Docs tagged “outputs”

Published tropism reports per serotype — tissue, level, model, citation — in alphabetical order with no score, plus the aav_packaging_feasible go/no-go.

Numbered positions, CDR and framework regions, and germline genes from ANARCI.

TAP, charge, pI, aggregation, immunogenicity, viscosity, and liabilities from the developability assessment.

Parameter posteriors, HDI intervals, diagnostics, and model comparison metrics from a Bayesian fit.

Humanness scores, classification, humanized sequences, and mutations from BioPhi.

Read the trials array — nct_id, phase, status, enrollment, sponsor_type and interventions — plus the PHASE1 to PHASE4 and RECRUITING status vocabularies.

Embeddings, attention maps, contact predictions, and function annotations from ESM-3.

Humanness scores, flagged positions, and closest germline from Humatch.

Germline V gene hits and framework-mutation counts from IgBLAST, for amino-acid antibody sequences.

Causal estimates, credible sets, colocalization posteriors, and diagnostic statistics.

ScFv candidates, CAR construct designs, safety scores, manufacturing feasibility, KIR match results, and cytotoxicity predictions.

Guide RNA tables, on-target scores, off-target site reports, and CRISPR screen gene rankings.

FlowSOM cluster assignments, segmentation masks, and spatial interaction scores.

Peak tables, differential regions, methylation calls, quality metrics, and statistical significance for all epigenomics tools.

Generated molecules, quality metrics, SAFE fragments, and downloadable artifacts from GenMol.

Gene records, pathway results, variant classifications, association scores, and cross-database links.

Generated Python protocols, experiment status updates, and result formats from Opentrons and Adaptyv Bio tools.

Preprocessed feature tables, annotated metabolites, differential results, and pathway enrichment scores.

Taxonomy reports, abundance profiles, diversity indices, distance matrices, and differentially abundant taxa.

What an MM-GBSA job returns on this platform, and why there is no binding free energy, binding classification or Kd estimate in it.

TMB values, MSI status, MHC binding predictions, and neoantigen rankings.

Matched patterns, fingerprints, statistics, and downloadable artifacts.

Pocket scores, druggability classification, residue lists, and PyMOL visualization scripts from P2Rank.

A PQR file with partial charge and radius in the occupancy and B-factor columns, a PROPKA pKa table with HID, HIE and HIP assignments, and a net charge.

Linker libraries, ternary complex coordinates, DC50 predictions, Dmax scores, and hook effect assessments.

PRIDE project metadata, file listings, EMDB entry details, and cryo-EM reconstruction parameters.

Read rp, rwp, convergence_flag and per-phase mass and volume fractions from a refine_xrd result, and why goodness of fit is always null for this tool.

Reaction classes, conditions, templates, atom maps, and similar reactions.

A 256-dimensional float vector per reaction, matches ranked by cosine similarity, and the score bands from very similar to no meaningful similarity.

Latent embeddings, UMAP coordinates, differential expression results, model checkpoints, and quality metrics.

mean_proportions per cell type in the summary, the spots-by-cell-types matrix in obsm['nnls_proportions'], and the is_heuristic caveat on every result.

Flux distributions, growth rates, essentiality classifications, shadow prices, and model construction summaries.

Ranked matches with identity, study, species, and context from OAS search.

Paratope residues, per-residue probabilities, and regions from Paragraph.

Result interpretation and data formats for PDB structure search and download.

Read pmid, title, abstract, authors and journal per article — plus the doi, pmcid and mesh_terms that only pubmed_search returns, never advanced search.

Read entry_type, function, GO terms and feature positions off each entry, then follow cross_references to PDB, ChEMBL and AlphaFold or fold the sequence.