DarwinOmics.ai

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
All catalog sections
99Adapters available

Browse Adapters

Every adapters entry

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 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 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 BAM Index BAM Index handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads BAM Merge BAM Merge handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable sequencing reads BAM Sort BAM Sort handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads samtools/samtools | 1,918 stars BAM To CRAM BAM To CRAM handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads BAM To FASTQ BAM To FASTQ handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads BCF To VCF BCF To VCF supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Adapters Runnable variant calls BED Intersect Native research data artifact adapter implementing deterministic BEDTools intersect-style half-open interval overlap for two in-memory interval sets labeled A: and B: in the name column. Adapters Runnable Data adapter BED Merge Research-certified native BEDTools merge equivalent over normalized parsed BED intervals. Adapters Runnable Data adapter BED Sort BED Sort converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. 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 Codonfm Codonfm converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter CRAM To BAM CRAM To BAM handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable sequencing reads CSV To H5AD CSV To H5AD converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Darwinomics Cgt Adverse Event Harmonize Harmonizes adverse event records into clinical event research data artifact rows. Adapters Runnable Data adapter Darwinomics Cgt Batch Record Normalize Normalizes batch records and process parameters into manufacturing run rows. Adapters Runnable Data adapter Darwinomics Cgt Efficacy Endpoint Harmonize Normalizes efficacy endpoint tables into clinical endpoint research data artifact rows. Adapters Runnable Data adapter Darwinomics Cgt Phenotype Flow Panel Ingest Converts flow cytometry panel results into structured phenotype panel rows. Adapters Runnable Data adapter Darwinomics Cgt Sample Manifest Ingest Converts sample sheets and assay manifests into research data artifact sample manifest rows. Adapters Runnable sample metadata Darwinomics Cgt Vector Batch Manifest Ingest Normalizes vector lot, construct, production, and inventory metadata into vector batch rows. Adapters Runnable Data adapter Darwinomics Dcrf Adapters The bridges between the outside world and research data artifact. Every file that enters the system goes through an adapter: FASTQ, BAM, VCF, TSV, H5AD, GFF3, Parquet, and 35 more formats. Adapters Runnable Data adapter Darwinomics Doc Docling Parser Darwinomics Doc Docling Parser converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Darwinomics Doc Grobid Scholar Parser Darwinomics Doc Grobid Scholar Parser converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Darwinomics Doc Landingai Ade Provider Darwinomics Doc Landingai Ade Provider converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Darwinomics Doc Liteparse Provider Rust-native LiteParse-compatible fast document parser that emits research data artifact document layout JSON for paper-reading pre-processing and model context construction. Adapters Runnable Data adapter Darwinomics Doc Llamaextract Provider Darwinomics Doc Llamaextract Provider converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Darwinomics Doc Llamaparse Provider Rust-native LlamaParse-compatible document parser that converts supplied paper text, source JSON, local files, PDF bytes, tables, figures, and references into research data artifact document layout JSON. Adapters Adapter Data adapter Darwinomics Doc Marker Parser Darwinomics Doc Marker Parser converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Darwinomics Doc Markitdown Parser Darwinomics Doc Markitdown Parser converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Darwinomics Doc Mineru Parser Darwinomics Doc Mineru Parser converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Darwinomics Doc Unstructured Parser Darwinomics Doc Unstructured Parser applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Adapters Adapter Data adapter Darwinomics Doc Vlm Structure Parser GROBID replacement: sends page images to Qwen3-VL-30B on OpenRouter with json_schema strict. Adapters Runnable Data adapter Darwinomics Paper Figure Pdf Cropper Crops figure regions from PDF using bounding boxes. Pure Rust, no AI. Adapters Runnable Data adapter Darwinomics Paper Figure Vlm Extractor Chart data extraction: sends cropped chart images to Qwen3-VL-235B on OpenRouter. Adapters Runnable Data adapter Darwinomics Pdf Page Renderer Renders PDF pages to PNG images using pdfium. Pure Rust, no AI. Adapters Runnable Data adapter Darwinomics Proto Database AlphaFold Db Darwinomics Proto Database AlphaFold Db 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 Darwinomics Proto Database Alphamissense Db Darwinomics Proto Database Alphamissense Db converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter google-deepmind/alphafold | 14,697 stars Darwinomics Proto Database Ccd Lookup Darwinomics Proto Database Ccd Lookup supports molecular design or docking analysis with structured inputs, scored outputs, and provenance for review. Adapters Adapter Data adapter Darwinomics Proto Database Ensembl Darwinomics Proto Database Ensembl converts incoming research evidence into sequence data while preserving traceability for the validation run. Adapters Adapter sequence data Darwinomics Proto Database Interproscan Darwinomics Proto Database Interproscan converts sequence data into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter sequence data Darwinomics Proto Database Ncbi Darwinomics Proto Database Ncbi converts incoming research evidence into sequence data while preserving traceability for the validation run. Adapters Adapter sequence data Darwinomics Proto Database Pdb Darwinomics Proto Database Pdb applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Adapters Adapter protein or structure data Darwinomics Proto Database Pubchem Darwinomics Proto Database Pubchem supports molecular design or docking analysis with structured inputs, scored outputs, and provenance for review. Adapters Adapter Data adapter Darwinomics Proto Database Sequence