See the executable workflow
Inspect the tools, dependencies, branches, containers, and contracts that make up the computation.
Products
Reusable software for reproducible biological research.
Scilytica turns recurring analytical and engineering needs into tools that can be tested, understood, and used beyond a single project.
Scilytica Toolkit
Reproducibility, designed into the analysis.
A Python toolkit emerging from Scilytica’s analytical work, beginning with reproducible single-cell and spatial analysis.
- Platform-aware ingestion for imaging-based spatial data, including 10x Genomics Xenium In Situ output bundles and Bruker CosMx SMI/AtoMx outputs
- Assay-aware preprocessing
- Frozen-reference mapping with documented provenance
- Controlled method evaluation with machine-readable outputs
The Toolkit is not yet available for general use. Capabilities and APIs may change as active development continues.
See the methods in practice →Ask about the Toolkit →Scilytica Workbench
Make scientific workflow changes inspectable and evidence-backed.
Scilytica Workbench is a workflow intelligence environment being developed for teams that build and evaluate scientific computational workflows. A shared workflow graph connects executable steps, containers, parameters, runtime behavior, proposed changes, and the evidence used to review them.
The current prototype focuses on local workflow development: source editing, workflow structure, reviewable change proposals, test evidence, source-control context, and controlled execution. AI assistance is optional and bounded. Validation, execution, and acceptance remain explicit human actions.
Workbench is a working engineering prototype. It is not available for production use.
Connect execution evidence
Relate task attempts, logs, runtime behavior, artifacts, and validation evidence back to the workflow graph.
Review before change
Keep proposed edits bounded and visible, with deterministic checks and explicit human disposition before acceptance.
Product direction
From workflow structure to evidence-backed change.
Workbench is intended to connect workflow creation, test and characterization runs, performance evidence, validation evidence, and controlled release records through one inspectable graph. The graph is more than a diagram: it is the organizing model for process contracts, containers, parameters, dependencies, runtime telemetry, artifacts, and change impact.
- Develop or import a workflow and understand how its computational steps connect.
- Run bounded tests, characterization campaigns, and validation sets while retaining task and environment evidence.
- Compare candidate changes against a baseline before deciding whether they should move forward.
- Keep evidence and human review attached to the exact workflow revision that produced them.
Nextflow is the first deeply implemented workflow adapter. The core product direction is designed to remain adaptable to additional workflow systems and execution backends.
The initial remote-execution direction is AWS-first, using portable containers and batch-oriented cloud infrastructure. Cloud execution, collaboration, administration, validation, and governance remain intended capabilities rather than claims about the current prototype.
Design partner program
Shape a complete path from workflow change to reviewed evidence.
Scilytica is preparing a design partner program for bioinformatics, computational-science, platform, and validation teams willing to share where workflow change review, reproducibility, runtime evidence, and infrastructure decisions break down today.
Early conversations will help define a narrowly useful path through workflow intake, bounded change, verification, controlled execution, evidence collection, and human review. This direction does not assume that Workbench replaces the workflow engine, source-control system, or quality system a team already trusts.
Technical and strategic collaborators may also inquire, but the primary purpose of the program is to learn from prospective users and their work.
Request a private previewExpert services today
Use the tools that fit the work.
Scilytica’s current services address specific scientific and engineering problems. Engagements can build on your existing environment and established open-source tools, incorporate Scilytica technology where appropriate, or combine both.
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