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academic
156

research-grants

Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.

lamm-mit
lamm-mit
research
open
academic
156

peer-review

Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.

lamm-mit
lamm-mit
research
open
academic
156

literature-review

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

lamm-mit
lamm-mit
research
open
academic
156

serpapi

SerpApi search engine results API via curl. Use this skill to scrape Google, Bing, YouTube, and other search engines.

nicepkg
nicepkg
research
open
bioinformatics
156

gwas-database

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

lamm-mit
lamm-mit
research
open
bioinformatics
156

geniml

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

lamm-mit
lamm-mit
research
open
bioinformatics
156

jax-modal-analysis

3D tetrahedral FEM modal analysis of a membrane STL. Takes a binary STL (mm units) + material properties JSON, repairs surface mesh, generates tetrahedral volume mesh via TetGen, assembles 3D stiffness/mass matrices with jax-fem, solves the generalised eigenvalue problem, and reports eigenfrequencies + mode shapes. Returns artifact JSON with eigenfrequencies_hz, eigenfrequencies_khz, modes_in_range, target_range_pass, and paths to summary PNG and CSV.

lamm-mit
lamm-mit
research
open
bioinformatics
156

torchdrug

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

lamm-mit
lamm-mit
research
open
bioinformatics
156

scientific-schematics

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

lamm-mit
lamm-mit
research
open
bioinformatics
156

neuropixels-analysis

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

lamm-mit
lamm-mit
research
open
bioinformatics
156

alphafold-database

Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

pytdc

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

rowan

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

rdkit

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

stable-baselines3

Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

uma

Run structure relaxation and phonon calculations using Meta's UMA (Universal Materials Accelerator) via fairchem

lamm-mit
lamm-mit
research
open
computational-chemistry
156

deepchem

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

chai

Use when predicting molecular structures (proteins, nucleic acids, small molecules, and complexes) with the Chai-1 foundation model via local inference or the Chai Discovery API.

lamm-mit
lamm-mit
research
open
computational-chemistry
156

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

lamm-mit
lamm-mit
research
open
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