PBDB Navigator

About

Built on the PBDB API, PBDB Navigator allows users to explore the Paleobiology Database through space, time, and taxonomy. The application is entirely client-side and depends on external services, including the Paleobiology Database, GPlates, and Phylopic.

You can find the current version at http://paleobiodb.org/navigator

Dependencies

This project requires Node.js, Grunt, and Topojson to be installed. To install Node.js on OS X see the instructions at the bottom of this document. Once Node is installed, you can install Grunt with npm install -g grunt-cli and Topojson with npm install topojson -g.

Organization

All working files (the ones you want to edit) are found in the assets directory, and all files to be used in the application (the compiled and minified versions) are found in the build directory. Each of the major application components (regular map, reconstruction map, time scale, taxa browser, interface) have their own Javascript file. All interface code is located in assets/js/navigator.js. Grunt combines and minifies all these files into build/js/script.min.js.

Setup

1. Clone or fork this repository, and navigate into it
2. npm install
3. Start a simple Python server with python -m SimpleHTTPServer and navigate to localhost:8000 in a web browser.

Helpful hints

To:

• Rebuild the plate cache: grunt shell:plates then grunt shell:badPlates
• Rebuild the rotation cache: grunt shell:rotations
• Rebuild the collections < Phanerozoic cache: grunt shell:oldCollections
• Validate HTML: grunt htmlhint
• Concatenate/minify Javascript: grunt uglify
• Concatenate/minify CSS: grunt cssmin
• Validate HTML, concatenate/minify Javascript and CSS: grunt

Contributing

PBDB Navigator is an open-source project and welcomes feedback/contributions from the community. If you see a bug and would like to fix it, please submit a pull request. If you see a bug or have a suggestion but do not know how to fix it, please open a new issue.

License

Paleobiology Database data is used under a CC-BY 4.0 Creative Commons license. Plate and collection rotation data from GPlates is used under a GNU General Public License (GPL), version 2, and taxonomic images from Phylopic.org are used under either a Public Domain or Creative Commons license.

All code unique to the PBDB Navigator interface is written by John Czaplewski unless otherwise specified, and uses a CC0 1.0 Universal Public Domain Dedication.

Setup Node.js on OS X

Adapted from https://gist.github.com/isaacs/579814#file-node-and-npm-in-30-seconds-sh :

1. echo 'export PATH=$HOME/local/bin:$PATH' >> ~/.bashrc
2. . ~/.bashrc
3. cd ~
4. mkdir node-latest
5. cd node-latest
6. curl http://nodejs.org/dist/node-latest.tar.gz | tar xz --strip-components=1
7. ./configure --prefix=~/local
8. make install (Takes a while...might have to agree to XCode terms and conditions here. If you get an XCode error, run sudo xcodebuild -license, view the license, and type agree to validate)
9. curl https://npmjs.org/install.sh | sh

If you get npm errno -13 with code EACCES while installing grunt, run sudo chown -R $USER /usr/local. This will make you the owner of /usr/local which will make sure you never have to use sudo with npm (via http://howtonode.org/introduction-to-npm)