Update 07_repos.qmd

develop/07_repos.qmd

@@ -1,10 +1,10 @@
 ---
-title: 7. Repositories for bio data
+title: 7. Repositories for biodata
 format: html
 date-modified: last-modified
 date-format: long
 date: 2023-11-30
-summary: In this lesson we navigate through different types of repositories and which ones are ideal to deposit your NGS datasets and data analyses.
+summary: In this lesson, we navigate through different types of repositories and which ones are ideal for depositing your NGS datasets and data analyses.
 ---
 
 :::{.callout-note title="Course Overview"}
@@ -34,7 +34,7 @@ Specialized repositories and archives securely store, curate, and disseminate sc
 There are two types of repositories:
 
 - **General repositories**: relevant to a wide range of disciplines (e.g. Zenodo). 
-- **Domain-specific**: repositories are customized for specific fields, providing specialized curation and context-specific features (e.g. ENA, GEO, Annotare etc.). 
+- **Domain-specific**: repositories are customized for specific fields, providing specialized curation and context-specific features (e.g. ENA, GEO, Annotare, etc.). 
 
 :::{.callout-note}
 # List of repositories for biological data
@@ -52,11 +52,11 @@ There are two types of repositories:
   - Functional Annotation of Animal Genomes (FAANG) Data Repository
   - Check ELIXIR Core Data Resources [here](https://elixir-europe.org/platforms/data/core-data-resources)
 
-Your institution might as well have their own repositories such as [ERDA](https://www.erda.dk/) (Electronic research data archive at University of Copenhagen).
+Your institution might as well have its repositories such as [ERDA](https://www.erda.dk/) (Electronic research data archive at the University of Copenhagen).
 :::
 
 ## Domain-specific repositories
-This tailored approach ensures alignment with standards and maximizes utility and impact of research findings. By catering to particular research areas, these repositories offer researchers a more focused audience, deeper domain expertise, and increased visibility within their specific research community. 
+This tailored approach ensures alignment with standards and maximizes the utility and impact of research findings. By catering to particular research areas, these repositories offer researchers a more focused audience, deeper domain expertise, and increased visibility within their specific research community. 
 
 Explore some examples of NGS data repositories below:
 
@@ -84,16 +84,16 @@ The repositories mentioned earlier adhere to established community standards for
 
 By adhering to standards, repositories ensure that submitted data is high quality, well-documented, and compliant with community best practices, promoting data discovery, reproducibility, and interoperability within the scientific community.
 
-Following all the recommendations in this course makes it straightforward to provide the necessary documentation and information for these repositories. For instance, repositories specific to NGS data will require the raw FASTQ files, sample metadata and protocols as well as final pre-processing results (for instance, read count matrices in BED files).  
+Following all the recommendations in this course makes it straightforward to provide the necessary documentation and information for these repositories. For instance, repositories specific to NGS data will require the raw FASTQ files, sample metadata, and protocols as well as final pre-processing results (for instance, read count matrices in BED files).  
 
 :::{.callout-warning}
-Keep in mind that these repositories are not intended for downstream analysis data and associated code. However, you should already have those version controlled by GitHub, which eliminates any concerns. You can then archive such repositories in a general repository like Zenodo.
+Keep in mind that these repositories are not intended for downstream analysis data and associated code. However, you should already have those versions controlled by GitHub, which eliminates any concerns. You can then archive such repositories in a general repository like Zenodo.
 :::
 
 
 ## General repositories
 
-[Zenodo](https://zenodo.org/) is one of the widely used repositories for a variety of research outputs. It is an open-access digital platform supported by the European Organization for Nuclear Research (CERN) and the European Commission. It caters to various research outputs, including datasets, papers, software, and multimedia files, making it a valuable resource for researchers worldwide.With its user-friendly platform, researchers can easily upload, share, and preserve their research data. Each deposited item receives a unique Digital Object Identifier (DOI), ensuring citability and long-term accessibility. Additionally, Zenodo offers robust metadata capabilities for enriching submissions with contextual information. Moreover, researchers can [link their GitHub]((https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content)) accounts to Zenodo, simplifying the process of archiving GitHub repository releases for long-term accessibility and citation.
+[Zenodo](https://zenodo.org/) is one of the widely used repositories for a variety of research outputs. It is an open-access digital platform supported by the European Organization for Nuclear Research (CERN) and the European Commission. It caters to various research outputs, including datasets, papers, software, and multimedia files, making it a valuable resource for researchers worldwide. With its user-friendly platform, researchers can easily upload, share, and preserve their research data. Each deposited item receives a unique Digital Object Identifier (DOI), ensuring citability and long-term accessibility. Additionally, Zenodo offers robust metadata capabilities for enriching submissions with contextual information. Moreover, researchers can [link their GitHub]((https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content)) accounts to Zenodo, simplifying the process of archiving the GitHub repository releases for long-term accessibility and citation.
 
 Once your accounts are linked, creating a Zenodo archive becomes as straightforward as tagging a release in your GitHub repository. Zenodo automatically detects the release and generates a corresponding archive, complete with a unique Digital Object Identifier (DOI) for citable reference. Therefore, before submitting your work to a journal, link your data analysis repository to Zenodo, obtain a DOI, and cite it in your manuscript which enhances reproducibility in research.