lamm-mit
- 209 skills
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- ▌ Chladni Physics · lamm-mit bundleRun a physics-based Chladni plate simulation for driven damped rectangular or square thin plates with material properties, plate dimensions, drive frequency, drive location, damping, modal response, and sand-particle settling. Use when asked for more realistic Chladni movies, physical resonance simulations, sand migration to nodal lines, material/thickness/frequency-controlled Chladni figures, or scientifically defensible Chladni artifacts beyond stylized analytic visuals. Produces text-free PNGs, sand-settling GIFs, plate-vibration GIFs, modal frequency CSV, physics NPZ data, parameters JSON, summary JSON, caption, and README by running a bundled Python simulator.
- ▌ Graphml Deep Analysis · lamm-mit bundleAnalyze Graph-PRefLexOR and Graph Explorer GraphML snapshots for deep scientific ideation insight. Use when a user selects or uploads a .graphml file and asks about graph structure, communities or modules, bridge concepts, critical connectors, relation chains, novelty or opportunity gaps, run provenance, or next research questions.
- ▌ Morphogenesis Postcard · lamm-mit bundleGenerate deterministic science-art postcard PNGs inside a shell/container skill environment. Use when asked for morphogenesis visuals, reaction-diffusion art, Turing patterns, dynamics-inspired scientific social posts, prompt-written visual rules/code, or reliable 4B-model-friendly visual artifacts. Always writes an inspectable Python visual-rule file, then renders PNG, parameters JSON, caption text, and README with the bundled renderer.
- ▌ Reaction Diffusion Poster · lamm-mit bundleCreate deterministic science-art visuals from Gray-Scott reaction-diffusion dynamics. Use when asked for Turing patterns, morphogenesis, dynamics art, reaction-diffusion simulations, or social-post-ready scientific images. Produces PNG posters, simulation data, captions, and a README by running a bundled Python renderer.
- ▌ Torchsim · lamm-mit bundleComprehensive TorchSim / torch-sim atomistic simulation skill for molecular dynamics, relaxation, high-throughput MLIP workflows, trajectory generation, trajectory analysis, validation, and movie production for materials systems.
- ▌ Beam Mechanics · lamm-mit bundleRun simple dimensionless 1D Euler-Bernoulli beam mechanics with selectable boundary conditions, point forces, distributed loads, point moments, springs, plots, CSV/JSON results, and deformation GIFs. Use when asked to analyze a simple beam, cantilever, fixed-fixed beam, overhang, support reactions, shear/moment/deflection plots, or a small educational beam mechanics movie/artifact.
- ▌ Chladni Plates · lamm-mit bundleCreate high-resolution Chladni plate resonance visuals and animations from analytic vibrating-plate mode superpositions. Use when asked for Chladni figures, nodal-line sand patterns, sound-wave or resonance visualization, vibrating square/rectangular/circular plates, cymatics-inspired scientific art, physics demonstration images, or GIF movies of plate dynamics. Produces text-free PNG images, GIF animations, frame sequences, field data, parameters JSON, captions, and README by running a bundled Python renderer.
- ▌ Fracture Mechanics · lamm-mit bundleRun parameterized 2D lattice fracture simulations from the Fracture and Mechanics notebook as offline artifacts. Use when asked to simulate a pre-cracked triangular lattice, Mode I tension, Mode II shear, Morse/Lennard-Jones/MLIP pair potentials, temperature effects, strain-rate effects, crack propagation, stress-strain curves, or fracture movies. Produces an animated movie, stress-strain plot, final lattice image, CSV data, JSON run metrics, and README by running a bundled Python script.
- ▌ Hierarchical Topopt · lamm-mit bundleRun fast 2D SIMP topology optimization with flexible boundary conditions, lightweight STL exports, and optional STL turntable renderings. Use when asked to optimize cantilevers, beams, bridges, plates, tension/shear strips, custom support/load layouts, density fields, compliance minimization, profile/flat/multimaterial STL meshes, polished STL previews, or rotating GIFs of optimized geometry. Produces density plots/data, boundary-condition previews and resolved node/DOF JSON, optimization history, summary files, optional STL meshes, and optional STL render artifacts by running bundled Python scripts.
- ▌ Ase · lamm-mit bundleAtomic Simulation Environment (ASE) for computational materials science. Perform DFT calculations, geometry optimization, band structure analysis, molecular property prediction, and periodic structure simulations. Supports VASP, MOPAC, Quantum ESPRESSO backends. For quick semi-empirical quantum chemistry, use mopac. For classical molecular dynamics, use openmm.
- ▌ Cas · lamm-mit bundleLook up chemicals in CAS Common Chemistry (name, CAS RN, SMILES, InChI; ~500k compounds)
- ▌ Dft · lamm-mit bundleSubmit, monitor, and retrieve DFT calculations on Artemis/SLURM via DREAMS framework
- ▌ Hpc · lamm-mit bundleSLURM HPC job management on Artemis — write submission scripts, submit jobs, monitor status, retrieve results
- ▌ Pdb · lamm-mit bundle3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.
