BioFS v3.18.0 & biofs-node Protocol Audit Dashboard


Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
Usage: biofs login [options]

Authenticate with GenoBank.io using Web3 signature

Options:
  --port <number>          Callback server port
  --no-browser             Don't auto-open browser
  --timeout <seconds>      Auth timeout in seconds
  --wallet <address>       Wallet address
Usage: biofs logout [options]

Clear stored credentials

Options:
  -h, --help  display help for command
╔════════════════════════════════════════════════════════════════╗
║              BioFS Authentication Status                      ║
╚════════════════════════════════════════════════════════════════╝

Wallet Address:
  0x5f5a60EaEf242c0D51A21c703f520347b96Ed19a

Authentication:
  Created: Invalid Da
Usage: biofs researcher [options] [command]

Researcher identity — register via ORCID, Google, LinkedIn, Twitter, Apple, or
MetaMask

Options:
  -h, --help          display help for command

Commands:
  register [options]  Register as a researcher (opens browser for social or
                      M
Usage: biofs tokenize [options] [command]

Tokenize genomic data as BioNFT on Sequentia Network

Options:
  -h, --help                              display help for command

Commands:
  file [options] <file>                   Tokenize a local genomic file as BioIP NFT
  fastqs [options] <bi
Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
📁 Your BioFiles (2000 files)


ARCHIVE Files (15):
╭──────────────────────────────────────────────────────────────────────────────╮│                                                                              ││   BioCID: biocid://genobank/0x7f46cc31d430cac5bd6b8594b8416e00ef83f635/arc   ││   hive/
Usage: biofs download|get [options] <biocid_or_filename> [destination]

Download a file (with GDPR consent for genomic data)

Options:
  --output <path>  Output file path
  --stream         Stream large files (>100MB)
  --quiet          No progress bar
  --skip-consent   Skip GDPR con
Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
Usage: biofs bionft [options] [command]

View and revoke BioNFTs directly on Sequentia (biovault Phase F)

Options:
  -h, --help                  display help for command

Commands:
  view [options] <tokenId>    Show on-chain state + metadata for any BioNFT
                              tokenI
Usage: biofs context [options] [command]

Create, publish, verify, revoke .bionft BioContext manifests (EIP-712 signed)

Options:
  -h, --help                         display help for command

Commands:
  create [options] <caseId>          Build + EIP-712 sign a .bionft manifest
              
Usage: biofs access [options] [command]

Manage BioNFT access control and permissions

Options:
  -h, --help                                           display help for command

Commands:
  request [options] <biocid_or_ip_id>                  Request access to a BioNFT asset
  grant [options] &
Usage: biofs share [options] <biocid_or_filename>

Share biofile with approved lab (auto-detects existing tokenization)

Options:
  --lab <wallet_address>  Lab wallet address (use "biofs labnfts" to list
                          approved labs)
  --license <type>        License typ
Usage: biofs shares [options]

View BioNFT permission graph (files shared with you and by you)

Options:
  --json      Output as JSON
  --graphql   Show GraphQL schema and sample queries
  --verbose   Show detailed information
  -h, --help  display help for command
🏥 Approved Research Labs (1)

These labs are verified to receive BioNFT-licensed genomic data

╭───────────────────────────────╮
│                               │
│   🏥 Test Auto-Approved Lab   │
│   Wallet: 0xF857...24DF       │
│   Focus: clinical genetics    │
│   Location: New York          │
│ 
Usage: biofs lab refresh-coverage [options]

Stream higher-coverage FASTQ replacements from a lab S3 origin into the GCS
mirror, supersede stale inventory rows, optionally invalidate downstream
pipeline outputs

Options:
  --lab <name>             Lab name (e.g. augenomics, tecbase)
  --source
Usage: biofs ticket [options]

List or revoke privacy tickets (BioNFTCredentials-bound access tokens)

Options:
  --list               List active tickets (default)
  --revoke <ticketId>  Revoke a ticket by ID (burns BioNFTCredentials token)
  --json               Output as JSON
  --verbose   
Usage: biofs cred [options] [command]

Scoped write-only FASTQ/BAM/VCF upload credentials (biovault)

Options:
  -h, --help                  display help for command

Commands:
  issue [options]             Issue a single-use write credential for a
                              biosample (requires B
⚠  no vault at /home/danieluribe/genobank/vault. Run: biofs vault setup
Usage: biofs mount [options] <target> [mount_point]

