OmniBioAI Ecosystem
Architecture · Codebase · Coverage · Health
Generated: 2026-08-29 23:06:58
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files
14,900
documentation
217,970
code lines
3,264,737
comment lines
262,152
blank lines
541,626
total lines
4,068,515
OmniBioAI ecosystem
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dev / clients
studio
Electron · v0.2.0
dev-hub
knowledge graph · :5173
sdk
Python SDK · :5190
iam-client
auth SDK
security-sdk
policy client
🔐 security plane
zero-trust boundary
api-gateway
JWT · trace prop · :8080
auth-service
bcrypt · JWT · :8001
policy-engine
RBAC/ABAC · :8002
hpc-policy-engine
GPU quota · :8003
security-audit
Redis streams · :8004
workbench
workbench
Django · 80+ plugins · :8000
lims
lab data · :7000
rag
PubMed · DeepSeek · :8090
workflow-bundles
WDL/Nextflow/CWL · :8098
control-center
health · images · :7070
services
toolserver
FastAPI bio tools · :9090
model-registry
ML versioning · :8095
opa
Open Policy Agent · :8181
ollama
Llama/DeepSeek · :11434
videos
tutorials · SDK · :8086
execution
tes
Slurm/AWS/Azure/GCP · :8081
tool-runtime
Docker/Singularity
tool-images
80+ bio tools · :8097
dev-docker
DGX · GPU env · :8082
healthy
down
not monitored
live from /health · auto-refreshes every 30s
repositories
32
tracked by cloc
code lines
3,264,737
excl. vendored
largest repo
omni-workbench
1,029,332 LOC
categories
5
core · sec · exec · infra · sdk
share by project
code lines · categorized by function
3,264,737
total LOC
infrastructure36.5%
execution20.6%
sdk / clients18.1%
core workbench17.3%
security7.5%
per-project breakdown
all repositories · sorted by code lines · click headers to sort
— items
per page
repository category files code comment blank share
repos scanned
36
clean
27
dirty
9
non-main branch
4
git working-tree status
every repo under the ecosystem root · same check as `bash omnibioai-utils/ecosystem_status.sh`
repositorybranchstatusdetails
omnibioai feature/snowflake-integration ✓ clean —
omnibioai-api-gateway main ✓ clean —
omnibioai-auth feat/443-mint-user-service-token ✓ clean —
omnibioai-billing main ✓ clean —
omnibioai-control-center main ✓ clean —
omnibioai-data main ✓ clean —
omnibioai-db-init main ✓ clean —
omnibioai-design-tokens main ✓ clean —
omnibioai-dev-docker main ✓ clean —
omnibioai-dev-hub main ✓ clean —
omnibioai-docs main ✗ dirty 1 untracked
omnibioai-ecosystem-regression main ✓ clean —
omnibioai-hpc-policy-engine main ✓ clean —
omnibioai-iam-client main ✓ clean —
omnibioai-landing main ✓ clean —
omnibioai-launcher main ✓ clean —
omnibioai-lims main ✓ clean —
omnibioai-model-registry main ✗ dirty 3 modified
omnibioai-policy-engine main ✓ clean —
omnibioai-rag feat/pubmedbert-768-query-support ✗ dirty 6 modified, 1 untracked
omnibioai-sdk main ✓ clean —
omnibioai-security-audit main ✗ dirty 1 unpushed
omnibioai-security-sdk main ✓ clean —
omnibioai-studio feat/regression-health-deployment ✗ dirty 2 modified
omnibioai-system-backups main ✓ clean —
omnibioai-tes main ✗ dirty 9 modified, 2 untracked
omnibioai-tool-images main ✗ dirty 2 modified
omnibioai-tool-runtime main ✓ clean —
omnibioai-toolserver main ✓ clean —
omnibioai-ui main ✓ clean —
omnibioai-usage-client main ✓ clean —
omnibioai-utils main ✓ clean —
omnibioai-videos main ✗ dirty 1 modified
omnibioai-work main ✓ clean —
omnibioai-workbench main ✓ clean —
omnibioai-workflow-bundles main ✗ dirty 6 modified
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monitored
—
services
healthy
—
UP
down
—
need attention
degraded
—
WARN
disk warnings
—
paths checked
status distribution
across all monitored services
—
of — UP
healthy—
down—
degraded—
response latency
per service · proportional bars · color = health
loading...
active users (7d)
1
active users (30d)
2
2 of 16 accounts are test/throwaway
sessions (30d)
17
approximate -- see note below
workflow success
51.9%
plugin-run level, not DAG-level
Only a handful of accounts exist in this deployment -- usernames matching /^test/ are flagged as test/throwaway, not real product users.
django_session isn't purged automatically (no clearsessions cron confirmed running) and expire_date reflects session expiry, not when the session started -- treat this as an approximate signal, not a precise count.
computed across individual plugin-step runs (RunStore/status.json), not DAG-level workflow outcomes -- there's no separable workflow identity to compute a true workflow success rate yet.
runs by day
last 30 days
top plugins
by run count · last 30 days
pluginruns
workflow_runner 13
drug_target_binding_affinity 6
multi_agent_bio_orchestrator 5
histopath_tumor_classifier 4
crispr_guide_efficiency_predictor 4
histopath_nuclei_segmentation 4
scrna_celltype_classifier 4
servicenow 4
protein_stability_ddg_predictor 2
variant_pathogenicity_classifier 2
atac_accessibility_classifier 2
ms_spectrum_classifier 2
nanopore_methylation_caller 2
spatial_domain_classifier 2
structural_variant_classifier 2
admet_property_predictor 1
microbiome_taxonomic_classifier 1
protein_function_classifier_esm 1
prs_deep_predictor 1
ptm_site_predictor 1
scrna_batch_integration_ae 1
microsoft_graph 1
top workflows
by run count · last 30 days
—
not available yet
workflow-level tracking not yet persisted -- DagExecutor doesn't write a durable workflow identity, only individual plugin-step runs are tracked.

