A molecular project can be hard to hand off, even when the model itself is easy to share. The analysis script may live in a separate folder, the useful notes may be in an email, and a colleague may not know which steps produced the result. Rebuilding that context takes time—and makes it harder to repeat or review the work.
SAMSON documents can hold more than molecular models: you can embed files and folders, including Python scripts and apps. That gives you a practical way to keep a model and its supporting workflow together in one document.
Put the working context beside the model
Think of a shareable document as a small project handoff. Alongside the molecular model, you might include the scripts used for a particular analysis, relevant data files, images, and notes explaining what to run and what to look for. The goal is not to include every file you have; it is to make the steps needed to understand or continue the work easier to find.
To add files or folders, drag and drop them into SAMSON and respond to the prompt to embed them. Alternatively, use Home > Embed files or Home > Embed folders.
Embedded files are stored within the SAMSON document. This makes the document self-contained with respect to those included files and allows you to transfer or share it. You can distribute it by email, GitHub, or SAMSON Connect Documents.
Make the next action obvious
A bundle of files is most useful when a colleague can tell what to do with it. Give scripts descriptive names, include a brief readme or notes file, and state which script to run first. If there are several scripts, describe their order and the expected input files. These small organizational steps do not change the science, but they can prevent a lot of back-and-forth.
To open an embedded Python script, double-click it to open it in the Code Editor. You can run a Python file from the editor using Run or its Run menu, or execute code in SAMSON’s integrated Python Console. The editor also includes Python templates that can help you get started with common scripting tasks.
Check what the workflow depends on
Embedding your scripts and data keeps those files with the document, but sharing a workflow still calls for a quick dependency check. If a script uses Python packages, note which packages and versions it expects. SAMSON’s Python Package Manager is available from Python Console > Edit > Manage packages…; it uses pip and can install packages from PyPI or a local package path. A colleague may need to install the same dependencies before running your script.
For packages you are actively developing, the Package Manager also supports editable/develop installation. This points Python to the package’s source files, so code changes are reflected without reinstalling. For a package you are simply using, the documentation recommends leaving editable mode unchecked. It also notes that editable packages may fail to load on some macOS installations after restarting SAMSON, so check that behavior if you rely on this mode.
A simple handoff checklist
- Include the model and the files needed to follow the workflow.
- Add a short note describing the purpose of each script and the order to run them.
- Record any Python package requirements and version constraints.
- Open and run the embedded script in SAMSON before sharing the document.
- Ask a colleague to test the handoff if reproducibility is important.
Embedding scripts does not replace documenting scientific choices, but it can keep the practical materials for a workflow close to the model they support. For details on Python scripting, package management, the Code Editor, and embedding files, learn more in the SAMSON scripting documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.