If you’re a molecular modeler juggling multiple tools to run simulations, analyze structures, or communicate with external software, you’re not alone. Many scientists find themselves switching between environments, writing glue code to bridge tools, or manually repeating tasks that could be automated. This not only adds friction to your workflow, but also increases the risk of errors and reduces reproducibility.
If you’re already using SAMSON, there’s a powerful yet often underused solution built right into the platform: custom apps. With a bit of development, you can build your own app to integrate external software, automate procedures, or even create entirely new functionalities inside SAMSON using its Application Programming Interface (API).
What is a SAMSON App?
In SAMSON, an app is a type of Extension that provides specific functionality. Unlike editors or visual models, apps can serve a wide range of purposes:
- Connect to external executables or cloud-based services
- Wrap and integrate your own code directly into the SAMSON interface
- Create new analysis tools or streamline demonstrations and workflows
Many apps—like the AutoDock Vina Extended App—already integrate well-known tools into SAMSON (see image below). But what if your lab uses a custom docking protocol, or you have in-house code for energy calculations? Making it part of SAMSON can dramatically simplify its usage and sharing within your team.
Where to Begin
SAMSON’s documentation provides a comprehensive guide to help you get started with app development. If this is your first time extending SAMSON, you’ll want to read the section on generating SAMSON Extensions. It walks you through the creation of an Extension using the Extension Generator, which sets up the basic scaffolding (files, build system, etc.) for your app.
You can then implement your logic using SAMSON’s API, which provides access to the molecular data, visualization tools, simulation engines, and more. Whether your app simply cleans molecular structures or connects to an entire pipeline, you’re free to tailor it to your needs.
Why This Matters
- Centralization: Bring your tools under one roof, reducing context switches and simplifying user training.
- Reusability: Once your app is built, it can be re-used by others in your team—or even shared on SAMSON Connect.
- Customization: Create exactly what you need, whether it’s a helper utility or a full interface to another software package.
Final Thoughts
Building your own app inside SAMSON can save you time, streamline your molecular modeling tasks, and make your workflow more reproducible. It might seem complex at first, but with the provided documentation and tools, even small teams or individual researchers can get started quickly.
If you’d like to explore this further, visit the documentation page for apps at https://documentation.samson-connect.net/users/latest/apps/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.