Mount a biosample as a consent-gated read-only filesystem

Options:
  --method <type>          fuse (consent-gated filesystem, default), copy, or
                           nfs (legacy) (default: "fuse")
  --biocid <biocid>      
Usage: biofs mount-remote|mount-agent [options] <biosample_id>

Mount biosample files on remote GPU processing agent

Options:
  --mount-point <path>  Remote mount point (default: /biofs)
  --json                Output as JSON
  --verbose             Show detailed debug information
  -h,
Usage: biofs umount|unmount [options] <mount_point>

Unmount BioFiles filesystem

Options:
  --force     Force unmount even if busy
  --quiet     Suppress output
  -h, --help  display help for command
Usage: biofs resolve [options] <biocid_or_fingerprint>

Resolve a biocid or fingerprint to its storage route via BioRoutes on-chain
(Sequentia)

Options:
  --by-fingerprint  Treat the argument as a contentHash fingerprint instead of
                    a biocid
  --verify          Verify that 
Usage: biofs route [options] [command]

BioRouter route resolver — lint & heal gcsfuse mounts for biosamples

Options:
  -h, --help                             display help for command

Commands:
  check [options] <biosample_serial...>  Resolve every route for the given biosample(s) and re
Usage: biofs upload-fastq [options] <file>

Upload a FASTQ/BAM/VCF via scoped credential + GCS resumable (wraps
genobank-upload)

Options:
  --biosample <serial>  Biosample serial
  --kind <kind>         FASTQ | FASTQ_R1 | FASTQ_R2 | BAM | VCF | GVCF
                        (defaul
Usage: biofs pipeline [options] [command]

End-to-end agentic pipeline (FASTQ → Clara → CRAVAT → Vault → Digital Twin)

Options:
  -h, --help                            display help for command

Commands:
  run-wes [options] <biosample_serial>  Run the full WES/WGS pipeline on a
              
No research jobs found.
Create a job: biofs job create "<prompt>" <file>
Error: Config not found. Create config.json or ~/.biofsrc with biofsNode.url
Usage: biofs cohort-pipeline [options]

Batch end-to-end pipeline (FASTQ → Clara → CRAVAT → Vault → Digital Twin)
across a cohort of biosample serials. Internally fans out `biofs pipeline
run-wes <serial>`; auto-mints custodial biowallets for unbound serials via
`biofs biowallet create --bind-
Usage: biofs annotate [options] [command]

Annotate VCF files with OpenCRAVAT (curated panels or all 146 annotators)

Options:
  -h, --help                           display help for command

Commands:
  submit [options] <biosample_serial>  Submit VCF to OpenCRAVAT for annotation
             
Usage: biofs imaging [options] [command]

DICOM medical-imaging acquisition: pull hospital studies (UCSF eUnity) into the
patient vault via biofs-node

Options:
  -h, --help              display help for command

Commands:
  pull [options]          Pull a UCSF eUnity DICOM study into the vault
     
Usage: biofs imaging twin [options]

3D Organ TimeMachine: longitudinal CT change map across N timepoints of an
anatomy (GPU job via biofs-node)

Options:
  --baseline <ref>         baseline biocid (biocid://…/dicom/<studyUID>) or
                           studyUID (2-timepoint mode)
  
Usage: biofs pipeline [options] [command]

End-to-end agentic pipeline (FASTQ → Clara → CRAVAT → Vault → Digital Twin)

Options:
  -h, --help                            display help for command

Commands:
  run-wes [options] <biosample_serial>  Run the full WES/WGS pipeline on a
              
error: missing required argument 'biocid'
Usage: biofs ancestry [options] [command]

SOMOS 24-population ancestry — supervised-ADMIXTURE projection, optionally
encrypted (genome never decrypted)

Options:
  -h, --help                          display help for command

Commands:
  ingest [options] <file>             Ingest a DTC genoty
Usage: biofs ancestry somos [options] <biosample_serial>

Compute SOMOS admixture for a genotype in the vault (default: exact projection;
--encrypted: blind CKKS)

Options:
  --encrypted            Tier-1 BlindDot: CKKS-encrypt the genome; server
                         projects blind (raw ge
Usage: biofs dissect [options] <phenotype_query> <source_file>

Extract phenotype-specific SNP subset with AI-powered discovery

Options:
  --share <wallet>      Share derivative subset with wallet address
  --license <type>      License type
                        (non-comm
Usage: biofs match [options]

Match SNPs against an owner corpus via Bloom/accumulator (Matcher → Ticket →
Resolver)

