Python pipeline Building Block for Harmony

What is the challenge?

Many customers, especially those in Academic institutions or those with a strong bioinformatics background already have powerful analysis solutions for some or many of their assays. We could see this at the HCS user group meeting in Madrid. At the moment, they need to leave the Harmony environment to run Phenix and CLS data with those scripts, by a number of users asked whether there could be a way to have an e.g. Python Building Block, that allows them to run their custom made solution within the Harmony environment to streamline their workflows.

In a nutshell: the customers like the streamlined Harmony workflow, and they would like to have a uniform workflow for all their assays. But at the same time, they would like to run the same Python scripts that they have always used also in Harmony. And they would love to have the option to use Python for analysis challenges, that they so far cannot do with Harmony.

What is the impact?

The users cannot run their custom made Python scripts within the Harmony environment, which creates the need for tedious data export or handling and it leads to non-uniform data management solutions.

Describe your idea

I am not sure if this is technically possible. But the users have been asking for a Harmony Building Block (probably an ABB) that allows them to run Python within the Harmony environment. Basically a Python Plugin for Harmony in Building Block format. They mentioned that this would be also great to form a more active user community where people can share their solutions with other Harmony users.

Requested by

Directly asked for by Caspar Jonker, Senior Scientist and Opera Phenix Plus user at Genmab, but also by Mario Barreras and Eoghan O'Duibhir, both of them imaging specialists and scientists at the Princess Maxima Center in Utrecht.