OmniBioAI
AI-Powered Bioinformatics Platform with registry-driven plugins and reproducible workflows
Plugins
Choose a category to focus the launcher.
Dashboard
9 app(s)
Alerting & Notifications
Threshold-based alerts, notifications, and alert history for OmniBioAI
System Health
Celery workers, queue depth, failed tasks, and disk/temp usage.
Provenance
Audit trail & lineage for OmniObjects (reproducible workflows)
Resource & Cost Monitoring
Track compute usage and cloud costs across projects and teams
Dataset Catalog
Central catalog of datasets: versions, size, freshness, schema, and lineage links
Audit & Activity Log
Platform-wide audit trail and activity timeline across OmniBioAI services
Data Manager
Upload, organize, and manage datasets & OmniObjects
Job Monitor
Central dashboard for monitoring all OmniBioAI runs (status, logs, progress, artifacts)
Plugin Manager
Admin UI to enable/disable plugins and regenerate compiled outputs
Workflows
6 app(s)
Workflow Dashboard
Monitor real-time progress of workflows and long-running tasks.
Workflow Runner
Generic registry-backed workflow execution UI with shared templates and services
Workflow Builder
Canvas-based drag-and-drop workflow builder for authoring reproducible pipelines
Visual Workflow Explorer
Interactive DAG-based explorer for WDL/Nextflow/Snakemake/CWL workflows
Workflow Compiler (SKILL.md → IR → DAG)
Compiles scientific SKILL.md protocols into structured IR and executable DAGs for OmniBioAI workflow engine
Workflow Registry Admin
Admin UI for registering workflow bundles
AI
11 app(s)
OnboardAI
Project documentation browser (plugins + docs) with Markdown rendering
AI Evidence Assistant
AI assistant with artifact-backed evidence and traceability
BioNarratorAI
Converts notebooks, pipelines, and experimental outputs into structured scientific narratives and publication-ready manuscripts
BioHypothesisAI
Generates novel biological hypotheses from scientific literature using knowledge graph reasoning and LLM-based abstraction
Agent Workflow Studio
Visual studio for designing, previewing, and running agent workflows
OmniBioAgent
Autonomous AI system for bioinformatics workflows (intent → DAG → execution).
LLM Fine-Tuner
Fine-tune LLMs on your biomedical data using LoRA/PEFT
Clinical BERT Fine-Tuner
Fine-tune BioBERT/PubMedBERT/ClinicalBERT on custom clinical text for classification
Literature RAG
Search PubMed, retrieve evidence, and generate grounded summaries with citations.
PubMed Search
Search PubMed with optional AI-powered summarization
OmniNotebookAI
Notebook-style AI research system with RAG, multi-source ingestion, and contextual querying
Analysis
42 app(s)
Omics Data QC Harmonizer
Cross-omics QC, batch detection, batch correction, and dataset harmonization engine for multi-cohort biological data integration
DESeq2 Differential Expression
Plugin scaffold
Volcano Plot Generator
Plugin scaffold
GSEA Pathway Enrichment
Plugin scaffold
Expression Heatmap
Plugin scaffold
PCA Dimensionality Reduction
Plugin scaffold
Splice Event Viewer
Plugin scaffold
Counts Matrix QC
Plugin scaffold
RNA-seq Report Generator
Plugin scaffold
Alpha Diversity Analysis
Plugin scaffold
Beta Diversity PCoA
Plugin scaffold
Taxonomic Abundance Plots
Plugin scaffold
Differential Abundance
Plugin scaffold
MAG Quality Assessment
Plugin scaffold
Microbiome Report Generator
Plugin scaffold
Protein Quantification
Plugin scaffold
PTM Phosphoproteomics Analysis
Plugin scaffold
Protein Interaction Network
Plugin scaffold
Proteomics QC Report
Plugin scaffold
DIA Proteomics Analysis
Plugin scaffold
Proteomics Report Generator
Plugin scaffold
Tumor Mutational Burden
Calculate tumor mutational burden (mutations/Mb) with TMB-H/Intermediate/TMB-L classification
MSI Detection
Detect microsatellite instability status (MSI-H/MSI-L/MSS) from per-locus repeat length data
Tumor Purity Estimator
Estimate tumor purity and ploidy from copy number segment data using BAF-deviation analysis
Neoantigen Predictor
Simplified peptide-HLA binding score predictor for candidate neoantigens (illustrative, not validated)
Clinical Genomics Report
Combined HTML clinical report: TMB, top mutated genes, copy number profile, and MSI status
SV Annotation
Annotate structural variants with size category and interchromosomal classification; produces distribution plots
