weight: 2
+---
+
+## Share and Access Data
+- [Share Data](/access-data/share-data/)
+- [Datasets](/access-data/datasets/)
\ No newline at end of file

content/access-data/datasets.md

+---
+title: Available Datasets
+menu:
+  share_access_data:
+    name: Available Datasets
+    weight: 2
+  footer_data:
+    name: Datasets
+    weight: 2
+layout: datasets
+---
+
+## Access-controlled datasets
+
+This is a manually curated list of available datasets with controlled-access. New datasets are added on an ongoing basis. If you would like your project to be listed here, please get in touch with us.
+
+------------------------------------------------------------
+| Name                                 | Access data catalog            | Data access documentation                                      | Contact                                  |
+|--------------------------------------|--------------------------------|----------------------------------------------------------------|------------------------------------------|
+| Swiss Pathogen Surveillance Platform | https://public.spsp.sib.swiss/ | https://public.spsp.sib.swiss/docs/data-access-and-re-use.html | aitana.neves@sib.swiss; aegli@imm.uzh.ch |
+------------------------------------------------------------
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content/access-data/share-data.md

+---
+title: Share Data
+menu:
+  share_access_data:
+    name: Share Data
+    weight: 1
+---
+
+## FAIR Data
+
+The Swiss National Science Foundation (SNSF) encourages researchers to share their data in alignment with the FAIR Data Principles, which promote the Findability, Accessibility, Interoperability, and Reusability of data. Researchers are expected to make their data available in publicly accessible digital repositories. For more details, you can visit the SNSF’s research policies page here (https://www.snf.ch/en/FAiWVH4WvpKvohw9/topic/research-policies).
+For researchers dealing with biomolecular data, the ELIXIR Deposition Databases for Biomolecular Data serve as a valuable resource. This platform helps you identify recommended databases for depositing your data, ensuring compliance with best practices in data sharing. You can explore these resources here (https://elixir-europe.org/platforms/data/elixir-deposition-databases).
+
+## Guidelines for Pathogen Genomic Data Submission
+
+When working with pathogen genomic data, it is essential to follow specific guidelines based on the nature of your metadata:
+* Non-Sensitive Metadata: If your metadata does not contain sensitive personal information, you can directly submit your data to the European Nucleotide Archive (ENA). To do so, you will need to register on their submission portal, which can be accessed here (https://www.ebi.ac.uk/ena/browser/submit).
+* Sensitive Personal Data: If your metadata includes sensitive personal data, it is recommended to submit your data to the Swiss Pathogen Surveillance Platform (SPSP). At SPSP, your data will be carefully curated and annotated before being shared with the ENA under a robust ethical and legal framework. Detailed submission instructions for new registered groups can be found here (https://public.spsp.sib.swiss/docs/instructions-for-new-registered-groups.html).
+SPSP also accepts submissions of data with non-sensitive metadata. To begin the submission process, registration on the SPSP website is required, which can be done here (https://spsp.ch/register-group/).
+
+By following these guidelines, you ensure that your pathogen genomic data is shared responsibly and in accordance with ethical standards, facilitating further research and collaboration within the scientific community.

content/analyse-data/_index.md

+---
+title: Bioinformatics resources
+menu: 
+  main:
+    name: Analyse data
+    identifier: analyse_data
+    weight: 3
+  analyse_data:
+    name: Bioinformatics resources
+    identifier: bioinformatics_resources
+    weight: 1
+aliases: 
+  - /resources
+---
+

content/analyse-data/nextclade.md

+---
+title: Nextclade
+description: "Nextclade is a user-friendly web portal and command line tool for clade assignment, mutation calling, and sequence quality checks."
+image: analyse-data/nextclade_logo.png
+redirect_url: https://clades.nextstrain.org/
+menu: 
+  bioinformatics_resources:
+    name: Nextclade
+    weight: 2
+---
\ No newline at end of file

content/analyse-data/training-material.md

+---
+title: Bioinformatics resources
+menu: 
+  analyse_data:
+    name: Training material
+    identifier: training_material
+    weight: 2
+---
+
+We list below material of interest for training and capacity building in FAIR pathogen data management and analysis.
+
+- [The International cookbook for wastewater practitioners - Vol. 1 SARS-CoV-2, Aug 2024.](https://publications.jrc.ec.europa.eu/repository/handle/JRC138489)
\ No newline at end of file

content/analyse-data/v-pipe.md

+---
+title: V-pipe
+description: "V-pipe is a bioinformatics pipeline for the analysis of viral genomic data. It supports the reproducible analysis of genomic diversity in intra-host virus populations, which is often involved in viral pathogenesis and virulence."
+image: analyse-data/v-pipe_logo.svg
+redirect_url: https://www.expasy.org/resources/v-pipe
+menu: 
+  bioinformatics_resources:
+    name: V-pipe
+    weight: 1
+---
\ No newline at end of file

content/analyse-data/v-pipe_logo.svg

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