GlycoBase

A comprehensive database for glycans. The full GlycoBase dataset is stored in Synapse and can be downloaded here.

GlycoBase can be accessed online here.

Prerequisites

System Requirements

• Python 3

• virtualenv (pip install virtualenv)

• R and RStudio

Local Development Instructions

Create the local virtual environment (first time set-up only)

The synapser R package developed by Sage Bionetworks depends on the older PythonEmbedInR package, which has compatibility issues. For this reason, this app interacts with the Synapse API using the Synapse Python client and uses the R package reticulate to call that Python code via the Shiny server.

Use the reticulate package to create a Python 3 virtualenv and install the Python packages pandas into it. In the R console:

> reticulate::virtualenv_create(envname = 'python35_env',
                                python = '/usr/bin/python3')

> reticulate::virtualenv_install('python35_env',
                                 packages = c('synapseclient', 'requests', 'pandas'))

Note: We also include synapseclient and requests, which can be used to (optionally) require the user to log in using their Synapse credentials. This functionality it currently turned off. Additionally, avoid running library(reticulate) as this will cause reticulate to initialize in the R session with your system version of Python rather than the one specified in the python arg of virtualenv_create(). If this happens, you may see an error similar to:

ERROR: The requested version of Python ('~/.virtualenvs/python35_env/bin/python') cannot be used, as
another version of Python ('/usr/bin/python') has already been initialized.

If you see this error, restart your R session and run the two commands above to create your virtual environment.

Running the app

In RStudio, open app.py and click the "Run App" button or run shiny::runApp() in the console. Open a web browser and go to http://127.0.0.1:7450 to see the app.

Secrets

Sensitive data like passwords and secret keys should never be checked into git in cleartext (unencrypted). If you need to store sensitive info, you can use the openssl cli to encrypt and decrypt the file.

Encrypt a file with shared secret

$ openssl enc -aes256 -base64 -in .Renviron -out .Renviron.encrypted

Decrypt a file with shared secret

$ openssl enc -d -aes256 -base64 -in .Renviron.encrypted -out .Renviron

Additional Resources

• See the full Synapse REST API docs for detailed explanations of all available endpoints.