Squonk (animal) logo with title text 'Squonk' and subtitle 'Data Manager'

Guided Tour

This page provides a high level overview of how to use the Squonk Data Manager. More detailed descriptions can be found in the individual How to guides that are referred to in this document.

Logging in

To do anything useful in the Squonk Data Manager you must login and be authenticated. Do this using the Account menu in the top right corner and click login. You are taken to Keycloak where you authenticate, and, assuming you are successful, you are taken back to the Data Manager where you can perform your work.

When finished use the Logout option in the Account menu.

More details can be found in the Logging in How To guide.

Defining your context

Once you are logged in you need to define the project you want to work in. The best way to so this is to use the Settings option in the Account menu in the top right corner. The settings panel opens full screen (close it when finished).

You can select a Context which includes the Organisation and Unit within that Organisation that you want to work in and the Project you want to work in.

More details can be found in the Setting your work context How To guide.

The Project Data tab

This shows the contents (files and directories) in your project. The interface is a simple file browser a bit like Windows Explorer and probably doesn't need much explanation. Note that the operations you can perform here are quite limited. If you want full control we suggest you run a Jupyter notebook in your project and use the file manager of the Jupyter lab interface, or a command line console to perform your operations.

Jobs and applications have full access to these project contents.

The Apps/Jobs tab

This is where you launch Applications and Jobs to do your work.

Those that are available (defined by the system administrator) are displayed as "cards". You can type into the "Search" box to filter these using terms that are defined for each job or app. For instance jobs implemented using RDKit should be labelled as "rdkit" so typing "rdkit" into the search box will show only cards that have this label. The labels for each job are displayed towards the bottom of the card in red.

To run a job or application click on the Run button. A dialog will appear allowing you to define the job inputs and options.

Inputs are project files that form the input to the job. Options are user specified parameters for execution of the job.

Specify these inputs and options and click the Run button at the bottom. The execution will be added to the bottom of the card. Click on it to see the execution details in the Results tab.

See the Running jobs How To guide for more details.

Launching an Application is very similar. Currently the only available application is a Jupyter Notebook. See the Running applications How To guide for more details.

The Results tab

This shows the execution of your Applications and Jobs. A high level summary of each running app or job is presented along with the ability to drill down into the specific details of each instance.

Details include the Status of the job and any events it might have generated. You are also able to view the input and output files and any log files that are generated.

When you are finished remember to TERMINATE your job or application to free up the resources it is using.

See the Inspecting job and application execution How To guide for more details.

The Datasets tab