Local LLMs

Ollama models installed on this machine · API key configuration status

Ollama — Local LLMs 🟢 running
Model Size Modified
llama3.1:8b-instruct-q4_K_M 4.9 GB 2026-07-28
meditron:latest 3.8 GB 2026-07-14
medllama2:latest 3.8 GB 2026-07-14
llama3.1:70b 42.5 GB 2026-06-19
qwen2.5-coder:32b 19.9 GB 2026-06-19
deepseek-r1:32b 19.9 GB 2026-06-19
gemma2:27b 15.6 GB 2026-06-18
deepseek-coder-v2:16b 8.9 GB 2026-06-18
qwen2.5-coder:14b 9.0 GB 2026-06-18
mxbai-embed-large:latest 0.7 GB 2026-06-18
deepseek-r1:latest 5.2 GB 2026-05-12
llama3:latest 4.7 GB 2026-05-12
nomic-embed-text:latest 0.3 GB 2026-05-09
Cloud API Keys
Claude API (Anthropic) NOT SET
OpenAI API NOT SET

Reference Data

Reference genomes, indexes, and databases available on this machine

Reference Genomes & Indexes
Organism Assembly STAR BWA Bowtie2 Salmon CellRanger ClinVar dbSNP gnomAD COSMIC
🧬 Human GRCh37 ✓✓✓✓✓ ✓✓✓✓
🧬 Human GRCh38 ✓✓✓✓✓ ✓✓✓✓
🧬 Human T2T-CHM13 ✓✓✓✓✓ ✓✓✓✓
🐭 Mouse GRCm38 ✓✓✓✓✓ ····
🐭 Mouse GRCm39 ✓✓✓✓✓ ····
🐀 Rat GRCr8 ✓✓✓✓· ····
🐟 Zebrafish GRCz11 ✓✓✓✓· ····
🪰 Drosophila BDGP6 ✓✓✓✓· ····
🧫 Yeast R64 ✓✓✓✓· ····
🐒 Chimpanzee Pan_tro_3.0 ✓✓✓✓· ····
🐵 Macaque Mmul_10 ✓✓✓✓· ····
🪱 C. elegans WBcel235 ✓✓✓✓· ····
🌿 Arabidopsis TAIR10 ✓✓✓✓· ····
🐷 Pig Sscrofa11.1 ✓✓✓✓· ····
🐔 Chicken GRCg7b ✓✓✓✓· ····

* Zebrafish (GRCz11) STAR index requires 141GB RAM — exceeds DGX Spark capacity (128GB). Salmon and Bowtie2 indexes available. STAR index will be added post-launch.