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- ▌ Uma · lamm-mit bundleRun structure relaxation and phonon calculations using Meta's UMA (Universal Materials Accelerator) via fairchem
- ▌ Chai · lamm-mitUse 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.
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- ▌ XLSX · lamm-mit bundleExtract and preview data from Excel and CSV spreadsheets for scientific analysis
- ▌ Arxiv · lamm-mit bundleSearch ArXiv for scientific preprints in biology, chemistry, and related fields
- ▌ Blast · lamm-mit bundleSearch NCBI BLAST for sequence homology and find similar sequences in biological databases
- ▌ Boltz · lamm-mitUse when predicting biomolecular structures (proteins, RNA, DNA, ligands) with the open-source Boltz diffusion model as an alternative to AlphaFold3.
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- ▌ Mopac · lamm-mit bundleSemi-empirical quantum chemistry with MOPAC. Fast QM calculations for geometry optimization, properties, activation barriers, reaction pathways. Methods PM6, PM7, PM6-D3H4X for 1000x faster than DFT. For full DFT accuracy, use ase. For classical MD, use openmm.
- ▌ Askcos · lamm-mit bundleRetrosynthetic template relevance prediction using a locally deployed ASKCOS TorchServe service. Returns ranked precursor suggestions with confidence scores from 5 template sets (reaxys, pistachio, pistachio_ringbreaker, bkms_metabolic, reaxys_biocatalysis). Requires local deployment at http://localhost:9410.
- ▌ Chembl · lamm-mit bundleSmall-molecule drug lookup by exact drug name or ChEMBL ID. Query MUST be a single drug name or ID — 1 to 3 words maximum. Valid examples: 'sotorasib', 'imatinib', 'ibrutinib', 'CHEMBL25', 'AMG 510'. If the topic is 'sotorasib KRAS G12C', the correct query is 'sotorasib'. If the topic is 'BTK inhibitors in CLL', search PubMed first to get a specific drug name, then query ChEMBL with that name. Strip protein names, mutation labels, and mechanism words — pass only the compound name.
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- ▌ Dreams · lamm-mit bundleAgentic materials discovery and DFT simulation framework using ASE, Quantum ESPRESSO, and Claude LLMs via LangGraph.
- ▌ Fabric · lamm-mit bundlePattern-based analysis using Fabric's 242+ specialized prompts for summarizing papers and extracting insights
- ▌ Openmm · lamm-mit bundleOpenMM molecular dynamics engine for protein and ligand simulations. Run NVE/NVT/NPT ensembles, compute free energies, analyze dynamics. Supports AMBER, CHARMM, OPLS force fields and GPU acceleration. For classical MD with periodic systems, use ase. For quick quantum chemistry, use mopac.
- ▌ Phonon · lamm-mit bundleCompute phonon properties and assess dynamic stability using ML potentials via phonopy
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- ▌ Scvelo · lamm-mitRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
- ▌ Adaptyv · lamm-mit bundleCloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
- ▌ Datamol · lamm-mit bundlePython cheminformatics library (RDKit wrapper). Input: SMILES strings you already possess. Output: computed molecular properties, fingerprints, conformers, clustering. Does NOT retrieve compounds from any database — querying by topic name returns only a metadata stub. Use pubchem or chembl to obtain SMILES first, then pass those SMILES here.
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- ▌ Molfeat · lamm-mit bundleMolecular ML featurization library (100+ featurizers: ECFP, descriptors, ChemBERTa). Input: SMILES strings you already possess. Output: numerical feature vectors for QSAR/ML models. Does NOT retrieve compounds from any database — querying by topic name returns only a metadata stub. Use pubchem or chembl to obtain SMILES first, then featurize here. For ADMET predictions use tdc.
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- ▌ Softjax · lamm-mit bundleSoft differentiable drop-in replacements for non-differentiable JAX functions (abs, relu, sort, argmax, comparison, logical operators, etc.) with adjustable softening strength.
- ▌ Uniprot · lamm-mit bundleProtein sequence, function, and annotation lookup. Query MUST be a bare gene symbol or protein name — 1 to 3 words maximum. Valid examples: 'KRAS', 'EGFR', 'BTK', 'TP53', 'Bruton tyrosine kinase', 'P01116'. If the topic is 'sotorasib KRAS G12C', the correct query is 'KRAS'. If the topic is 'imatinib BCR-ABL resistance', the correct query is 'BCR-ABL'. Strip the drug name, mutation label, and all mechanism words — pass only the protein or gene name.
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- ▌ CSV Read · lamm-mit bundleRead a CSV or XLSX file and return columns, shape, dtypes, and first N rows as JSON.
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- ▌ Sequence · lamm-mit bundleAnalyze biological sequences using Biopython - translate, align, parse FASTA/GenBank
- ▌ Symtorch · lamm-mit bundleApproximate deep learning model components with symbolic equations using PySR
- ▌ Alphafold · lamm-mitUse when running AlphaFold2 predictions on custom protein sequences, validating designed sequences via self-consistency, predicting binder-target complexes, or interpreting AF2 confidence metrics (pLDDT, pTM, ipTM).
