Docs tagged “inputs”
37 Ivy Biosciences docs pages tagged inputs.
- AAV inputs and parameters
Target tissue, serotype and payload limit for the literature lookup; a protein sequence for the optimizer. No species, route or promoter parameter exists.
- ANARCI inputs and parameters
Submit up to 100 variable-region sequences and pick the scheme that sets CDR boundaries — imgt, chothia, kabat, aho or wolfguy — or name a known antibody.
- Antibody developability inputs and parameters
Sequences, the metrics enum, structure input, and numbering scheme for the developability assessment.
- Bayesian Optimization inputs and parameters
Data format, model types, priors, and sampler settings for Bayesian statistical and PK/PD modeling.
- BioPhi inputs and parameters
VH/VL sequences, mode, target humanness, and residues to preserve for BioPhi.
- Causal Genomics inputs and parameters
GWAS summary statistics formats, instrument selection criteria, LD reference panels, and configuration options for all causal genomics tools.
- Cell & Gene Therapy inputs and parameters
Target antigens, ScFv sequences, signaling domain options, HLA types, KIR genotypes, and configuration options for all cell therapy tools.
- ClinicalTrials.gov v2 API parameters: phase and status
Query, condition, drug, status and limit parameters over the ClinicalTrials.gov v2 API, plus how to filter by phase when the tool has no phase parameter.
- CRISPR inputs and parameters
Gene targets, PAM types, scoring models, mismatch thresholds, and screen analysis options for all CRISPR tools.
- Cytometry inputs and parameters
File formats, marker panels, FlowSOM clustering parameters, and segmentation options for the cytometry tools.
- Epigenomics inputs and parameters
BAM file requirements, peak calling parameters, genome assemblies, statistical thresholds, and methylation options for all epigenomics tools.
- ESM-3 inputs and parameters
Sequence formats, model size options, and embedding configuration for ESM-3.
- GenMol inputs and parameters
Run modes, fragment constraints, SMILES formats, and quality filter configuration for GenMol.
- Genomics inputs and parameters
Query formats, database selection, organism codes, and filter options for all genomics tools.
- Humatch inputs and parameters
Up to 50 sequences, the chain_type that picks the heavy or light model — mislabel it and the score is meaningless; the threshold moves only the human call.
- IgBLAST inputs and parameters
Sequences, organism, domain system, and alignment options for IgBLAST.
- Lab Automation inputs and parameters
Protocol types, labware definitions, pipette configurations, and experiment parameters for all lab automation tools.
- Metabolomics inputs and parameters
Data formats, normalization methods, annotation databases, and filter options for all metabolomics tools.
- Metagenomics inputs and parameters
FASTQ formats, database selection, diversity metrics, statistical methods, and configuration options for all metagenomics tools.
- MM-GBSA inputs and parameters
Complex structures, the solvent model, and minimization toggle for MM-GBSA calculations.
- OAS search inputs and parameters
Sequences, chain, species, region, threshold, and database tier for OAS search.
- Oncology Analytics inputs and parameters
VCF formats, HLA types, peptide sequences, and configuration options for the oncology analytics tools.
- OpXRD inputs and parameters
Search filters, similarity queries, and operation configuration for OpXRD.
- P2Rank inputs and parameters
PDB formats, model selection, and visualization options for P2Rank pocket prediction.
- Paragraph inputs and parameters
Up to 20 sequences and the probability threshold that decides which residues are paratope — plus why only imgt works, since a chothia request is rejected.
- PDB Search inputs and parameters
Input formats, parameters, and validation for PDB structure search and download.
- PDB2PQR inputs and parameters
PDB structures, pH settings, force field options, and processing flags.
- PROTAC inputs and parameters
Warhead SMILES, E3 ligand structures, linker constraints, and scoring options for all PROTAC design tools.
- Proteomics inputs and parameters
Query formats, organism filters, instrument filters, PTM filters, and resolution thresholds for PRIDE and EMDB tools.
- PubMed Search inputs and parameters
Input formats, parameters, and validation for PubMed literature search.
- PyWPEM inputs and parameters
Pick one of 14 operations, then supply an XRD intensity CSV, a CIF by URL or inline text, a wavelength preset such as CuKa1Ka2, and the two-theta range.
- Reaction Classifier inputs and parameters
Pass a reactants>>products SMILES, then set confidence_threshold, include_conditions, include_atom_mapping or include_template — 1 to 50 per batch.
- RXNFP inputs and parameters
Reaction SMILES format and parameters for fingerprinting and similarity search.
- scvi-tools inputs and parameters
AnnData requirements, model selection, training configuration, covariate options, and output controls.
- Spatial Omics inputs and parameters
Spatial data formats, reference atlases, and configuration options for the spatial omics tools.
- Systems Biology inputs and parameters
Model formats, objective functions, media conditions, knockout specifications, and configuration options for all systems biology tools.
- UniProt Search inputs and parameters
Ask Ivy in chat with an accession, a gene symbol or a free-text query, name an organism to filter by, and ask for the sequence when you need it.