Isoform Detection Quantification
Plugin scaffold
Long-read Sequencing Report
Plugin scaffold
rMATS Splicing Analysis
Plugin scaffold
SUPPA2 Isoform Analysis
Plugin scaffold
Sashimi Plot Generator
Plugin scaffold
LeafCutter Splicing
Plugin scaffold
IRFinder Intron Retention
Plugin scaffold
Splicing Analysis Report
Plugin scaffold
Omics QC Report Generator
Generate QC reports from harmonized omics QC data
RNA-seq Analysis Intelligence
Differential expression and downstream intelligence from RNA-seq workflow outputs (DESeq2, QC, plots)
KEGG Search
Query KEGG pathways, compounds, genes, and diseases
Advanced Single Cell
Advanced single-cell integration and analysis
Exome Analysis
Exome sequencing pipelines and interpretation helpers
Omics QC Metrics Extractor
Extract and normalize QC metrics from raw omics datasets
Proteomics
Proteomics / Mass spectrometry analysis workflows
Genomics
37 app(s)
FASTQ Trimmer
Adapter trimming and quality filtering using fastp
FASTQ Quality Control (FastQC + MultiQC)
Standalone FASTQ QC using FastQC and MultiQC
Variant QC & Filtering
Stage-1 variant quality control and filtering for VCF files
CNVkit (Copy Number Analysis)
Copy number variation analysis using CNVkit with batch, reference, and segmentation workflows
VCF Liftover (hg19 ↔ hg38)
Genomic coordinate liftover using UCSC liftOver with chain files (hg19 ↔ hg38) with full RunStore + OmniObject integration
BEDTools Intersect
Genomic interval intersection using bedtools intersect for overlap and annotation workflows
Polygenic Risk Score (PRS) Builder
Build and evaluate Polygenic Risk Scores (PRS) from GWAS summary stats + cohort genotypes; produces PRS scores, weights, and evaluation plots.
eQTL Linker
Variant-to-gene eQTL linking and GWAS locus overlap visualization (LocusZoom-style).
SpliceAI Variant Annotation
Deep learning-based splice site effect prediction on VCF files using SpliceAI (Illumina)
Phasing & Haplotype Analysis
Cohort-, reference-, and trio-aware genotype phasing and haplotype analysis with QC and reproducible artifacts
Population PCA Structure
Plugin scaffold
Restriction Digest
Simulate restriction enzyme digestion and visualize fragments
ADMIXTURE Analysis
Plugin scaffold
ORF Finder
Find and translate open reading frames in a DNA sequence
FST Population Differentiation
Plugin scaffold
Linkage Disequilibrium Analysis
Plugin scaffold
Selection Scan iHS XP-EHH
Plugin scaffold
Variant Pathogenicity Classifier Fine-Tuner
Fine-tune a variant pathogenicity classifier on lab-specific curated variants
Nanopore Run QC
Plugin scaffold
Genome Assembly QC
Plugin scaffold
DeepVariant Variant Caller
DeepVariant (CPU/GPU) runner scaffold via TES/container runtime
Phenotype Association
Association analysis between genotypes and phenotypes (GWAS, PheWAS, covariate-aware models)
Rare Variant Burden Testing
Gene-based rare variant burden testing (SKAT, burden tests) with covariate-aware models and pathway enrichment
Read Simulator
Synthetic read simulator for WGS, WES, and RNA-seq. Supports single-end and paired-end layouts. Produces FASTQ and simulation manifest for benchmarking and testing pipelines.
Pathogenicity Scoring
Rank variants using SnpEff consequence/impact and optional predictors (future: CADD/REVEL/SpliceAI).
GWAS & Population Genetics
Population QC, ancestry analysis (PCA), and GWAS using containerized pipelines
GEO Search
Search NCBI GEO for datasets, series, and samples
GWAS Catalog Search
Search GWAS Catalog for variant-trait associations and studies
Gene Annotation
Gene & functional annotation utilities
Genome Viewer
IGV-style genome visualization plugin
Network Analysis
Network and graph analysis workflows
Object Transform Engine
VCF/TSV/JSON transformation engine with OmniObject support
OmniLink: Enhancer-to-Target Mapping
WIP: Variant → enhancer → gene mapping engine
Pathway Enrichment
Pathway and enrichment analysis workflows
SV/Fusion Circos (Interactive)
Interactive Circos visualization for structural variants and gene fusions with hover and filtering
Variant Annotation
VCF-based variant annotation pipelines
SRA/BioProject/BioSample Submission Manager
Prepare, validate, and submit sequencing data and metadata to NCBI SRA/BioProject/BioSample for publication.
