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End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level cou…
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summa…
Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.
Write and run custom ORCA input files for advanced electronic structure methods or settings not available through the SCINE wrapper, including multi-reference methods, excited states, relativistic eff…
Dock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking generated complexes.
Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
Predict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.
Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.
Design or audit the identification strategy for an observational study. Use when the task concerns estimands, causal assumptions, threats to identification, or defensible research design rather than m…
Use when creating, reading, or updating workflow checkpoint files (workflow-state.json, progress.log, init.sh) — the file-centric state system for cross-session computational workflows
Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.
Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.
Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.
Calculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.
Generate transition state structures for chemical reactions using React-OT.
Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.
run cellpose-based segmentation for common bioimage analysis tasks in python, cli, or gui workflows, including 2d, 3d, batch processing, model selection, parameter tuning, result export, and optional …
Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.
Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
Run a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.
Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
Scripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral plotting.
Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.