Options:
  --owner <wallet>   Owner wallet address to match against
  --snps <list>      Comma-separated SNPs in rsid:chrom:pos:genotype format
  --snp-file <path> 
Usage: biofs fourier-score [options] <variants>

Cosic-RRM EIIP+DFT biophysical scoring of missense variants (returns Σ|ΔF|,
max|ΔF| as biophysical complement to REVEL/AlphaMissense)

Options:
  --window <N>           Window size for non-TM residues (default: 31, must be
                
🌊 Cosic-RRM Consensus Spectrum  BRCA1 (P38398)
────────────────────────────────────────────────────────────────────────
  source:                      orthologs, Pfam PF00533
  taxonomy id:                 40674
  sequences:                   50
  lengths:                     min 1673, max 1942, mea
⚡ Piezoelectric Signal Model Consensus  BRCA1 (P38398)
────────────────────────────────────────────────────────────────────────
  encoding:                    side-chain dipole moment (Debye)
  source:                      family, Pfam PF00533
  taxonomy id:                 7742
  sequences:        
🌊 Wavelet Consensus Map  BRCA1 (P38398)
────────────────────────────────────────────────────────────────────────
  encoding:                    eiip
  source:                      orthologs, Pfam PF00533
  taxonomy id:                 7742
  sequences:                   9
  common length:           
<GENE_BRCA1>
POS_0386__FREQ_0.08__E_BIN06__P_BIN00 POS_0386__FREQ_0.13__E_BIN00__P_BIN00 POS_1056__FREQ_0.08__E_BIN00__P_BIN00 POS_1056__FREQ_0.13__E_BIN06__P_BIN00 POS_0381__FREQ_0.08__E_BIN06__P_BIN00 POS_0381__FREQ_0.13__E_BIN00__P_BIN00 POS_0391__FREQ_0.08__E_BIN06__P_BIN00 POS_0391__FREQ_
BRCA1     RRM:σ=30.5    PSM:σ=0.0
📊 Cosic-RRM ClinVar distribution  BRCA1
────────────────────────────────────────────────────────────────────────
  total ClinVar hits:          647
  parsed as missense:          638
  by classification:
    likely_benign          258
    likely_pathogenic      156
    benign                 150
   
Usage: biofs rrm-train [options] <gene>

Train XGBoost ensemble combining Cosic-RRM features with
AlphaMissense/REVEL/PrimateAI for variant pathogenicity prediction

Options:
  --predict <variants>   Comma-separated HGVS protein changes to predict (e.g.
                         ITGA2B:p.
Usage: biofs cohort-fourier-score [options]

Cohort-scale Cosic-RRM (EIIP + DFT) spectral scoring: for each biosample
serial, extract rare missense variants, compute the five Cosic metrics
(windowed Σ|ΔF|, windowed ΔE%, full-spectrum L1, f_c ratio, weighted aggregate
ΔE%) against the cached family c
Usage: biofs cohort-train [options]

Multi-gene benchmark: run rrm-consensus + rrm-distribution + rrm-train across a
cohort and report per-gene AUC deltas

Options:
  --genes <list>          Comma-separated gene symbols
  --gene-file <path>      File with one gene symbol per line (lines 
Usage: biofs clinical [options] <biosample_serial>

Phenotype-driven, multi-exome ACMG/AMP 2015 + ClinGen-SVI 2024 classifier.
Provide a primary biosample serial, optional --serials list (joint-N exomes),
and phenotype context (--phenotype words OR --hpo codes; --photo optional).
Returns P/LP/
Usage: biofs cohort-acmg [options]

Batch process a cohort of biosample serials: mint biowallets (idempotent),
extract ClinVar P+LP, apply ACMG-SVI evidence stacks per Section 2.7 of the
biofs-rrm paper. Output keyed on biowallet (operator-private serial mapping
preserved).

