Managing data in molecular modeling workflows can become overwhelming. Scripts, models, images, experimental results—these often reside in scattered folders across different machines. This increases the risk of broken references, version confusion, and forgotten dependencies.
If you’re using SAMSON, the integrative platform for molecular design, there’s a built-in solution to this problem: Universal File Embedding.
What is Universal File Embedding?
In SAMSON, Documents act as containers that store molecules, simulation models, and other data. Thanks to Universal File Embedding, these Documents can also include external files and folders—like Python scripts, datasets, PDFs, or even entire Python apps—making the Document fully self-contained.
Why it Helps
- Portability: You can move or share a single file knowing everything you need is inside.
- Reproducibility: Embedded scripts and parameters remain linked to the specific molecular models you used.
- Collaboration: Share a fully packaged experimental setup with peers or collaborators.
- Project Management: Reduce clutter and consolidate your work context.
How to Embed Files or Folders
There are two simple ways to embed data in your SAMSON Document:
- Drag-and-Drop: Just drag your file or folder into the SAMSON interface. You’ll be prompted with options to embed or open them.
- Use the Menu: Navigate to Home > Embed files or Home > Embed folders.
Once embedded, the file becomes part of the SAMSON Document and is stored within it. This means you no longer have to worry about sending along supplementary files when sharing your work.
Good Use Cases
- Python scripting: Attach custom analysis or visualization scripts that interact with the molecule in your document.
- Data permanence: Keep simulation outputs directly tied to the corresponding model.
- Documentation: Embed PDFs of relevant research articles or lab notes for future reference.
Example Dialog
Here’s what the embedding dialog looks like:
You’ll be asked whether you’d like to embed the file or open it. If you choose embedding, the file is saved directly into your SAMSON Document file.
Practical Benefits
File embedding makes it easier to maintain consistent data and ensures nothing gets left behind when transferring work across machines or sharing with colleagues. It’s especially useful for academic users working on reproducibility, or industry users needing to create dependable workflows for team-based modeling.
Looking Ahead
Since Documents can be shared via SAMSON Connect, embedding ensures your collaborators won’t open a project that’s missing crucial files. Everything they need is already inside.
To learn more, visit the SAMSON Documentation – Loading Molecules.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.