Machine Learning
31 app(s)
OmniML Studio
Machine learning tutorials, experiments, and model development hub
Variant Effect Intelligence
Variant annotation, pathogenicity prediction, and functional impact ranking using ML
Single-Cell Omics Intelligence
Single-cell RNA/ATAC analysis with ML-based clustering, cell-type annotation, and state inference
Anomaly Detection Omics
Unsupervised anomaly detection in omics datasets
Auto ML Biomarker Discovery
Automated ML pipeline for biomarker selection from multi-omics data
Single-Cell Cell Type DL
Deep learning cell-type classification for single-cell RNA-seq using PyTorch
Deep Learning Variant Classifier
Deep learning model for pathogenic vs benign variant classification
Drug Response Predictor
ML model for drug sensitivity and response prediction
Drug Target Intelligence
Drug–target ML inference and ranking
Explainable AI Interpreter
SHAP/LIME based model explanation for biological insights
Gene Expression Regulatory AI
Deep learning for gene regulatory network inference
Histopathology Computer Vision
Whole-slide image preprocessing and CV inference
Multi-Omics Integration AI
MOFA+, SNF, and deep learning based multi-omics integration
Single Cell Trajectory Inference
AI-based cell trajectory and pseudotime analysis
Variant Pathogenicity Classifier (PyTorch)
MLP classifier over variant annotation features (CADD, gnomAD AF, conservation, consequence) predicting benign / VUS / pathogenic.
Structural Variant Classifier (1D-CNN)
1D CNN over binned read-depth log2-ratio signal, classifying windows as DEL / DUP / INV / NEUTRAL.
scRNA-seq Cell Type Classifier
MLP over Scanpy HVG/PCA embedding predicting cell type label.
scRNA-seq Batch Integration Autoencoder
Unsupervised autoencoder producing batch-corrected low-dimensional cell embeddings (scVI-lite style).
Histopathology Tumor Classifier (CNN)
Compact ResNet-style CNN over H&E patch tiles, classifying tumor vs normal.
Histopathology Nuclei Segmentation (U-Net)
U-Net segmentation producing nuclei masks plus per-image count/density.
Protein Function Classifier (ESM2 embeddings)
Fine-tuned classification head on frozen ESM2 embeddings predicting functional/GO category from sequence.
Protein Stability ΔΔG Predictor
MLP regression over ESM2 embedding deltas predicting the free-energy change (ddG, kcal/mol) of point mutations.
ADMET Property Predictor
Multi-task MLP over RDKit Morgan fingerprints predicting solubility, permeability, and hERG cardiotoxicity risk from SMILES.
Drug-Target Binding Affinity Predictor
MLP over ligand Morgan fingerprint + target protein ESM2 embedding predicting binding affinity (pKi/pIC50).
Protein Language Model Fine-Tuner
LoRA fine-tuning of ESM-2 on custom labeled protein sequences for function, localization, or stability prediction.
scRNA Foundation Model Fine-Tuner
Fine-tune a Geneformer-style rank-value transformer on lab-specific single-cell data for cell type annotation
DNA Sequence Foundation Model Fine-Tuner
LoRA fine-tuning of the Nucleotide Transformer DNA foundation model on custom labeled genomic sequences.
Histopathology Foundation Model Fine-Tuner
Fine-tuning of the Phikon histopathology foundation model on custom labeled tile images.
Chemistry Language Model Fine-Tuner
LoRA fine-tuning of the ChemBERTa SMILES foundation model on custom labeled molecules.
Antibody Language Model Fine-Tuner
LoRA fine-tuning of the AbLang antibody language model on custom labeled antibody sequences.
Biomedical Vision-Language Model Fine-Tuner
LoRA fine-tuning of the BiomedCLIP vision-language model on custom (image, caption) pairs.
Utilities
10 app(s)
Object Registry Explorer
Browse OmniObject registry: status, sizes, paths, and metadata
OmniBioAI Catalog
Unified platform catalog of tools, workflows, plugins, and compute backends with version and capability visibility.
Sample Sheet Generator
Plugin scaffold
Plate Layout Designer
Plugin scaffold
MultiQC Report Aggregator
Plugin scaffold
PDF Report Builder
Plugin scaffold
LIMS Integration
Integrate external LIMS (LIMS-X) with OmniBioAI for sample and project metadata
Collaboration
Multi-user collaboration, sharing, and activity
Run Inspector
Run provenance, reproducibility, and audit viewer
Circrna
3 app(s)
Clinical
3 app(s)
Clinical Report Generator
Generate auditable, clinician-ready reports from clinical insight pipelines (VCF, phenotype, evidence, literature)
Clinical Database Mapping
Maps filtered and scored variants to clinical databases (ClinVar, OMIM, PharmGKB) as a deterministic, auditable RunStore stage
REDCap Integration
Import patient cohorts and research data from REDCap. Export analysis results back to REDCap projects.
