If you’re a molecular modeler juggling multiple tools, supplementary data, scripts, or even presentation figures, you’ve likely experienced the frustration of losing track of crucial files. Whether you’re preparing a publication, sharing a molecular model with collaborators, or switching between different machines, keeping everything organized can be tedious and error-prone.
Fortunately, SAMSON, the integrative platform for molecular design, offers a feature that can smooth your workflow considerably: Universal File Embedding. This tool allows you to store all essential files—Python scripts, datasets, papers, images, even entire folders—directly within your molecular project document. Let’s take a look at how this works, and why it can make your modeling life easier.
Why embed files?
File embedding helps solve several practical issues:
- Self-containment: Everything needed for your project stays within one document file. You won’t have to chase down linked dependencies later.
- Easy sharing: Send a single file to collaborators or upload it to SAMSON Connect. No need to zip archives or worry about missing folders.
- Reproducibility: Embedded Python scripts or notebooks ensure that simulations or analyses are preserved exactly as you ran them.
How to embed files and folders
There are two ways to embed external resources into your SAMSON document:
- Drag and Drop: Simply drag files or folders into your open SAMSON window. You’ll be prompted to choose whether to embed them or link externally.
- Via Menu: Navigate to Home > Embed files or Home > Embed folders to browse and embed content manually.
Once embedded, files are stored inside the project document. That means when you move the document or upload it, everything comes with it.
Common use cases
- Embedding Python scripts to automate model preparation or post-process analysis.
- Storing a research poster or article alongside the model it describes.
- Including Excel datasets or CSV results with your simulation outputs.
- Packaging training data required for machine learning applications running within SAMSON.
This approach not only improves organization but also enhances collaboration. Rather than sending a mix of models, scripts, and notes, you can distribute a single file that contains everything.
Sharing embedded documents
When you’re ready to share, SAMSON makes it easy via SAMSON Connect. Upload your embedded document through the Home > Publish menu and choose your visibility preferences—Public, Hidden, or Restricted. Embedded files stay part of the document, ensuring consistency across reviewers or collaborators.
This is especially useful in teaching environments or research groups where sharing reproducible, editable systems is key.
To learn more, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get the platform at https://www.samson-connect.net.