Docs tagged “quickstart”

Name a target tissue for per-serotype tropism reports with citations and no ranking, then codon-optimize a protein transgene against the 4.7 kb limit.

Five steps from a target SMILES to scored retrosynthesis routes — pick stocks and a policy, submit, then read score, steps and the purchasability flag.

Number an antibody sequence and read its CDRs with ANARCI in a few steps.

Paste VH/VL or name a therapeutic, pick the metrics, and read the composite developability score with charge, pI, aggregation and liability flags.

Point at a CSV, pick regression, hierarchical, dose_response or pkpd, set the outcome and predictors, then read r_hat and divergences before the posterior.

Call biophi_humanness for an OASis score and class, or biophi_humanize and biophi_graft to return a humanized VH/VL with the mutations made.

Step-by-step workflows for Mendelian randomization, fine-mapping, colocalization, and LD score regression.

Step-by-step workflows for CAR-T ScFv design, construct assembly, safety prediction, NK-CAR design, and KIR matching.

Start a conversation, submit queries, and understand AI responses in the Chat Workspace.

Ask Ivy in chat for measured activity against a target — name a ChEMBL ID like CHEMBL203, an activity type like IC50 and a nM cutoff, then read the pChEMBL rows.

Install with the curl script or npm, sign in with ivybloom auth login --browser, then fold a sequence with ivybloom run esmfold and download the result.

Search ClinicalTrials.gov by condition and filter by development phase.

Step-by-step workflows for guide RNA design, off-target analysis, and CRISPR screen hit identification.

Step-by-step workflows for FlowSOM clustering and IMC segmentation and spatial analysis.

Step-by-step workflows for ATAC-seq peak calling, ChIP-seq analysis, differential accessibility, and methylation profiling.

Step-by-step guide to generating protein embeddings with ESM-3 on the platform.

Step-by-step guide to generating your first molecules with GenMol on the platform.

Step-by-step workflows for gene lookup, pathway search, variant interpretation, and cross-database linking.

Paste a sequence, set the chain to H or L, and read back a humanness score, the closest human germline V gene, and the low-humanness positions to target.

Assign the germline V gene and read the annotation with IgBLAST in a few steps.

Generate an OT-2 serial dilution or cherry-picking protocol with opentrons_generate_protocol and download the Python file for the Opentrons App.

Step-by-step workflows for data preprocessing, metabolite annotation, differential analysis, and pathway enrichment.

Step-by-step workflows for taxonomic classification, community profiling, diversity analysis, and differential abundance testing.

Step-by-step guide to rescoring docked complexes with MM-GBSA on the platform.

Run a KA-Search over natural repertoires: set chain, species and region — full, cdr3 or cdr_all — then read ranked matches with identity, study and CDR3.

Step-by-step workflows for TMB/MSI calculation, MHC binding prediction, and neoantigen prediction.

Run search_patterns by element, then similarity_search on two_theta_values and intensities — cosine above 0.85 is a strong match, 0.70-0.85 is related.

Step-by-step guide to predicting binding sites on a protein structure with P2Rank on the platform.

Paste a sequence and set the chain type; Paragraph folds the antibody first, then returns paratope residues with a probability and region for each.

Download a PDB structure by ID or search it by name, review it in the 3D viewer, then chain it straight into DiffDock docking or P2Rank pocket prediction.

Protonate a structure at pH 7.4 with the amber force field, read the predicted pKa and histidine states, then download the PQR file for docking or APBS.

Step-by-step workflows for linker enumeration, ternary complex modeling, and degradation scoring.

Step-by-step workflows for searching PRIDE datasets, exploring EMDB cryo-EM structures, and retrieving detailed metadata.

Type a plain-English query, read the matching titles and abstracts off the canvas, then ask the model to pull the genes, compounds and diseases it names.

Simulate a pattern from a CIF with simulate_xrd, then run fit_background before refine_xrd, which needs its variance and both background CSVs.

Classify a reaction SMILES into a named class with an RXNO ID, add ORDerly catalyst, base, solvent and temperature suggestions, or batch a whole route.

Fingerprint one reaction SMILES or a batch from a retrosynthetic route, then search the reference index for the most similar known reactions.

Step-by-step workflows for batch correction with scVI, cell type annotation with scANVI, and doublet detection with SOLO.

Upload a spatial .h5ad and an annotated scRNA-seq reference, both as raw integer counts, then read per-spot proportions from obsm['nnls_proportions'].

Open a campaign in Studio, run one tool from its window, and find the result.

Step-by-step workflows for FBA simulation, metabolic model construction, and gene essentiality prediction.

Search for a protein in UniProt and chain the sequence into structure prediction.