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The Hyve at i2b2 tranSMART Tübingen Symposium 2019

October 29, 2019 | By Marinel Cavelaars

Looking back at a successful i2b2 tranSMART symposium in Tübingen on October 8-9, we’d like to give you an impression of The Hyve’s contribution to this year’s event. 

 

 

Presentations

Keynote: Large scale observational clinical research with OHDSI 

Data scientist and software developer Maxim Moinat, an active member of the OHDSI community and co-lead of the technical work package in the EHDEN consortium, was invited to give a keynote about the international OHDSI collaborative. Maxims presentation showed that the objective of the OHDSI community is very similar to the objective of the i2b2 tranSMART community but the approach in terms of use of standards, methodology and technology is quite different.

 

Overview of the features and architecture of Glowing Bear and tranSMART

In recent years, The Hyve has built Glowing Bear, the user interface for tranSMART 17.2, and has transformed the structure of the platform to be more modular and easier to maintain. 

In his presentation, software architect Gijs Kant gave an overview of the added features and the changes to the data model and architecture.


Easy and secure deployment of Glowing Bear and tranSMART

Software engineer Ewelina Grudzién explained how dockerization of all Glowing Bear - tranSMART components and main compose scripts makes deployment not only faster, but also allows for easier management of the configuration, improved security and easier monitoring of the individual components.

Related read: Glowing Bear delivery standardized by Docker

 

 



Building ETL pipelines to tranSMART 17.2: new tools for the data loader

Data engineer Alessia Peviani presented the tools that are available to build Extract, Transform, Load (ETL) data pipelines to import data into tranSMART 17.2. She shared examples of real use cases, varying from simple cases using Jupyter Notebook to sophisticated automated data loading pipelines.

 

Hands-on session

At the end of the symposium The Hyve organized a two-part workshop. We were happy to see so many people interested in this session. The first part of the workshop focused on tranSMART data loading tools. The majority of the 22 participants managed to load data to a tranSMART 17.2 database using Python tools in Jupyter Notebook on ready-to-use virtual environments, as well as browse the loaded data afterwards using the Glowing Bear user interface. 

The second part of the workshop concerned querying data in tranSMART. It gave the participants an opportunity to learn more about the tranSMART 17.2 REST API and how to write more intuitive query constraints in Python using the tranSMART API client package.

The materials used during the workshop can be found in thehyve/workshop-tuebingen2019 GitHub repository.