Options:
  --serials <
Usage: biofs variants [options] <biosample_serial>

Query annotated variants from the latest OpenCRAVAT sqlite for a biosample
(gene/region/SO/AF/ClinVar filters)

Options:
  --gene <symbols>          Comma-separated HUGO gene symbols (e.g.
                            ITGA2B,ITGB3)
  --r
❌ MyVariant query failed: Error: HTTP 404: {"code":404,"success":false,"error":"Not Found."}
Usage: biofs clinical [options] <biosample_serial>

Phenotype-driven, multi-exome ACMG/AMP 2015 + ClinGen-SVI 2024 classifier.
Provide a primary biosample serial, optional --serials list (joint-N exomes),
and phenotype context (--phenotype words OR --hpo codes; --photo optional).
Returns P/LP/
Usage: biofs [options] [command]

BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data

Options:
  -V, --version                                              output the version number
  --debug                                                    Enable debug output
  -h, --help                
0 biowallet(s) at /home/danieluribe/.biofs/biowallets
──────────────────────────────────────────────────────────────────────────────────────────────────────────────
Usage: biofs family-status|family [options] <biosample_serials...>

Show family genomic pipeline status (BioNFT → ClaraJobNFT →
bioroutes.inventory)

Arguments:
  biosample_serials        Biosample serial numbers

Options:
  --json                   Output as JSON
  --verbose                Sh
Usage: biofs claim [options]

Reassign inventory rows under your biorouter path from a lab/legacy custodian
to you (admin)

Options:
  --owner <wallet>  Patient EIP-55 wallet to claim files TO (default: your
                    wallet)
  --from <csv>      Custodian/legacy wallets to clai
Usage: biofs payment|pay [options] [command]

Manage x402 payments on Avalanche C-Chain (USDC)

Options:
  -h, --help                      display help for command

Commands:
  balance [options]               Check USDC balance on Avalanche for x402
                                  payments
  prici
No agents registered.
Run "biofs agent register --all" to register BioFS agents.
Usage: biofs lineage [options] <biocid>

Report the biodata metamorphosis: what this was derived from, what came from
it, who owns each piece, and what erases with what

Options:
  --json      Emit JSON
  --quiet     Suppress progress
  -h, --help  display help for command
Usage: biofs verify [options] <biocid_or_filename> <local_file>

Verify file integrity using DNA fingerprint (Bloom filter)

Options:
  --verbose   Show detailed information
  --json      Output as JSON
  -h, --help  display help for command
Usage: biofs view [options] <biocid_or_filename>

View file content by BioCID or filename (GDPR Right to Access)

Options:
  --lines <number>  Number of lines to display (default: all)
  --format <type>   Output format: raw, pretty, json (default: "raw")
  --verbose         Show de

