Define the question
Explain the study in the language you already use. Work with an agent to clarify the comparison and the biological context.
01 / PIPELINE DESIGN
A clear plan for
your research question.
Work with an agent to turn a biological question into an analysis pipeline. Make the inputs, decisions, and steps explicit before the work begins.
PIPELINE DESIGN IN THE WORKSPACE
DESKTOP APP CONCEPT
Explore the documents and controls. All data and execution states are illustrative.
HOW IT SUPPORTS YOUR WORK
Begin with the study, not the command line.
Your experimental context matters. Start with the samples you have, the comparison you want to make, and the questions you need the analysis to answer.
Develop the approach
Discuss the analytical steps, inputs, and assumptions. See how each part of the pipeline contributes to the question.
Prepare for execution
Refine the plan before moving to the execution engine. Keep the analysis grounded in the study design.
AN EXAMPLE RESEARCH CONTEXT
From “what changed?” to a defined comparison.
An example gene-expression study begins with a treatment and a control. The first task is to establish the sample groups, consider variation, and decide what a meaningful comparison looks like.
- Research question
- How does expression differ between conditions?
- Study context
- Treatment and control; sample-level variation
- Analysis plan
- Inspect inputs → assess quality → compare → review
A conversation around the work EXAMPLE
Your experimental context shapes the next step.
A CLOSER LOOK
Questions about
pipeline design.
Do I need to arrive with a finished pipeline?
No. The intent is to develop the approach with an agent, starting from the research question and the data available.
Does the agent choose the scientific approach for me?
The agent helps work through the options and construct the pipeline. The researcher supplies the study context and assesses whether the approach is appropriate.
LET’S TALK RESEARCH
Tell us what your lab is working on.
Bring your questions, your data challenges, and where you want to go next.