- FactorForge package, web UI, CLI, and documentation
- Eijex MCP public access surface
- AgentOS workflow-integrity code and synthetic fixtures
- ValidationHub schemas and registry code
Open evidence infrastructure for plant expression
Design sequences.
Govern workflows.
Preserve evidence.
Eijex develops open-source, human-supervised research software connecting reproducible plant CDS design with reviewable evidence infrastructure.
FactorForge is available now. Shared database integration remains a research checkpoint.
View Eijex on GitHubOpen-source software for reproducible plant bio-design, human-supervised workflow governance, and evidence traceability.
From design to evidence
One workflow. Clear responsibility at every step.
FactorForge creates reviewable design candidates, AgentOS guides human-supervised decisions, and ValidationHub preserves the evidence behind each handoff.
- 01
Design
FactorForge
Create reproducible CDS candidates and run deterministic computational checks.
Learn about FactorForge - 02
Review
AgentOS
Apply policies, record approvals, and keep human judgment in control.
Learn about AgentOS - 03
Preserve
ValidationHub
Store reviewed evidence as structured, traceable research records.
Learn about ValidationHub
One identity and provenance trail connects the entire workflow.
Shared infrastructure is being validated as a research checkpoint—not presented as a completed production database.
Eijex MCP provides public access to supported tools while scientific source-of-truth records remain with their owning systems.
Implementation status
What exists today—and what still has to be proven.
Public software availability and database integration are different milestones. This view keeps them separate.
- Captured GCP PostgreSQL 16 research instance
- Separate tested FactorForge SQLite metadata path
- Byte-pinned candidate-asset manifest registration
- Ordered migrations and schema-version policy
- PostgreSQL, SQLite, and specification reconciliation
- Access, restore, state-isolation, and leakage tests
- Public or synthetic end-to-end lineage fixture
These checkpoints show that implementation has begun.
They do not establish a synchronized production database, a completed evidence ledger, or biological performance.
They do not establish a synchronized production database, a completed evidence ledger, or biological performance.
Open-source stack
Public tools with explicit responsibility boundaries.
Public software releases are staged independently from permissioned research data.
FactorForge
AvailableCDS Design Review
Pre-synthesis sequence review for plant CDS workflows, with reproducible candidates, deterministic checks, and citable review artifacts.
pip install factorforge-cdsEijex MCP
AvailablePublic Tool Access
MCP-compatible access to public FactorForge capabilities with explicit tool and data boundaries.
mcp.eijex.comAgentOS
Public codeWorkflow Control Plane
Human-supervised orchestration for policy checks, approval gates, audit trails, and evidence-safe public projection.
Human approval at public boundariesValidationHub
Public codeEvidence Registry
Schema-driven infrastructure for reviewing and curating validation evidence while permissioned records remain outside public repositories.
Open schemas · Permissioned evidenceFactorForge available via
pip install factorforge-cdsconda install factorforge-cdssoondocker pull ghcr.io/eijex/factorforge-cds:latestResearch program
Software claims and research evidence advance separately.
Each research track has its own scope, evidence gate, and publication path. Neither substitutes computational results for physical observations.
1Computational case study
Paper 1 — Reproducible CDS design
A frozen N. benthamiana computational study and reproducibility package. It makes no expression, yield, or wet-lab claim.
Current status: Computational scope frozen
2Planning scaffold
Paper 2 — Evidence infrastructure
A research plan for traceable design-to-evidence infrastructure, now recording a partial database implementation checkpoint.
Current status: Evidence gate not yet complete
Research Notes
The decisions, dead ends, and lessons behind the work.
Engineering investigations and computational observations from building reproducible, evidence-aware bio-design software.
Rule/LM ArchitectureCurrent
Why rule authority still matters in a language-model system
A code-level audit changed the question from whether a language model could replace deterministic design rules to how learned proposals could remain bounded by them.
· 2 minRead note →
Design & ValidationEngineering note
Why every CAI value needs an authority record
Two CAI values for the same sequence were both mathematically correct—and still misleading when shown without their references.
· 2 minRead note →
Design & ValidationPublic-redacted case study
Why a CDS-level pass does not guarantee expression
Codon choice, protein architecture, experimental context, and measured yield belong to connected—but different—evidence layers.
· 2 minRead note →
Reliability & ReleaseEngineering note
When an MFE calculation became an availability risk
Two plausible debugging theories were wrong. A traceback showed that an unbounded cubic-time folding call was the real cause.
· 2 minRead note →
Research Notes are editorial records, not peer-reviewed publications or biological validation evidence. Incomplete and superseded work remains visible when it helps explain how a decision changed.
Open code · permissioned data
Public software does not mean public research records.
Code, public schemas, documentation, and synthetic fixtures are open. Raw sequences, partner documents, personal information, and permissioned experimental evidence are governed separately and are not published in the software repositories.