Research operating system

Keep every analysis traceable from first run to final methods.

SCORIAL gives computational biology teams a governed workspace for project memory, validation, decisions, sessions, and methods.

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Researchers, founders, and technical teams building more reproducible computational biology workflows.

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Embryology proteomics graph

A real research workflow, kept traceable from raw spectra to methods.

Example: an embryo proteomics study comparing developmental progression with LC-MS/MS evidence, QC gates, analytical decisions, and final methods all tied together.

SCORIAL
study record

Question

Which protein programs separate viable progression from arrest?

Evidence

Raw spectra, QC plots, protein groups, stage annotations.

Output

Ranked proteins, pathway modules, defensible methods.

Embryology cohort

Embryology metadata

Stage, morphology score, culture condition, operator notes.

MaxQuant / FragPipe

LC-MS/MS raw files

Vendor files, blank media controls, FASTA release, cRAP.

Blocked if violated

QC gates

1% PSM/protein FDR, 2 unique peptides, TIC drift checks.

ProteinGroups -> analysis

Quant matrix

LFQ/TMT intensities, missingness class, normalization state.

limma / MSstats

Stage-aware contrasts

Blastocyst vs arrested embryo signatures with batch covariates.

Export without IDs

Methods + SCORIAL.md

Search parameters, decisions, checksums, and final text.

Trace

Raw file -> search params -> protein matrix -> figure.

Catch

FDR, cRAP, missingness, normalization, MBR risk.

Decide

LFQ vs TMT, imputation model, stage-aware contrast.

Export

SCORIAL.md and methods text without sample identifiers.

Active checks

TMT isotope purity correction logged before quantification.

Missingness labeled MNAR/MCAR before imputation.

UniProt release and contaminant database checksum preserved.

No embryo-stage contrast runs before normalization is complete.

Operating loop

Built for the points where research work breaks.

Slack decisions that never reach the manuscript

Methods sections rewritten from memory

Parameter changes no one can trace later

Analysis sessions that disappear into terminal history

Memory

Project context that survives handoffs

Objectives, datasets, assumptions, constraints, and session history stay connected in one workspace.

Validation

Claims checked before they harden

Risky cohort logic, unsupported methods language, and missing compute details are routed into review.

Methods

Publication text with a source trail

Methods drafts come from approved workspace state instead of reconstructed memory.

Platform

Every surface is tied to the same project record, without sending visitors into the app.

Capture

Project setup
Session notes
Constraints

Govern

Validation queue
Decision log
Risk review

Export

Methods draft
SCORIAL.md
Publication state

Governance

Designed for teams that need answers they can defend.

SCORIAL keeps outputs close to the evidence, constraints, and decisions that produced them.

Operating principles

  • Claims stay linked to sources.
  • Decision rationale is recorded before export.
  • Constraints remain visible across the workspace.
  • Sensitive workspace data stays behind authenticated routes.