Core
1 app(s)
Data
1 app(s)
Drug Discovery
13 app(s)
Molecular Docking Analysis
Plugin scaffold
Binding Site Predictor
Plugin scaffold
ChEMBL Search
Search ChEMBL for drug compounds, targets, and bioactivities
Chemoinfo Intelligence
Structure-to-Insight analytics using RDKit and AI
Molecule Validation
Validate and canonicalize SMILES molecules using RDKit.
Molecular Descriptors
Compute all RDKit 2D descriptors and Morgan fingerprints.
ADMET Prediction
Rule-based ADMET property prediction from molecular descriptors.
Druglikeness Scoring
Score druglikeness with Lipinski, Veber, Egan, Ghose, REOS, and QED.
Toxicity Prediction
Structural alert-based toxicity prediction (Brenk, PAINS, hERG, Ames, DILI).
Target Prediction
Predict molecular targets using Morgan fingerprint similarity.
Pathway Mapping
Map predicted targets to KEGG/Reactome pathways.
Mechanism Analysis
LLM-powered mechanism of action synthesis from all upstream evidence.
Drug Report Generator
Self-contained HTML + JSON drug discovery insight report.
Epigenomics
22 app(s)
ATAC-seq Peak Calling
Plugin scaffold
TF Footprinting Analysis
Plugin scaffold
Differential Accessibility
Plugin scaffold
ATAC Motif Enrichment
Plugin scaffold
Chromatin Accessibility QC
Plugin scaffold
ATAC-seq Report
Plugin scaffold
DMR Detection Analysis
Plugin scaffold
Chromatin State Segmentation
Plugin scaffold
Hi-C Contact Map Analysis
Plugin scaffold
TAD Loop Caller
Plugin scaffold
Bisulfite-seq QC
Plugin scaffold
Epigenomics Report
Plugin scaffold
ChIP-seq QC Metrics
Extract normalized ChIP-seq QC metrics (FRiP, mapping, dup, peaks) from workflow outputs into OmniObjects.
ChIP-seq Peak Set Ops
Replicate-aware peak operations: overlap, consensus peak sets, and optional IDR integration.
ChIP-seq Peak Annotation
Annotate peaks to genes/features (promoter/intron/intergenic), generate tables and summary plots.
ChIP-seq Motif Analysis
Motif enrichment analysis from peak sequences (HOMER/MEME), returns top motifs and candidate regulators.
ChIP-seq Signal Plots
Generate deepTools plots (heatmaps, metaplots) from bigWig signal over peaks/TSS/regions.
ChIP-seq Differential Binding
Differential binding analysis between conditions (DiffBind/csaw), produces differential peaks and plots.
ChIP-seq Report Generator
Compile ChIP-seq QC + peak annotation + motifs + signal plots into a final auditable HTML/PDF report OmniObject.
JASPAR Search
Search JASPAR transcription factor binding profiles and PWM matrices
ATAC-seq Accessibility Classifier (1D-CNN)
1D-CNN over binned Tn5 coverage signal classifying windows as open/closed/intermediate chromatin — unlike atac_peak_calling's mean+k-sigma threshold, this is a learned classifier.
Nanopore Methylation Caller (1D-CNN)
1D-CNN over windowed raw nanopore current signal classifying per-position methylation state (unmethylated/methylated/ambiguous) — unlike methylation_qc's threshold on precomputed bisulfite beta values, or nanopore_qc/longread_report which never touch raw signal.
Infrastructure
5 app(s)
Infrastructure AI Copilot
AI-powered infrastructure intelligence, workflow diagnostics, and operational reasoning for OmniBioAI.
Zenodo Integration
Publish analysis results to Zenodo with DOI generation. Import public datasets from Zenodo. Supports open science and reproducible research.
AWS S3 Integration
Import datasets from AWS S3 buckets and export analysis results back to S3. Supports any S3-compatible storage including MinIO.
eLabFTW Integration
Export analysis results to eLabFTW electronic lab notebook. Create experiments, upload files, and add tags directly from OmniBioAI pipelines.
