Phage Design: from KYC to FASTA
A complete walkthrough of the current research preview: institutional verification, mock design jobs, candidate review, audit trail, and safe export.
Phase 0 is a mock pipeline
It does not run Evo 2, does not generate viable genomes, and does not clear sequences for synthesis. Exports are watermarked and must not be sent to a synthesis provider.
Before you start
You need a real account and a verifiable research affiliation. The module is not open to anonymous or personal-email users.
- A Lalax account with a verified email.
- An institutional email address and a real institution/lab.
- A role in the project: PI, researcher, postdoc, PhD student, or industry scientist.
- Willingness to sign the research-use and no-synthesis agreements.
What is allowed in Phase 0
- Host
- E. coli C only (non-pathogenic lab strain, PhiX174 host).
- Reference
- PhiX174 (NC_001422.1), fixed. No uploaded genomes.
- Output
- Synthetic mock candidates and a watermarked FASTA export.
- Not allowed
- Clinical use, environmental release, synthesis, arbitrary pathogens, or custom hosts.
STEP 01
Request institutional access
Phage Design is gated. Until an administrator approves your institution, the workbench shows the verification form instead of the design form.
- 1Sign in and open /dashboard/phage-design.
- 2Complete the institutional form: name, institution, department, lab, role, country, and intended research use.
- 3Confirm the three agreements: research-use only, no synthesis without local biosafety review, and data-processing consent.
- 4Submit and wait for manual review. The page shows a pending state with a refresh button.
- 5If rejected, read the reviewer notes, correct the form, and resubmit. If revoked, contact support.
STEP 02
Create your first mock design job
Phase 0 runs a mock pipeline. It generates synthetic, non-functional candidates to test the workflow, the audit trail, and the export format.
- 1Give the job a clear name so the audit trail is easy to review.
- 2Host is fixed to E. coli C and the reference genome is fixed to PhiX174 (NC_001422.1). Arbitrary hosts and uploaded genomes are rejected.
- 3Choose 1-12 candidates, a GC range, and a minimum ORF count. These constraints drive the mock filter.
- 4Add notes for the audit trail if you need to explain the research context.
- 5Tick the research-use attestation and click Run mock design.
STEP 03
Review candidates and the audit trail
The results table is intentionally explicit about what Phase 0 does and does not do.
- 1Status: candidate means the sequence passed the mock constraints; filtered means it failed the GC or ORF threshold.
- 2Length and GC are computed from the generated sequence.
- 3ORFs are counted with a simple ATG-to-stop scan in the mock pipeline.
- 4Viability and novelty scores are heuristic placeholders, not biological predictions.
- 5Risk flags always include mock_pipeline, not_screened, and no_synthesis. Filtered candidates also show the failed constraint.
- 6The audit trail records job creation and mock pipeline completion.
STEP 04
Export safely
FASTA export exists so you can test the downstream workflow. It is not a synthesis order and it is not a validated genome.
- 1Click FASTA on a completed job.
- 2Every file is watermarked: RESEARCH USE ONLY - NOT FOR SYNTHESIS.
- 3Do not send exported sequences to a DNA synthesis provider.
- 4Phase 1 will add real Evo 2 inference, in silico filtering, and a biosafety screening report behind institutional verification.
How to read the results
| Column | Meaning |
|---|---|
| Candidate | Generated candidate label. |
| Status | candidate or filtered. |
| Length | Nucleotide length of the mock sequence. |
| GC | GC percentage. |
| ORFs | Open reading frames found by the mock scanner. |
| Viability | Heuristic 0-1 score; not a biological prediction. |
| Novelty | Heuristic 0-1 score; not a biological prediction. |
| Flags | mock_pipeline, not_screened, no_synthesis, and any failed constraint. |
Do not synthesize or release
The mock scores are not evidence of viability, host range, or safety. Any future laboratory work requires local institutional biosafety review and provider screening.
Reviewing access requests
Admins open /dashboard/admin/phage-access. Admin accounts bypass the KYC gate for testing, but all non-admin users must be approved explicitly.
Review checklist
- Email domain matches the institution.
- Institution and lab are verifiable.
- Role and intended use are coherent.
- No sanctions, export-control, or clinical red flags.
- Research-use and no-synthesis agreements are signed.
Decision states
- Approve: grants workbench access.
- Reject: user can correct and resubmit.
- Revoke: immediately blocks an approved account.
- Every decision is written to the access audit log.
There are no email notifications yet: the admin must review the queue from the admin page.
Troubleshooting
Institutional verification required
Your KYC request is not approved. Open /dashboard/phage-design and check the status.
Verification pending
An administrator has not reviewed the request yet. Use Refresh status or contact your admin.
Previous request rejected
Read the reviewer notes, correct the form, and resubmit.
Access revoked
The account is blocked from the module. Contact support; the form is intentionally hidden.
Trial limit reached
Phase 0 allows two mock jobs per account. Existing jobs remain visible.
Job not found
The job was deleted or belongs to another account. Jobs are scoped to the authenticated user.
What comes after Phase 0
Real generation
Evo 2 7B Microviridae or the hosted Evo 2 40B API in an isolated GPU worker.
Real filtering
The published phage pipeline: ORF validation, genetic architecture, homology, and tropism checks.
Real safety
Biosafety screening, institutional review, synthesis-partner handoff, and full audit.
Ready to try the workflow?
Open the workbench, submit your institutional request, and run a mock job once approved.
Open the workbench