Connect the analytical steps.
Build a pipeline from individual tasks. Define how data moves between them, which steps depend on others, and which can run in parallel.
THE BIOINFORMATICS PIPELINE ENGINE
Gobble.
From analysis plan
to execution.
Connect analytical steps into a pipeline, run the work, and follow its progress. Gobble keeps inputs, outputs, and execution state organized throughout the analysis.
Built in Go. Designed for bioinformatics workflows.
HOW THE ENGINE WORKSgobble.
YOUR STARTING POINTData + analysis plan
The inputs and the work to be done.
Gobble engine
- 01Check the plan
Inputs, outputs, and dependencies
- 02Execute the steps
Tasks in the right order
- 03Track the work
Progress, logs, and run state
READY TO EXPLOREResults + execution record
Outputs to inspect, interpret, and build on.
Illustrative workflow
WHAT THE ENGINE DOES
Structure for the pipeline.
Clarity through the run.
Gobble handles the execution work around the analysis, so each step has a defined place in the research workflow.
Check the plan before execution.
Validate the pipeline and inspect the work it describes. Make inputs, outputs, and resource requirements clear before starting.
Put the pipeline to work.
Run the analysis steps in their intended order, manage their dependencies, and collect the outputs they produce.
Understand what is happening.
Follow progress across the pipeline. Inspect individual tasks and their logs to see what has finished and what needs attention.
Continue from the run state.
Resume a pipeline with its recorded state in view. Reuse compatible completed tasks and carry out the work that remains.
Make the workflow reusable.
Package a pipeline as a runner that another researcher can execute. Keep the defined workflow together when passing it on.
BIOINFORMATICS WORKFLOWS
Different kinds of data.
A common engine.
The biological question shapes the workflow. Gobble provides the structure for running its analytical steps.
- WGSWhole-genome sequencing
- RNA-seqBulk RNA sequencing
- Methyl-seqDNA methylation
- ATAC-seqChromatin accessibility
- scRNA-seqSingle-cell RNA sequencing
THE ENGINE’S ROLE IN YOUR RESEARCH
Your question.
A workflow to carry it forward.
The researcher brings the scientific context. An agent helps shape the analysis. Gobble manages the pipeline execution.
Sets the direction.
Defines the question and interprets the results in the context of the experiment.
Develops the approach.
Helps turn the research goal into analytical steps and pipeline code.
Carries out the workflow.
Executes the steps and keeps their outputs and run state organized.
Explore the Gobble project.View the source on GitHub
LET’S TALK RESEARCH
Let’s talk about your pipeline.
Bring your questions, your data challenges, and where you want to go next.