Frequently Asked Questions




CyberGISX essentials

CyberGISX is a platform that supports geospatial community engagement and enables interactive notebook development. The community notebook showcase web page facilitates sharing research and resources contained in interactive notebooks. This platform is supported by a Jupyter Notebook based interactive code base that has been developed specifically to facilitate geospatial cyberinfrastructure and software use. Many powerful cyberGIS and geospatial libraries have already been built into the system! Built-in support for commonly used software libraries, shared data sources, and access to high-performance computing and big data resources are also available.

Once you have found an interesting notebook on the Community Notebooks page, clicking “See the notebook” below the short notebook description will direct you to an informational page for that notebook. You can quickly scroll through a static snapshot of the notebook displayed on the page. If you are registered with CyberGISX, click “Open with CyberGISX” to open the notebook in the development environment.

Registering with CyberGISX

You need a valid and accessible email address and a GitHub username. Your GitHub username will be used as your CyberGISX username. Both your email and GitHub username must be unique. Two CyberGISX users can not share an email address or a GitHub account.

Navigate to the registration page by clicking the “Register” button on the main menu. Then fill out the form and click “Submit”. After you complete the form, you will be sent an email for verification. Then, click on the “Log In” button and log in with GitHub. After that and once you have been approved by the CyberGISX admin team, you will be able to open the CyberGISX platform and and have access to increased functionality within the CyberGISX website.

You need a valid and accessible email address and a GitHub username. Your GitHub username will be used as your CyberGISX username. Both your email and GitHub username must be unique. Two CyberGISX users can not share either an email address or a GitHub account.

If you do not currently have a GitHub account, go to https://github.com/ and select the “Sign up” button in the GitHub menu bar. Then enter a username you wish to use, a valid email address, and a password and click “Sign up for GitHub”. You will need to verify your GitHub account by opening a link in an email GitHub will send you after you register. After you verify your email you may see instructions on how to start to set up your GitHub account, however, you do not need to do anything further to be able to use your GitHub account on CyberGISX. You can skip the suggested step or close out of the page.

An easy way to find your GitHub username is to go to your GitHub profile page and look at the website address – your GitHub username will appear after the main website like this: https://github.com/<your GitHub username>.

Getting started with CyberGISX

Once you have registered with CyberGISX, click on the “Log In” button on the CyberGIS menu bar. This will redirect you to the GitHub login page. After logging in with your GitHub account, you will be directed to the notebook dashboard.

From the dashboard you can create and then edit a new notebook. On the top right corner of the dashboard menu you can select the “New” button and select one of the drop down options to create a new notebook, text file, or folder. If you are just starting out, it is recommended that you select “Python 3” in this drop down menu item. This will create a new notebook that uses Python.

First register with CyberGISX, then in the notebook dashboard, you can upload the notebook from your home computer to the CyberGISX Jupyter environment. To do this, in the notebook dashboard navigate to the folder that you want to store the notebook in. Then in the top right corner of the dashboard menu select “Upload” and a window will open that allows you to select a file for uploading. Once you have selected your file it will appear in the file list. Click the blue “upload” button on the right side of the new file in the file list to complete the upload process.

Creating notebooks with CyberGIS

Using Software

Only Python 3 is currently supported, although this may change in the future. We are currently working towards supporting R as well.

See this document for a list of available libraries.

Yes, but we request that you only install new libraries if you know what you are doing. You can type “conda install -y lib” or “pip install -y lib==version” from a terminal launched from the notebook dashboard. These libraries will be only available to you and not to other users on CyberGISX. If you believe additional libraries should be included in our base install you may contact us with your recommendations.

Handling Data

You can upload data and other files from your home computer to the CyberGISX Jupyter environment. After that, you can access these resources from within your notebook. If the data you wish to use is large and may be of use to many users, contact us at help@cybergis.org to inquire about storage on the shared data directory.

Currently, the shared data directory is accessible at /home/jovyan/shared_data/.

Accessing Computing infrastructure

This notebook demonstrates how you can access HPC resources. You can access Keeling or other remote computers such as XSEDE’s Comet, however, certain restrictions apply. Contact us at help@cybergis.org for more information.

By default, each notebook server has access to 2 cores and 4GB of memory. We have a limit of 10G of data in your home directory. If you need more space to store your input data you may contact us at help@cybergis.org. Additionally, datasets that would be of broad interest could be, upon request, stored in the shared directory.

Developing a Notebook

Within the notebook editor menu, select “Kernel” then “Restart” or “Restart & Clear All”. This will forcefully stop any running code. If you have made changes in an external file that do not appear in the notebook, you may need to restart the kernel to see the updated code.

Engaging the CyberGISX Community

You can download your notebook code as an .ipynb file from either the notebook dashboard or editor. If you accessed non-web-based external data or other resources from within your notebook you will have to also download them and place them locally in the same file structure relative to your notebook for the code to work properly.

Send the notebook and any required data to us at help@cybergis.org, and we will consider adding your notebook to the Community Notebooks page. The notebook code needs to be fully self-contained.

We have a notebook submission process currently under development.

Once you have been approved and have logged into CyberGISX, you can click on your username on the top right menu to view your public profile page. You can edit your profile page by hovering over your username and clicking the “Edit Profile” menu item. It is recommended that you do not change your email address on this page.

Hover over your username on the top right menu and click the “New Blog Post” menu item to start a new post. Refer to this page for more instructions.

Click on your username on the top right menu to view your profile page. You can see and edit your blog posts from this page. Refer to this page for more instructions.

Accessing support

Many general software tutorials can be found online Additionally, Stackoverflow.com is a useful debugging resource. The CyberGIS Helpdesk may be able to help with certain research projects. To inquire, contact us at help@cybergis.org.

 

For further questions, contact us at help@cybergis.org.