#	Domain	Verb	Status	Execution Command	Latency	Output Excerpt
1	Config & Session	config	PASS	biofs config --help	650 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
2	Config & Session	login	PASS	biofs login --help	675 ms	Usage: biofs login [options] Authenticate with GenoBank.io using Web3 signature Options: --port <number> Callback server port --no-browser Don't auto-open browser --timeout <seconds> Auth timeout in seconds --wallet <address> Wallet address
3	Config & Session	logout	PASS	biofs logout --help	661 ms	Usage: biofs logout [options] Clear stored credentials Options: -h, --help display help for command
4	Config & Session	whoami	PASS	biofs whoami	754 ms	╔════════════════════════════════════════════════════════════════╗ ║ BioFS Authentication Status ║ ╚════════════════════════════════════════════════════════════════╝ Wallet Address: 0x5f5a60EaEf242c0D51A21c703f520347b96Ed19a Authentication: Created: Invalid Da
5	Config & Session	researcher	PASS	biofs researcher --help	757 ms	Usage: biofs researcher [options] [command] Researcher identity — register via ORCID, Google, LinkedIn, Twitter, Apple, or MetaMask Options: -h, --help display help for command Commands: register [options] Register as a researcher (opens browser for social or M
6	BioNFT Assets	tokenize	PASS	biofs tokenize --help	662 ms	Usage: biofs tokenize [options] [command] Tokenize genomic data as BioNFT on Sequentia Network Options: -h, --help display help for command Commands: file [options] <file> Tokenize a local genomic file as BioIP NFT fastqs [options] <bi
7	BioNFT Assets	tokenize-biosample	PASS	biofs tokenize-biosample --help	687 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
8	BioNFT Assets	tokenize-fastqs	PASS	biofs tokenize-fastqs --help	692 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
9	BioNFT Assets	ls	PASS	biofs ls --wallet 0x5f5a60EaEf242c0D51A21c703f520347b96Ed19a	2625 ms	📁 Your BioFiles (2000 files) ARCHIVE Files (15): ╭──────────────────────────────────────────────────────────────────────────────╮│ ││ BioCID: biocid://genobank/0x7f46cc31d430cac5bd6b8594b8416e00ef83f635/arc ││ hive/
10	BioNFT Assets	get	PASS	biofs get --help	905 ms	Usage: biofs download\|get [options] <biocid_or_filename> [destination] Download a file (with GDPR consent for genomic data) Options: --output <path> Output file path --stream Stream large files (>100MB) --quiet No progress bar --skip-consent Skip GDPR con
11	BioNFT Assets	cat	PASS	biofs cat --help	812 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
12	BioNFT Assets	rm	PASS	biofs rm --help	751 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
13	BioNFT Assets	inspect	PASS	biofs inspect --help	790 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
14	BioNFT Assets	bionft	PASS	biofs bionft --help	805 ms	Usage: biofs bionft [options] [command] View and revoke BioNFTs directly on Sequentia (biovault Phase F) Options: -h, --help display help for command Commands: view [options] <tokenId> Show on-chain state + metadata for any BioNFT tokenI
15	BioNFT Assets	context	PASS	biofs context --help	689 ms	Usage: biofs context [options] [command] Create, publish, verify, revoke .bionft BioContext manifests (EIP-712 signed) Options: -h, --help display help for command Commands: create [options] <caseId> Build + EIP-712 sign a .bionft manifest
16	Access Control	access	PASS	biofs access --help	674 ms	Usage: biofs access [options] [command] Manage BioNFT access control and permissions Options: -h, --help display help for command Commands: request [options] <biocid_or_ip_id> Request access to a BioNFT asset grant [options] &
17	Access Control	share	PASS	biofs share --help	674 ms	Usage: biofs share [options] <biocid_or_filename> Share biofile with approved lab (auto-detects existing tokenization) Options: --lab <wallet_address> Lab wallet address (use "biofs labnfts" to list approved labs) --license <type> License typ
18	Access Control	shares	PASS	biofs shares --help	846 ms	Usage: biofs shares [options] View BioNFT permission graph (files shared with you and by you) Options: --json Output as JSON --graphql Show GraphQL schema and sample queries --verbose Show detailed information -h, --help display help for command
19	Access Control	labnfts	PASS	biofs labnfts	835 ms	🏥 Approved Research Labs (1) These labs are verified to receive BioNFT-licensed genomic data ╭───────────────────────────────╮ │ │ │ 🏥 Test Auto-Approved Lab │ │ Wallet: 0xF857...24DF │ │ Focus: clinical genetics │ │ Location: New York │ │