Benchling Integration
Import samples/sequences from Benchling and export analysis results back to Benchling
Metabolomics
15 app(s)
Peak Alignment
Retention time alignment and peak grouping across samples
Metabolite Annotation
Annotate features against HMDB, KEGG, and MassBank databases
Batch Effect Correction
Correct batch effects using ComBat or limma removeBatchEffect
Batch Effect Detection
Detect batch effects using PCA and clustering analysis
Biomarker Discovery
Random Forest and LASSO-based biomarker selection
Feature Matrix Builder
Build feature intensity matrix from aligned peaks
Metabolomics Data Importer
Import and convert raw metabolomics files (mzML, .raw, .wiff, .d) to standardized format
Missing Value Imputation
Impute missing values using kNN, min/2, or QRILC methods
Normalization
Normalize feature matrix using TIC, PQN, or quantile normalization
Outlier Detection
PCA-based sample outlier detection and flagging
Peak Detection
LC-MS peak detection using centWave/matchedFilter algorithms
Report Generator
Generate comprehensive HTML/PDF metabolomics analysis report
Metabolomics Sample QC
Sample quality control: TIC plots, missing values, injection order analysis
Statistical Analysis
t-test, ANOVA, fold-change analysis with multiple testing correction
MS/MS Spectrum Compound Classifier
MLP over binned MS/MS spectra classifying compound class directly from spectral patterns — unlike metabolomics_annotate's static m/z-to-database lookup, which never uses fragmentation patterns.
Microbiome
2 app(s)
Microbiome Taxonomic Classifier (1D-CNN)
1D-CNN over one-hot encoded sequence reads, classifying each read into a taxonomic label — unlike taxonomic_abundance, which only re-aggregates an already-classified OTU table.
AMR Gene Classifier (1D-CNN)
1D-CNN over one-hot encoded protein sequence predicting antimicrobial-resistance drug class (or none).
Orchestration
1 app(s)
Population Genetics
1 app(s)
Proteomics
2 app(s)
PTM Site Predictor (ESM2 windowed embeddings)
MLP on windowed ESM2 embeddings around candidate residues, predicting PTM type — unlike ptm_analysis, which only aggregates PTMs already identified by upstream mass spec, never reading sequence.
Enzyme EC-Number Classifier (ESM2)
Classification head on frozen ESM2 embeddings predicting a protein's top-level Enzyme Commission class (or non-enzyme).
Single Cell
12 app(s)
Cell-Cell Communication Visualization
Visualize ligand-receptor interactions and pathway enrichment across cell types
Clustering
Consumes a count matrix (upload or OmniObject), runs clustering (Scanpy), and registers clustered outputs.
Marker Identification
Deterministic identification of cluster-specific marker genes from clustered single-cell datasets
Scanpy Import
Convert 10x count matrix to AnnData for scRNA-seq analysis.
Single-Cell LOOM Viewer
Interactive visualization and annotation of single-cell datasets using LOOM format
Scanpy QC Metrics
Compute QC metrics and plots for scRNA-seq data.
Scanpy QC Filter
Apply QC thresholds to filter low-quality cells.
Scanpy Clustering
PCA / UMAP / Leiden clustering for scRNA-seq data.
Scanpy Markers
Rank marker genes per cluster for scRNA-seq data.
Single-Cell Annotation
Assign cell types to clusters and generate an annotation report.
Single Cell Analysis
scRNA-seq workflow and exploration
CITE-seq Multimodal Cell-Type Classifier
Dual-branch MLP fusing paired RNA + surface-protein (ADT) measurements to classify cell type.
Spatial
7 app(s)
QC Plots (Visium)
Generate Visium QC plots from Space Ranger outputs.
Threshold Recommendation (Visium)
Compute and validate QC thresholds and produce thresholds.json.
Spatial Analysis (Visium)
Filter, normalise, HVG, PCA, UMAP of Visium data via scanpy.
Spatial Clustering (Visium)
Leiden clustering on Visium AnnData via scanpy.
Spatial Marker Identification (Visium)
Identify cluster marker genes via rank_genes_groups.
Spatial Report Generation (Visium)
Generate final auditable HTML/PDF spatial transcriptomics report.
Spatial Domain Classifier (GAT)
Graph Attention Network over a spatial k-NN graph (built from physical coordinates, not expression similarity) classifying each spot into a spatial domain.
Structure
4 app(s)
Agentic PyMOL
Describe what you want to see in plain English — an AI agent drives PyMOL to render it
Protein Structure Visualizer
Plugin scaffold
Protein Evolution Analysis
Plugin scaffold
AlphaFold (Protein Structure)
Protein structure prediction using AlphaFold/ColabFold via local Docker execution