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Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downl…
Vision-language pre-training framework bridging frozen image encoders and LLMs. Use when you need image captioning, visual question answering, image-text retrieval, or multimodal chat with state-of-th…
Guides researchers through structured ideation frameworks to discover high-impact research directions. Use when exploring new problem spaces, pivoting between projects, or seeking novel angles on exis…
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.
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analys…
Autonomous VTI sourcing. Discovers popular repositories that depend on a target SDK, fans out a fleet of subagents to scout each one for silent footguns, proves every candidate RED→GREEN, auto-promote…
Review branch changes against `master` using a diff-to-master workflow that emphasizes correctness, regressions, API breaks, side effects, and missing tests. Use when the user asks to review a branch …
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.
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Sends an agent on a scouting mission to find real-world coding traps (footguns in popular SDKs/protocols), synthesize the finding into a proven brainblast rule pack, and submit it to the pack registry…
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.