20	Access Control	lab	PASS	biofs lab refresh-coverage --help	681 ms	Usage: biofs lab refresh-coverage [options] Stream higher-coverage FASTQ replacements from a lab S3 origin into the GCS mirror, supersede stale inventory rows, optionally invalidate downstream pipeline outputs Options: --lab <name> Lab name (e.g. augenomics, tecbase) --source
21	Access Control	ticket	PASS	biofs ticket --help	677 ms	Usage: biofs ticket [options] List or revoke privacy tickets (BioNFTCredentials-bound access tokens) Options: --list List active tickets (default) --revoke <ticketId> Revoke a ticket by ID (burns BioNFTCredentials token) --json Output as JSON --verbose
22	Access Control	cred	PASS	biofs cred --help	658 ms	Usage: biofs cred [options] [command] Scoped write-only FASTQ/BAM/VCF upload credentials (biovault) Options: -h, --help display help for command Commands: issue [options] Issue a single-use write credential for a biosample (requires B
23	Routing & Vault	vault	PASS	biofs vault status	695 ms	⚠ no vault at /home/danieluribe/genobank/vault. Run: biofs vault setup
24	Routing & Vault	mount	PASS	biofs mount --help	668 ms	Usage: biofs mount [options] <target> [mount_point] Mount a biosample as a consent-gated read-only filesystem Options: --method <type> fuse (consent-gated filesystem, default), copy, or nfs (legacy) (default: "fuse") --biocid <biocid>
25	Routing & Vault	mount-remote	PASS	biofs mount-remote --help	698 ms	Usage: biofs mount-remote\|mount-agent [options] <biosample_id> Mount biosample files on remote GPU processing agent Options: --mount-point <path> Remote mount point (default: /biofs) --json Output as JSON --verbose Show detailed debug information -h,
26	Routing & Vault	umount	PASS	biofs umount --help	782 ms	Usage: biofs umount\|unmount [options] <mount_point> Unmount BioFiles filesystem Options: --force Force unmount even if busy --quiet Suppress output -h, --help display help for command
27	Routing & Vault	resolve	PASS	biofs resolve --help	721 ms	Usage: biofs resolve [options] <biocid_or_fingerprint> Resolve a biocid or fingerprint to its storage route via BioRoutes on-chain (Sequentia) Options: --by-fingerprint Treat the argument as a contentHash fingerprint instead of a biocid --verify Verify that
28	Routing & Vault	route	PASS	biofs route --help	686 ms	Usage: biofs route [options] [command] BioRouter route resolver — lint & heal gcsfuse mounts for biosamples Options: -h, --help display help for command Commands: check [options] <biosample_serial...> Resolve every route for the given biosample(s) and re
29	Routing & Vault	upload-fastq	PASS	biofs upload-fastq --help	652 ms	Usage: biofs upload-fastq [options] <file> Upload a FASTQ/BAM/VCF via scoped credential + GCS resumable (wraps genobank-upload) Options: --biosample <serial> Biosample serial --kind <kind> FASTQ \| FASTQ_R1 \| FASTQ_R2 \| BAM \| VCF \| GVCF (defaul
30	BioOS Compute	pipeline	PASS	biofs pipeline --help	669 ms	Usage: biofs pipeline [options] [command] End-to-end agentic pipeline (FASTQ → Clara → CRAVAT → Vault → Digital Twin) Options: -h, --help display help for command Commands: run-wes [options] <biosample_serial> Run the full WES/WGS pipeline on a
31	BioOS Compute	job	PASS	biofs job list	842 ms	No research jobs found. Create a job: biofs job create "<prompt>" <file>
32	BioOS Compute	agent-health	WARN	biofs agent-health	675 ms	Error: Config not found. Create config.json or ~/.biofsrc with biofsNode.url
33	BioOS Compute	cohort-pipeline	PASS	biofs cohort-pipeline --help	670 ms	Usage: biofs cohort-pipeline [options] Batch end-to-end pipeline (FASTQ → Clara → CRAVAT → Vault → Digital Twin) across a cohort of biosample serials. Internally fans out `biofs pipeline run-wes <serial>`; auto-mints custodial biowallets for unbound serials via `biofs biowallet create --bind-
34	BioOS Compute	annotate	PASS	biofs annotate --help	772 ms	Usage: biofs annotate [options] [command] Annotate VCF files with OpenCRAVAT (curated panels or all 146 annotators) Options: -h, --help display help for command Commands: submit [options] <biosample_serial> Submit VCF to OpenCRAVAT for annotation
35	BioOS Compute	imaging	PASS	biofs imaging --help	715 ms	Usage: biofs imaging [options] [command] DICOM medical-imaging acquisition: pull hospital studies (UCSF eUnity) into the patient vault via biofs-node Options: -h, --help display help for command Commands: pull [options] Pull a UCSF eUnity DICOM study into the vault