Fetch Darwinomics Proto Database Sequence Fetch converts incoming research evidence into sequence data while preserving traceability for the validation run. Adapters Adapter sequence data Darwinomics Proto Database Uniprot Darwinomics Proto Database Uniprot converts incoming research evidence into sequence data while preserving traceability for the validation run. Adapters Adapter sequence data Darwinomics Provider BioNeMo NIM Darwinomics Provider BioNeMo NIM converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter NVIDIA-BioNeMo/bionemo-recipes | 806 stars Darwinomics Provider Proto Mcp Darwinomics Provider Proto Mcp converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter 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 FASTA To Sequence Parses plain-text UTF-8 FASTA research data artifact rows into research data artifact rows. Adapters Runnable sequence data FASTQ Interleave FASTQ Interleave converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter FASTQ To BAM FASTQ To BAM handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable sequencing reads GA4GH TES Client GA4GH TES Client converts sample metadata into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable sample metadata 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 GFF To BED Native deterministic GFF3-to-BED adapter. Each research data artifact value contains one complete UTF-8 GFF3 v3 document; the output value is exact BED text matching pinned gffread v0.12.9 for the certified transcript/exon/CDS subset. Adapters Runnable Data adapter GPU Container Executor GPU Container Executor converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter GTF To GFF3 Research-certified native research data artifact GTF2.2-to-GFF3 normalizer pinned to GenomeTools gt gtf_to_gff3 fixture semantics. Adapters Runnable Data adapter H5AD To CSV H5AD To CSV converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Huggingface Gated Models Huggingface Gated Models converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Inline Image To Dcrfimage Inline Image To Dcrfimage processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Adapters Runnable image or spatial data iRODS Fail-closed iRODS AVU request adapter analysis element. The checked-in two-column research data artifact interface is insufficient to represent the official iRODS metadata operation, entity type, target name, and optional units; execution... Adapters Runnable sample metadata Isa Tools Isa Tools converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Labkey Normalize LabKey field names to lower camel case and infer each non-null scalar in authoritative LabKey 24.3 Date, Integer, Double, Boolean, String order. Adapters Runnable Data adapter Loom To H5AD Loom To H5AD converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Msa Search Msa Search converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter MTX To H5AD MTX To H5AD converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Mzml To Mgf Mzml To Mgf converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Mzxml To Mzml Mzxml To Mzml converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Nemo Agent Toolkit Nemo Agent Toolkit converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter NVIDIA-BioNeMo/bionemo-recipes | 806 stars Nifti To Mgh Nifti To Mgh converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter OME Zarr Export OME Zarr Export processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Adapters Runnable image or spatial data OME Zarr Import OME Zarr Import processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Adapters Runnable image or spatial data OMERO OMERO processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Adapters Runnable image or spatial data Open Shell Runner Open Shell Runner converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter openBIS openBIS converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Openfold3 Openfold3 applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Adapters Adapter Data adapter aqlaboratory/openfold | 3,391 stars Pangenome Deepvariant Pangenome Deepvariant handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads google/deepvariant | 3,740 stars Parabricks Fq2bam Parabricks Fq2bam handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable Data adapter Pdb To Mmcif Pdb To Mmcif converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Proteina Complexa Proteina Complexa applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Adapters Adapter Data adapter Proto Language Proto Language converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Proto Tools Proto Tools converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Python Tool Env Python Tool Env converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Adapter Data adapter Rapids Singlecell Rapids Singlecell supports single-cell analysis, annotation, or embedding workflows with reproducible matrix and metadata handling. Adapters Runnable sequencing reads Raw To Mzml Raw To Mzml converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter REDCap REDCap converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Result Normalizer Result Normalizer converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter SAM To BAM SAM To BAM handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable sequencing reads SRA To FASTQ SRA To FASTQ converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Terra Fail-closed deterministic research data artifact projection with exact Arrow schema, canonical entity:/attribute: keys, null preservation, bounded values, stable deduplication, and reserved-identifier validation. Adapters Runnable Data adapter Tool Schema Importer Tool Schema Importer converts incoming research evidence into DarwinOmics-ready evidence while preserving traceability for the validation run. Adapters Runnable Data adapter Universal Deepvariant Universal Deepvariant handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads google/deepvariant | 3,740 stars VCF Annotate VCF Annotate handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads VCF Index VCF Index handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads VCF Merge VCF Merge handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads VCF Sort VCF Sort handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Adapters Runnable aligned sequencing reads VCF To BCF VCF To BCF supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Adapters Runnable variant calls