Power Users Welcome: More Control with Via Foundry’s SDK and CLI
Automatic cars are great, many people use them. They’re smooth, easy to use, and ideal for anyone who just wants to get from A to B, whether it's a first-time driver or someone who needs a comfortable ride.
But if you're a professional racecar driver on a track, that simplicity becomes a constraint. When you’re coming out of a corner at speed, aiming for the apex, you don’t want the car making decisions for you. You need to feel the engine respond. You need control. Gear by gear, move by move.
Not because automatic cars are bad. They just aren’t built for precision handling.
Visual interfaces are similar. In Via Foundry, the point-and-click UI makes complex analysis approachable. You can launch pipelines, explore results, and collaborate across teams without writing code. For many researchers, that’s the fastest way to get from question to insight.
But if you're a power user, a pro racer in the data world, that ease can feel limiting.
You want to tweak parameters mid-run, rerun pipelines across datasets, automate tasks, and structure your work for scale. Clicking through steps you’ve already mastered slows you down. You can still accomplish what you need to, but you're not moving at your own pace.
What you need isn’t a simpler interface. It’s a programmable one. One that lets you work the way you think: in code, in scripts, in logic you control.
You Don’t Have To Choose Between Ease and Control - Via Foundry Gives You Both
If you prefer a visual, intuitive interface, you can explore data, run pipelines, and collaborate across teams with just a few clicks. If you prefer code, you get full programmatic access.
These tools, both the UI and the programmatic interfaces, are secured by organizational admin controls and aligned with standards like SOC 2 and ISO 27001. This way, you can move between visual and code-based work while knowing your data and processes are protected.
For coders, Via Foundry offers three powerful ways to build, automate, and scale your work:
- The SDK (Python or R) – Script your analysis in notebooks and build custom logic around your workflows.
- The CLI – Trigger pipelines, move files, and manage jobs straight from the terminal.
- Workbench – Launch JupyterLab or RStudio in fully configured cloud environments for exploratory or interactive work. (We’ll cover Workbench in a separate article. It’s a different kind of tool built for hands-on research rather than scripting or automation.)
Stick Shift Options for Coders
A. SDK: Work Programmatically in Notebooks
A Software Development Kit (SDK) lets developers interact with a platform through code, using libraries, helper functions, and APIs.
Via Foundry’s SDK gives you full scripting access to your analysis workflows and results, through either Python or R. It’s ideal for those who prefer to work in environments like Google Colab, Jupyter, or RStudio, letting you interact directly with Via Foundry pipelines, data, and outputs through a familiar coding interface.
Example: Just as the AWS SDK for Python lets you manage AWS resources through code, the Via Foundry SDK lets you interact directly with Via Foundry pipelines, data, and outputs, through a Pythonic interface.
What you can do:
- Set up and authenticate: Install the SDK in your notebook environment, authenticate once using a token, and reuse it across machines or users.
- Access pipeline results: Load a specific pipeline run by report ID and programmatically explore outputs, like the gene expression matrix from the RSEM module.
- Work outside of Foundry: Pull data into local or cloud-based environments like Colab or RStudio, perform custom analysis, then push results (such as plots or derived datasets) back into your workspace for sharing and reuse.
- Analyze with your own code: Use tools like pandas, matplotlib, or scanpy to transform, explore, and visualize results within your preferred workflow.
- Upload results and artifacts: Push plots, data files, or full notebook session history back into your workspace in Via Foundry, keeping everything connected.
- Enable reproducibility: If session tracking is enabled, others can trace exactly how results were generated, including the code, environment, and parameters used.
When to use the SDK:
If you’re the kind of user who prefers a hands-on grip, someone who thinks in code, iterates through problems, and wants full control over each step, the SDK will feel natural. It’s built for IDEs (Integrated Development Environments) including notebooks like Google Colab or Jupyter, where you can script your analysis, reuse workflows, and explore results on your own terms. If reproducibility matters to you, if you like seeing exactly what went into each result, and if you want to move fluidly between exploration and automation, the SDK is the right tool.
B. Command Line Interface (CLI): Terminal-Based Control
A Command Line Interface (CLI) is a way to interact with software by typing commands into a terminal or shell. It may exist on its own or be part of a larger toolkit. For example, the Via Foundry CLI lets you access many SDK capabilities directly from the command line.
Example: Just as the AWS CLI allows you to manage AWS resources without opening a browser, the Via Foundry CLI lets you run pipelines, manage files, and automate jobs in Via Foundry using simple commands.
What you can do:
- Launch and monitor pipelines
Start jobs with a single command and track their progress from the terminal. There’s no need to open the UI or click through forms. - Manage files easily
Upload and download datasets or results using quick commands. This is especially useful in server-based or remote work environments. - Automate bulk tasks
Loop over multiple samples, apply the same workflow at scale, and avoid repetitive setup. Useful for large datasets and batch processing. - Integrate with existing systems
Use Via Foundry commands inside your broader infrastructure. Include them in shell scripts, cron jobs, or complex bioinformatics workflows. - Work faster
Skip UI load times and mouse clicks. For those who already work in the terminal, this is the most direct way to get things done.
When to use the CLI:
If you’re the kind of driver who prefers to shift gears yourself, the CLI gives you that level of control. It’s built for coders who already work in a terminal and want to stay in flow. Use it to run large jobs, automate routine tasks, or connect Via Foundry to your existing infrastructure. You’re still using the same powerful capabilities of Via Foundry, just through the CLI’s streamlined shell interface rather than the SDK’s scripting environment.
Via Foundry: Built for the Way You Actually Work
Not every task needs a script. Not every analysis fits inside a form. Most teams shift between interfaces based on the problem, the deadline, or who's at the keyboard.
Via Foundry supports that reality. Use the visual interface to move quickly through well-known steps. Switch to code when you need precision, automation, or customization. The tools are there when you need them, and out of the way when you don’t.
You’re not locked into a single workflow. You’re supported across all of them.
Ready to dig in? Book a demo here.
