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

To register with CyberGISX, follow the instructions on CyberGISX quick guide page in the "To Register" section.

As the CyberGISX platform is designed to use an email address as the user's unique identifier, we encourage our prospective users to register by selecting an organizational login (i.e. university, national lab, facility, or project) as their identity provider in CILogon.  However, if your organization is not listed in the CILogon identity provider list, we encourage you to select Google as an identity provider.

Note: Please make sure to remember and log in to the CyberGISX platform with your selected identity provider.

Getting started with CyberGISX

Once you have registered with CyberGISX, click on the “Launch CyberGISX” button on the CyberGIS menu bar. 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.

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 Notebook" menu item to start creating a new notebook page. Once you have created a page for your notebook using the form on this page, you can view a preview of your notebook on the web and allow other people to see your notebook. If someone has a CyberGISX account, they can use the page that is created to open your notebook in CyberGISX. 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 notebook pages from this page. Refer to this page for more instructions.

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.