Annotation Databases
ClinVar ✓ Available
COSMIC ✓ Available
dbSNP ✓ Available
gnomAD ✓ Available
Gene Ontology ✓ Available
InterPro ✓ Available
Pfam ✓ Available
UniProt ✓ Available

AI Knowledge Base

PubMed literature indexed locally · FAISS vector search · RAG pipeline

RAG Service RUNNING
28.1M
PubMed Abstracts
282
Domains Ingested
283
FAISS Indexes
229.75 GB
Index Size
Indexed Domains (showing first 20) 283 total
.cache AI_Drug_Discovery ALS_MND Addiction_Substance Aging_Longevity Allergy_Asthma Alzheimer_CaseStudy Alzheimer_Disease Antimicrobial_Resistance Autoimmune Bioinformatics Biomarker_Discovery Brain_Tumors Breast_Cancer CRISPR_Editing CRISPR_GenomeEditing Cancer_CaseStudy Cardiovascular Cell_Atlas Clinical_Trials
data_source classification: explicit field if present in model_meta.json, otherwise inferred from naming/metric patterns — 92/92 versions are inferred, not confirmed.
tasks
5
0 with ≥1 real version
total versions
92
all registered
real
0
confirmed/inferred real data
synthetic
0
dummy/placeholder data
unknown
92
unclassified
all model versions
sorted by most recent · click headers to sort
— items
per page
task model version data source metric
running / total
—
containers
SIF built
—
images
SIF missing
—
not built
SIF storage
—
GB total
plugin images
—
tracked
plugins present
—
local images
—
ContainerImageStatusUptimePorts
loading…
active now
45
running/queued/created
recent (shown)
20
last 20, any state
active runs
RunStore status — refreshes on page reload · note: CREATED/RUNNING entries may include stale/orphaned status files that were never finalized, not necessarily live activity
pluginrun idstateupdatedsteps
workflow_runner 920d1aa4-b96a-404b-9661-f7e2d99463c9 RUNNING 2026-08-28T01:10:53.313540+00:00 0
workflow_runner b9f6fd21-2aa6-41d7-aa30-4a4240ff7383 RUNNING 2026-08-28T01:00:18.454165+00:00 0
workflow_runner e669ef1d-90eb-40b5-a47d-610f0f30d932 RUNNING 2026-08-28T00:59:53.761490+00:00 0
workflow_runner 553237b2-e79c-496a-93b5-4a38ed74fd46 RUNNING 2026-08-28T00:58:30.247586+00:00 0
workflow_runner 172321bf-56ce-4bb3-90db-9a8771025e67 RUNNING 2026-08-28T00:49:34.479053+00:00 0
workflow_runner ca81a537-eb75-40e6-8125-533c7ccf10d1 RUNNING 2026-08-28T00:48:15.324921+00:00 0
workflow_runner e6f8c1c7-3218-414a-9992-76f48b2e6143 RUNNING 2026-08-28T00:46:14.077884+00:00 0
workflow_runner 0891ed97-48e7-4333-9b8d-4e53ad195304 RUNNING 2026-08-28T00:44:54.114413+00:00 0
workflow_runner bc4cdcfa-d49a-4f52-a4ac-2a9c720ab97f RUNNING 2026-08-28T00:44:01.595855+00:00 0
workflow_runner cb5c8d1d-0663-419b-9264-4ddb61923272 RUNNING 2026-08-28T00:43:08.609152+00:00 0
workflow_runner 836929eb-5889-4feb-939e-4f2b2acffd82 RUNNING 2026-08-28T00:41:59.185995+00:00 0