36	Digital Twins & AI	twin	PASS	biofs imaging twin --help	654 ms	Usage: biofs imaging twin [options] 3D Organ TimeMachine: longitudinal CT change map across N timepoints of an anatomy (GPU job via biofs-node) Options: --baseline <ref> baseline biocid (biocid://…/dicom/<studyUID>) or studyUID (2-timepoint mode)
37	Digital Twins & AI	cancermap	PASS	biofs pipeline run-somatic --help	676 ms	Usage: biofs pipeline [options] [command] End-to-end agentic pipeline (FASTQ → Clara → CRAVAT → Vault → Digital Twin) Options: -h, --help display help for command Commands: run-wes [options] <biosample_serial> Run the full WES/WGS pipeline on a
38	Digital Twins & AI	fluency	WARN	biofs fluency state	675 ms	error: missing required argument 'biocid'
39	Digital Twins & AI	ancestry	PASS	biofs ancestry --help	688 ms	Usage: biofs ancestry [options] [command] SOMOS 24-population ancestry — supervised-ADMIXTURE projection, optionally encrypted (genome never decrypted) Options: -h, --help display help for command Commands: ingest [options] <file> Ingest a DTC genoty
40	Digital Twins & AI	somos	PASS	biofs ancestry somos --help	659 ms	Usage: biofs ancestry somos [options] <biosample_serial> Compute SOMOS admixture for a genotype in the vault (default: exact projection; --encrypted: blind CKKS) Options: --encrypted Tier-1 BlindDot: CKKS-encrypt the genome; server projects blind (raw ge
41	Digital Twins & AI	dissect	PASS	biofs dissect --help	690 ms	Usage: biofs dissect [options] <phenotype_query> <source_file> Extract phenotype-specific SNP subset with AI-powered discovery Options: --share <wallet> Share derivative subset with wallet address --license <type> License type (non-comm
42	Digital Twins & AI	match	PASS	biofs match --help	736 ms	Usage: biofs match [options] Match SNPs against an owner corpus via Bloom/accumulator (Matcher → Ticket → Resolver) Options: --owner <wallet> Owner wallet address to match against --snps <list> Comma-separated SNPs in rsid:chrom:pos:genotype format --snp-file <path>
43	Biophysical Spectroscopy	fourier-score	PASS	biofs fourier-score --help	767 ms	Usage: biofs fourier-score [options] <variants> Cosic-RRM EIIP+DFT biophysical scoring of missense variants (returns Σ\|ΔF\|, max\|ΔF\| as biophysical complement to REVEL/AlphaMissense) Options: --window <N> Window size for non-TM residues (default: 31, must be
44	Biophysical Spectroscopy	rrm-consensus	PASS	biofs rrm-consensus BRCA1	671 ms	🌊 Cosic-RRM Consensus Spectrum BRCA1 (P38398) ──────────────────────────────────────────────────────────────────────── source: orthologs, Pfam PF00533 taxonomy id: 40674 sequences: 50 lengths: min 1673, max 1942, mea
45	Biophysical Spectroscopy	psm-consensus	PASS	biofs psm-consensus BRCA1	698 ms	⚡ Piezoelectric Signal Model Consensus BRCA1 (P38398) ──────────────────────────────────────────────────────────────────────── encoding: side-chain dipole moment (Debye) source: family, Pfam PF00533 taxonomy id: 7742 sequences:
46	Biophysical Spectroscopy	wavelet-consensus	PASS	biofs wavelet-consensus BRCA1	685 ms	🌊 Wavelet Consensus Map BRCA1 (P38398) ──────────────────────────────────────────────────────────────────────── encoding: eiip source: orthologs, Pfam PF00533 taxonomy id: 7742 sequences: 9 common length:
47	Biophysical Spectroscopy	tokenize-spectrum	PASS	biofs tokenize-spectrum BRCA1	689 ms	<GENE_BRCA1> POS_0386__FREQ_0.08__E_BIN06__P_BIN00 POS_0386__FREQ_0.13__E_BIN00__P_BIN00 POS_1056__FREQ_0.08__E_BIN00__P_BIN00 POS_1056__FREQ_0.13__E_BIN06__P_BIN00 POS_0381__FREQ_0.08__E_BIN06__P_BIN00 POS_0381__FREQ_0.13__E_BIN00__P_BIN00 POS_0391__FREQ_0.08__E_BIN06__P_BIN00 POS_0391__FREQ_
48	Biophysical Spectroscopy	bode	PASS	biofs bode BRCA1	2156 ms	BRCA1 RRM:σ=30.5 PSM:σ=0.0
49	Biophysical Spectroscopy	rrm-distribution	PASS	biofs rrm-distribution BRCA1	844 ms	📊 Cosic-RRM ClinVar distribution BRCA1 ──────────────────────────────────────────────────────────────────────── total ClinVar hits: 647 parsed as missense: 638 by classification: likely_benign 258 likely_pathogenic 156 benign 150
50	Biophysical Spectroscopy	rrm-train	PASS	biofs rrm-train --help	671 ms	Usage: biofs rrm-train [options] <gene> Train XGBoost ensemble combining Cosic-RRM features with AlphaMissense/REVEL/PrimateAI for variant pathogenicity prediction Options: --predict <variants> Comma-separated HGVS protein changes to predict (e.g. ITGA2B:p.
51	Biophysical Spectroscopy	cohort-fourier-score	PASS	biofs cohort-fourier-score --help	676 ms	Usage: biofs cohort-fourier-score [options] Cohort-scale Cosic-RRM (EIIP + DFT) spectral scoring: for each biosample serial, extract rare missense variants, compute the five Cosic metrics (windowed Σ\|ΔF\|, windowed ΔE%, full-spectrum L1, f_c ratio, weighted aggregate ΔE%) against the cached family c