- ▌ Biopython · lamm-mit bundleComputational molecular biology library (sequence I/O, alignment, phylogenetics). Input: FASTA/GenBank/PDB files you already have. Output: parsed sequences, alignments, phylogenetic trees, structural analysis. Does NOT search databases — invoking by topic returns only a placeholder stub. For literature use pubmed, for protein lookup use uniprot, for sequence homology use blast.
- ▌ Geomaster · lamm-mitComprehensive geospatial science skill covering 70+ topics in remote sensing, GIS, spatial analysis, and machine learning for Earth observation. Processes satellite imagery (Sentinel, Landsat, MODIS), vector/raster data, point clouds. Supports 8 programming languages with 500+ code examples.
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- ▌ Paperclip · lamm-mit bundleOnboard and manage Paperclip AI for research-paper knowledge and agent orchestration
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- ▌ Diagramming · lamm-mit bundleGenerate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows
- ▌ Doc To Lora · lamm-mit bundleA method to instantly internalize document contexts into language models using LoRA without fine-tuning.
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- ▌ Job Results · lamm-mit bundleRead and parse results from completed SLURM jobs — check status, retrieve output, filter candidates
- ▌ Nistwebbook · lamm-mit bundleLook up chemical data from NIST Chemistry WebBook (thermochemistry, spectra, properties)
- ▌ Peptide Msa · lamm-mit bundlePerform a simple multiple-sequence alignment (MSA) for short peptides and return aligned sequences + consensus.
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- ▌ Python Exec · lamm-mit bundleExecute arbitrary Python code and return stdout. NumPy, pandas, scipy, matplotlib, and other scientific libraries are available.
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- ▌ Youtu Agent · lamm-mit bundleFlexible, high-performance framework for building, running, and evaluating autonomous agents with automated generation, experience learning, and RL training capabilities.
- ▌ Autoresearch · lamm-mit bundleAutonomous AI agent that modifies and iteratively improves a GPT language model training setup, running experiments within a 5-minute time budget to optimize validation bits-per-byte.
- ▌ Fem Analysis · lamm-mit bundleModal analysis of a membrane STL using Kirchhoff plate FEM (scipy eigensolver). Takes a binary STL + material properties JSON, constructs a 2D rectangular FEM mesh, assembles stiffness and mass matrices, extracts the first N eigenfrequencies, and reports whether any mode falls in a target frequency range. Returns artifact JSON with eigenfrequencies_hz, mode_shapes_png, and target_range_pass.
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- ▌ Minerals Viz · lamm-mit bundleGenerate charts (PNG/SVG) for critical minerals data — production, trade, import reliance, and time series
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- ▌ Pdb Database · lamm-mit bundlePython API for RCSB PDB 3D structures (search, fetch coordinates, metadata). Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers — pass only the target protein name or PDB accession.
- ▌ Stl Renderer · lamm-mit bundleRender publication-quality PNG views of any binary STL file — isometric (3-D perspective), top-down XY projection, and XZ cross-section at Y midpoint. All dimensions derived from the STL bounding box; nothing hardcoded. Optionally uploads to imgur and returns URLs. Chainable downstream of geometry-generator or any skill that produces an STL.
- ▌ Text To Lora · lamm-mit bundleGenerate task-specific LoRA adapters from natural language descriptions using a trained T2L model for instant transformer adaptation.
- ▌ Tooluniverse · lamm-mit bundleAccess 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more
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- ▌ Bioreason Pro · lamm-mit bundleMultimodal reasoning LLM for protein function prediction integrating protein embeddings with biological context to generate structured reasoning traces and functional annotations.
- ▌ Corpus Search · lamm-mit bundleSemantic search over critical minerals PDF corpus — rare earth, lithium, cobalt, nickel supply chain, trade policy, extraction, and materials research via Pinecone
- ▌ Drug Research · lamm-mit bundleGenerates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections. Covers identity, chemistry, pharmacology, targets, clinical trials, safety, pharmacogenomics, and ADMET properties. Use when users ask about drugs, medications, therapeutics, or need drug profiling, safety assessment, or clinical development research.
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- ▌ Latex Posters · lamm-mit bundleCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
- ▌ Minerals Data · lamm-mit bundleQuery and analyze structured CSV datasets on critical minerals production, trade, and supply chains
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- ▌ Osti Database · lamm-mit bundleSearch OSTI.gov for DOE technical reports on critical minerals, energy, and materials science
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- ▌ Qmmm Adaptive · lamm-mit bundleQM/MM hybrid simulations with adaptive sampling for enzyme mechanisms and reaction dynamics. Combines quantum mechanics (reactive center) with molecular mechanics (protein/solvent) for accurate transition state and reaction pathway calculations. Supports metadynamics, umbrella sampling, and accelerated MD for enhanced conformational sampling.
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- ▌ Bgs Production · lamm-mit bundleQuery BGS World Mineral Statistics for production, imports, and exports by commodity, country, and year
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- ▌ Code Execution · lamm-mitAgentic computation — iteratively write code, run commands, read results, and reason about next steps
- ▌ Comtrade Trade · lamm-mit bundleQuery UN Comtrade bilateral trade flows (USD, kg) for critical minerals by HS code, country, and year