workflow_runner 189cce27-71f4-42ed-bace-f8be1e26a56b RUNNING 2026-08-28T00:40:37.243499+00:00 0
workflow_runner c86aef77-81f2-4ad5-9fbf-18d38ec970ce RUNNING 2026-08-28T00:40:10.732943+00:00 0
protein_stability_ddg_predictor d8863e9f053c RUNNING 2026-07-27T19:21:55.243997+00:00 0
single_cell_trajectory_inference run-scti-submit RUNNING 2026-05-29T05:28:56.719605+00:00 0
omics_qc_metrics_extractor 07cc0db5f6044ced89f6049a922104ea RUNNING 2026-05-29T05:21:26.898236+00:00 0
multi_omics_integration_ai run-moi-submit RUNNING 2026-05-29T05:20:58.048713+00:00 0
metabolomics_sample_qc run-submit RUNNING 2026-05-29T05:20:35.278230+00:00 0
metabolomics_biomarkers run-bm-submit RUNNING 2026-05-29T05:20:05.859046+00:00 0
gene_expression_regulatory_ai run-grn-submit RUNNING 2026-05-29T05:16:24.691133+00:00 0
explainable_ai_interpreter run-xai-submit RUNNING 2026-05-29T05:15:56.912868+00:00 0
drug_response_predictor run-drp-stub RUNNING 2026-05-29T05:15:40.586645+00:00 0
deep_learning_variant_classifier run-dlvc-stub RUNNING 2026-05-29T05:13:02.545208+00:00 0
deep_learning_variant_classifier run-dlvc-submit RUNNING 2026-05-29T05:13:02.282716+00:00 0
auto_ml_biomarker_discovery run-automl-bad RUNNING 2026-05-29T05:11:18.268438+00:00 0
auto_ml_biomarker_discovery run-automl-submit RUNNING 2026-05-29T05:11:15.868171+00:00 0
anomaly_detection_omics run-anom-submit RUNNING 2026-05-29T05:11:07.662457+00:00 0
drug_response_predictor run-drp-submit RUNNING 2026-05-29T05:03:36.202793+00:00 0
omics_qc_metrics_extractor a2982d3e372941f88d265ce208806a4a RUNNING 2026-05-25T18:44:54.916080+00:00 0
omics_qc_metrics_extractor 3c919d6c0afc4fc19991df035279bc8f RUNNING 2026-05-25T18:42:47.547647+00:00 0
omics_qc_metrics_extractor 7f846078a963475499622aa7294e866b RUNNING 2026-05-25T18:41:33.648976+00:00 0
omics_qc_metrics_extractor 40c1447570f344948db5772fb622119c RUNNING 2026-05-25T18:18:23.169200+00:00 0
omics_qc_metrics_extractor 0cca7e4ff5fd4754bf9b42baddccc764 RUNNING 2026-05-25T18:18:10.321835+00:00 0
omics_qc_metrics_extractor 78582f34b5714b94971a6150c893d9ce RUNNING 2026-05-25T18:15:31.526460+00:00 0
omics_qc_metrics_extractor a53a3080f53549ccadbfe4704cf764ea RUNNING 2026-05-25T17:38:48.715359+00:00 0
omics_qc_metrics_extractor 7a94f9a4fca54672bc5f892b05aa371f RUNNING 2026-05-25T17:22:17.623922+00:00 0
omics_qc_metrics_extractor eb5dc4bbdc2440b18c43d63df5922797 RUNNING 2026-05-25T17:13:28.971771+00:00 0
omics_qc_metrics_extractor b876655c6948491c8852172226a5b443 RUNNING 2026-05-25T17:06:15.667811+00:00 0
variant_qc_filtering 2d76130c3ce34656 CREATED 2026-05-25T08:47:54.698227+00:00 0
bedtools_intersect 6617499fb668439c8b35653f02786dd5 CREATED 2026-05-25T08:21:06.323334+00:00 0
bedtools_intersect 5360c14a90b74d73a6f7a913a81463ac CREATED 2026-05-25T08:20:52.320482+00:00 0
