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Open Source Science

https://github.com/clavellab/hibc

Shiny application to display data and metadata for The Human Intestinal Bacterial Collection (HiBC)

https://github.com/clavellab/hibc

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Shiny application to display data and metadata for The Human Intestinal Bacterial Collection (HiBC)

Basic Info
  • Host: GitHub
  • Owner: ClavelLab
  • Language: R
  • Default Branch: main
  • Size: 3.4 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created 11 months ago · Last pushed 10 months ago
Metadata Files
Readme

README.md

hibc

hibc is the code repository for the website of "Human Intestinal Bacteria Collection". It contains the R code to generate the website in the form of a Shiny interactive application. The application is then build as a Docker container and served online to the public at https://hibc.rwth-aachen.de.

Development

Whilst all the code is accessible and pull-requests are welcome, some of the features for the deployment of the shiny application are restricted to RWTH personnel.

Create the R project via Rstudio

  1. Clone the repository using git clone https://git.rwth-aachen.de/clavellab/hibc
  2. Open the Rstudio project in hibc/app/app.Rproj to create the app project
  3. Rstudio warns you that One or more packages recorded in the lockfile are not installed because a couple of R packages and dependencies are needed.
    1. Install the dependencies by typing renv::restore() in the Console and agree to the installation of the packages.
    2. Check that all dependencies are set by typing renv::status() in the Console where you should have No issues found
  4. Preview the Shiny app via the "Run app" button or by typing shiny::runApp() in the R console.

Build the docker container locally

You can test if the Shiny application is ready for deployment by building the docker container locally.

```bash

build the Dockerfile

docker build -t hibc-shiny .

run the shiny app

docker run -it -d -p 3838:3838 hibc-shiny

access locally on your browser with

firefox http://localhost:3838 ```

Create a release to trigger the deployment

Once the edits and tests are satisfying, the deployment of the website is triggered by the creation of a tagged release.

  1. Tag the git commit using git tag -a vX.Y.Z where X, Y and Z follows the https://semver.org
  2. Push the tag to the remote with git push --tags
  3. Create a Gitlab release using the Releases section or https://git.rwth-aachen.de/clavellab/hibc/-/releases/new

Citation

Hitch, T.C.A., Masson, J.M., Pauvert, C., Bosch, J., Nüchtern, S., Treichel, N.S., Baloh, M., Razavi, S., Afrizal, A., Kousetzi, N., Aguirre, A.M., Wylensek, D., Coates, A.C., Jennings, S.A.V., Panyot, A., Viehof, A., Schmitz, M.A., Stuhrmann, M., Deis, E.C., Bisdorf, K., Chiotelli, M.D., Lissin, A., Schober, I., Witte, J., Cramer, T., Riedel, T., Wende, M., Winter, K.A., Amend, L., Riva, A., Trinh, S., Mitchell, L., Hartman, J., Berry, D., Seitz, J., Bossert, L.C., Grognot, M., Allers, T., Strowig, T., Pester, M., Abt, B., Reimer, L.C., Overmann, J., Clavel, T., 2025. HiBC: a publicly available collection of bacterial strains isolated from the human gut. Nat Commun 16, 4203. https://doi.org/10.1038/s41467-025-59229-9

Acknowledgements

This work is supported by the NFDI4Microbiota (https://nfdi4microbiota.de), a German consortium of the National Research Data Infrastructure that supports and train the microbiology community for better research data production and management.

Owner

  • Name: The Clavel lab
  • Login: ClavelLab
  • Kind: organization
  • Location: Germany

This is the official GitHub account for the research group of Prof. Thomas Clavel.

GitHub Events

Total
  • Push event: 2
  • Create event: 4
Last Year
  • Push event: 2
  • Create event: 4

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 173
  • Total Committers: 7
  • Avg Commits per committer: 24.714
  • Development Distribution Score (DDS): 0.26
Past Year
  • Commits: 55
  • Committers: 2
  • Avg Commits per committer: 27.5
  • Development Distribution Score (DDS): 0.018
Top Committers
Name Email Commits
cpauvert c****t 128
Lukas C. Bossert l****t@m****l 17
Jojo-AGClavel 8****l 10
Jonathan Hartman h****n@i****e 9
The Clavel lab 7****b 3
Lukas C. Bossert g****t@t****e 3
Thomas Hitch t****h@g****m 3
Committer Domains (Top 20 + Academic)
texografie.de: 1 itc.rwth-aachen.de: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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