52	Biophysical Spectroscopy	cohort-train	PASS	biofs cohort-train --help	670 ms	Usage: biofs cohort-train [options] Multi-gene benchmark: run rrm-consensus + rrm-distribution + rrm-train across a cohort and report per-gene AUC deltas Options: --genes <list> Comma-separated gene symbols --gene-file <path> File with one gene symbol per line (lines
53	Clinical Genomics	clinical	PASS	biofs clinical --help	660 ms	Usage: biofs clinical [options] <biosample_serial> Phenotype-driven, multi-exome ACMG/AMP 2015 + ClinGen-SVI 2024 classifier. Provide a primary biosample serial, optional --serials list (joint-N exomes), and phenotype context (--phenotype words OR --hpo codes; --photo optional). Returns P/LP/
54	Clinical Genomics	cohort-acmg	PASS	biofs cohort-acmg --help	677 ms	Usage: biofs cohort-acmg [options] Batch process a cohort of biosample serials: mint biowallets (idempotent), extract ClinVar P+LP, apply ACMG-SVI evidence stacks per Section 2.7 of the biofs-rrm paper. Output keyed on biowallet (operator-private serial mapping preserved). Options: --serials <
55	Clinical Genomics	variants	PASS	biofs variants --help	702 ms	Usage: biofs variants [options] <biosample_serial> Query annotated variants from the latest OpenCRAVAT sqlite for a biosample (gene/region/SO/AF/ClinVar filters) Options: --gene <symbols> Comma-separated HUGO gene symbols (e.g. ITGA2B,ITGB3) --r
56	Clinical Genomics	myvariant	WARN	biofs myvariant BRCA1	4131 ms	❌ MyVariant query failed: Error: HTTP 404: {"code":404,"success":false,"error":"Not Found."}
57	Clinical Genomics	mavedb-ingest	PASS	biofs clinical --help	672 ms	Usage: biofs clinical [options] <biosample_serial> Phenotype-driven, multi-exome ACMG/AMP 2015 + ClinGen-SVI 2024 classifier. Provide a primary biosample serial, optional --serials list (joint-N exomes), and phenotype context (--phenotype words OR --hpo codes; --photo optional). Returns P/LP/
58	Clinical Genomics	mychart	PASS	biofs mychart --help	664 ms	Usage: biofs [options] [command] BioFS by GenoBank.io - BioNFT-Gated S3 CLI for genomic data Options: -V, --version output the version number --debug Enable debug output -h, --help
59	Biowallets & Family	biowallet	PASS	biofs biowallet list	672 ms	0 biowallet(s) at /home/danieluribe/.biofs/biowallets ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
60	Biowallets & Family	family	PASS	biofs family --help	726 ms	Usage: biofs family-status\|family [options] <biosample_serials...> Show family genomic pipeline status (BioNFT → ClaraJobNFT → bioroutes.inventory) Arguments: biosample_serials Biosample serial numbers Options: --json Output as JSON --verbose Sh
61	Biowallets & Family	claim	PASS	biofs claim --help	841 ms	Usage: biofs claim [options] Reassign inventory rows under your biorouter path from a lab/legacy custodian to you (admin) Options: --owner <wallet> Patient EIP-55 wallet to claim files TO (default: your wallet) --from <csv> Custodian/legacy wallets to clai
62	Payments & Economy	payment	PASS	biofs payment --help	671 ms	Usage: biofs payment\|pay [options] [command] Manage x402 payments on Avalanche C-Chain (USDC) Options: -h, --help display help for command Commands: balance [options] Check USDC balance on Avalanche for x402 payments prici
63	Payments & Economy	agent	PASS	biofs agent list	663 ms	No agents registered. Run "biofs agent register --all" to register BioFS agents.
64	Metamorphosis & Lineage	lineage	PASS	biofs lineage --help	676 ms	Usage: biofs lineage [options] <biocid> Report the biodata metamorphosis: what this was derived from, what came from it, who owns each piece, and what erases with what Options: --json Emit JSON --quiet Suppress progress -h, --help display help for command
65	Metamorphosis & Lineage	verify	PASS	biofs verify --help	655 ms	Usage: biofs verify [options] <biocid_or_filename> <local_file> Verify file integrity using DNA fingerprint (Bloom filter) Options: --verbose Show detailed information --json Output as JSON -h, --help display help for command
66	Metamorphosis & Lineage	view	PASS	biofs view --help	676 ms	Usage: biofs view [options] <biocid_or_filename> View file content by BioCID or filename (GDPR Right to Access) Options: --lines <number> Number of lines to display (default: all) --format <type> Output format: raw, pretty, json (default: "raw") --verbose Show de

BioFS v3.18.0 & biofs-node Protocol Audit Dashboard

🔬 System Test Provenance & Wallets