bedtools_intersect 9df779ea092140dc9bb727cf8c7f83fe CREATED 2026-05-25T08:13:07.562235+00:00 0
bedtools_intersect 771a8a7f86f34358aa3d92e4f74e08d8 CREATED 2026-05-25T08:12:50.887219+00:00 0
bedtools_intersect 3eb06ec27647452c97c26b9472cf6e9f CREATED 2026-05-25T08:12:37.772414+00:00 0
bedtools_intersect 1e3000ad1ee6438e8f928947360ed93d CREATED 2026-05-25T08:12:24.355555+00:00 0
recent run history
last 20 runs, any state
pluginrun idstateupdatedsteps
workflow_runner 920d1aa4-b96a-404b-9661-f7e2d99463c9 RUNNING 2026-08-28T01:10:53.313540+00:00 0
workflow_runner b9f6fd21-2aa6-41d7-aa30-4a4240ff7383 RUNNING 2026-08-28T01:00:18.454165+00:00 0
workflow_runner e669ef1d-90eb-40b5-a47d-610f0f30d932 RUNNING 2026-08-28T00:59:53.761490+00:00 0
workflow_runner 553237b2-e79c-496a-93b5-4a38ed74fd46 RUNNING 2026-08-28T00:58:30.247586+00:00 0
workflow_runner 172321bf-56ce-4bb3-90db-9a8771025e67 RUNNING 2026-08-28T00:49:34.479053+00:00 0
workflow_runner ca81a537-eb75-40e6-8125-533c7ccf10d1 RUNNING 2026-08-28T00:48:15.324921+00:00 0
workflow_runner e6f8c1c7-3218-414a-9992-76f48b2e6143 RUNNING 2026-08-28T00:46:14.077884+00:00 0
workflow_runner 0891ed97-48e7-4333-9b8d-4e53ad195304 RUNNING 2026-08-28T00:44:54.114413+00:00 0
workflow_runner bc4cdcfa-d49a-4f52-a4ac-2a9c720ab97f RUNNING 2026-08-28T00:44:01.595855+00:00 0
workflow_runner cb5c8d1d-0663-419b-9264-4ddb61923272 RUNNING 2026-08-28T00:43:08.609152+00:00 0
workflow_runner 836929eb-5889-4feb-939e-4f2b2acffd82 RUNNING 2026-08-28T00:41:59.185995+00:00 0
workflow_runner 189cce27-71f4-42ed-bace-f8be1e26a56b RUNNING 2026-08-28T00:40:37.243499+00:00 0
workflow_runner c86aef77-81f2-4ad5-9fbf-18d38ec970ce RUNNING 2026-08-28T00:40:10.732943+00:00 0
microsoft_graph 9fcedab97a3848be9ef4f02f9b475ec5 COMPLETED 2026-08-16T17:26:39.577468+00:00 1
servicenow 910755bda82a48c99ebea5a1e5f36b8c FAILED 2026-08-16T16:58:54.608355+00:00 1
servicenow 8581f15422c7414b94069d51e7ea9837 FAILED 2026-08-16T16:58:39.903744+00:00 0
servicenow b70b15a9e61444d99260fa9fe2b49cda FAILED 2026-08-16T16:58:14.421928+00:00 1
servicenow 4e7c38c2cd904b749a5e613b29a2668f FAILED 2026-08-16T16:57:11.462719+00:00 0
multi_agent_bio_orchestrator retry_fix_check_b_1786741138 COMPLETED 2026-08-14T20:58:58.475715+00:00 1
multi_agent_bio_orchestrator retry_fix_check_a_1786741138 COMPLETED 2026-08-14T20:58:58.422680+00:00 5
cloc counts exclude vendored/runtime directories and selected extensions per cloc policy.
Coverage is best-effort and does not fail the report when a repository has test or configuration issues.
Health data is live — fetched from the Control Center /health endpoint with 30-second auto-refresh.
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