Neotoma Lakes App

The Neotoma Paleoecology Database (“Neotoma”) is more than a database! Neotoma is a database, a software ecosystem, and a community.

Neotoma provides an underlying cyberinfrastructure that enables the development of common software tools for data ingest, discovery, display, analysis, and distribution, while giving domain scientists control over critical taxonomic and other data quality issues.

What is Neotoma Lakes app?

The Neotoma Lakes app is an R-Shiny application designed to assist in improving lake entries within the Neotoma database.

1. Begin by entering the SiteID:
2. Water bodies from the Hydrolakes DB near the site will be displayed in blue. Clicking on these water bodies allows you to access information within the Hydrolakes DB associated with each lake on the right panel. If one of these lakes represents better the Neotoma DB Site, you can submit it along with comments.
3. If you cannot find a polygon representing your water body in the Hydrolakes DB, you have the option to create your own polygon. In doing so, you’ll be able to view the information about the polygon in the right panel and submitting it to improe the database.

App Access and Local Deployment

Accessing the App

The application can be accessed through the link available in the ‘About’ section of this GitHub repository.

Running the App Locally

To run the app on your local machine using Docker, follow these steps:

1 - Clone or Download the Repository Example using the terminal:

git clone [email protected]:flor14/neotoma-lakes.git

2 - Install Docker Desktop

Install Docker Desktop if you haven’t done so yet and open it.

3 - Building the App

Navigate to the folder where the project is located. Execute the docker build command to generate the Docker image:

cd neotomalakes
docker build -t neotomalakesapp .

This step can take some minutes. Then, start the app with this command:

docker run --rm -p 3838:3838 neotomalakesapp

Note: If you are using a Mac M1/M2, please add the argument --platform linux/amd64 to the last command.

The app will now be accessible locally at http://localhost:3838.

Community guidelines

Report Issues:

• Questions, feedback, bug reports: please open an issue in the issue tracker of the project here.

Contribution to the software:

• Please open an issue in the issue tracker of the project that describes the changes you would like to make to the software and open a pull request with the changes. The description of the pull request must reference the corresponding issue.

• Join the Neotoma Community