Platform capabilities

2143 research-facing analytical elements for computational biology validation.

Browse the 2143 research-facing platform elements DarwinOmics uses to reproduce submitted analyses, compare reported outputs, and generate structured validation reports.

739Models

650Tools

432Pipelines & Workflow Elements

223Visualizations

99Adapters

Browse by category

Catalog sections

Biology AI, statistical models, and predictive engines Models Sequence and protein language models, variant-effect predictors, structure predictors, cell and spatial models, drug-discovery models, and other ML components DarwinOmics can use to reproduce or compare computational analysis steps. ESMscGPTCellTypistAlphaFoldDNABERTVariant effect 739 available Executable analysis tools and native computational steps Tools QC, trimming, alignment, quantification, differential analysis, annotation, variant calling, proteomics, microbiome, image, and matrix operations with captured inputs, parameters, outputs, and provenance. FastQCSTARSalmonDESeq2GATKSAMtools 650 available

Workflow-scale analysis elements Pipelines & Workflow Elements nf-core/imported pipelines, Darwinomics executable pipeline contracts, Darwin catalog workflow wrappers, BioNeMo workflows, prototypes, and workflow engine support. The full count is workflow-scale elements; named imported pipelines are shown where the source is a complete workflow. nf-coreRNA-seqSingle-cellWGSATAC-seqBioNeMo 432 available Result views, plots, reports, and interactive inspection surfaces Visualizations Volcano plots, heatmaps, UMAP/PCA/t-SNE, genome views, protein and molecule viewers, networks, dashboards, quality reports, and comparison visualizations regenerated from supplied analysis artifacts. VolcanoHeatmapPCAUMAPGenome browser3D structure 223 available Data bridges, importers, exporters, and provenance handoffs Adapters FASTA, image, workflow, repository, provenance, and compute handoff adapters that move submitted evidence into DarwinOmics research data contracts without losing traceability. FASTAOME-ZarrGA4GHTerraOMEROProvenance 99 available

Live modules

Featured catalog entries

QC FastQC Run FastQC quality control only. Pipelines & Workflow Elements Runnable sequencing reads s-andrews/FastQC | 602 stars Darwin Starsolo Single-cell RNA-seq quantification using STARsolo: barcode demultiplexing, alignment, and count matrix generation Pipelines & Workflow Elements Runnable Workflow alexdobin/STAR | 2,216 stars Salmon Run Salmon 1.10.2 quasi-mapping quantification over a hash-pinned transcript/read research data artifact request and return exact transcript-level quantification rows. Tools Runnable Analysis tool COMBINE-lab/salmon | 901 stars Darwin DESeq2 Research-certified Darwin catalog wrapper over darwinomics-tool-deseq2. It emits exact DESeq2 1.52.0 default Wald fixture parity rows for the active certified count matrix and fails closed outside that certificate. Pipelines & Workflow Elements Adapter expression matrices thelovelab/DESeq2 | 465 stars GATK4 GATK4 supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Tools Runnable Analysis tool broadinstitute/gatk | 1,970 stars Nano Samtools Sort Nano Samtools Sort handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads samtools/samtools | 1,918 stars

AlphaFold2 Multimer AlphaFold2 Multimer applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Adapters Adapter protein or structure data google-deepmind/alphafold | 14,697 stars Beyond Esm2 Graph Enhanced Protein Sequence Modeling With Efficient Protein/nucleotide language model: Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient. From Huazhong University of Science and Technology,Fudan University,Northwestern Polytechnical University. Models Runnable Biology model facebookresearch/esm | 4,140 stars Darwin scGPT Generative pre-trained transformer for single-cell transcriptomics with cell type annotation and perturbation prediction. Pipelines & Workflow Elements Runnable Workflow bowang-lab/scGPT | 1,589 stars

Celltypist Celltypist renders dimensionality-reduction views from matrices or embeddings for clustering, separation, and quality-control review. Models Runnable Biology model Teichlab/celltypist | 491 stars Nano Volcano Plot Nano Volcano Plot renders volcano plots from differential-analysis statistics, making effect size and significance patterns inspectable in the validation report. Visualizations Runnable Visualization ComplexHeatmap ComplexHeatmap renders heatmaps from expression, feature, or tabular matrices so clustered patterns and annotations can be compared against the submitted figure. Visualizations Runnable Visualization

UMAP Viewer UMAP Viewer renders dimensionality-reduction views from matrices or embeddings for clustering, separation, and quality-control review. Visualizations Runnable Visualization lmcinnes/umap | 8,216 stars Darwin RNA-seq Complete RNA-seq analysis: QC, trimming, alignment, quantification, and differential expression Pipelines & Workflow Elements Runnable Workflow Rapids Singlecell Rapids Singlecell supports single-cell analysis, annotation, or embedding workflows with reproducible matrix and metadata handling. Adapters Runnable sequencing reads GPU WGS WGS pipeline using NVIDIA Parabricks for 30-50x faster alignment and variant calling. Pipelines & Workflow Elements Runnable Workflow GA4GH WES Client Validate one or more research data artifact rows, serialize each as the WES 1.0.1 RunWorkflow multipart/form-data request, POST to {wes_base_url}/runs, and parse the server-issued RunId into research data artifact. Adapters Runnable Data adapter Atac Footprint Plot Atac Footprint Plot turns tabular analysis results into report-ready plots that can be checked against the figures in a submitted study. Visualizations Runnable aligned sequencing reads Darwin Diaproteomics Data-independent acquisition (DIA) proteomics analysis using spectral library generation, OpenSWATH, and PyProphet for quantitative proteomics. Pipelines & Workflow Elements Runnable Workflow AICSImageIO Import AICSImageIO Import processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Adapters Runnable image or spatial data Anvil Normalize authenticated AnVIL Terra entity records and Gen3 flat-file index records into deterministic research data artifact rows using pyAnVIL 0.1.1rc3 entity-key and drs_file semantics. Adapters Runnable Data adapter Bio Formats Import Bio Formats Import processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Adapters Runnable image or spatial data Citation Provenance Citation Provenance converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter FAIRDOM Seek Canonicalize FAIRDOM-SEEK/ISA-Tab metadata into exact research data artifact key/value rows while preserving i_, s_, and a_ scope, nullability, and strict YYYY-MM-DD dates. Adapters Runnable Data adapter