lamm-mit/scienceclaw

paperclip

Onboard and manage Paperclip AI for research-paper knowledge and agent orchestration

scienceclaw-post

Generate a structured scientific post and publish it to Infinite. Runs a focused single-agent investigation (PubMed search → LLM analysis → hypothesis/method/findings/conclusion) and posts the result. Faster than scienceclaw-investigate — best for targeted,…

infinite

Infinite platform integration for AI agent collaboration

csv-read

Read a CSV or XLSX file and return columns, shape, dtypes, and first N rows as JSON.

python-exec

Execute arbitrary Python code and return stdout. NumPy, pandas, scipy, matplotlib, and other scientific libraries are available.

scientific-report-pdf

Generate a structured scientific PDF report from a JSON description. Accepts a JSON file specifying title, authors, abstract, sections (headings, text, tables, figures), and inline data panels (heatmap, bar, scatter, line). Produces a publication-style A4 PDF…

code-execution

Agentic computation — iteratively write code, run commands, read results, and reason about next steps

uma

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

dft

Submit, monitor, and retrieve DFT calculations on Artemis/SLURM via DREAMS framework

hpc

SLURM HPC job management on Artemis — write submission scripts, submit jobs, monitor status, retrieve results

job-results

Read and parse results from completed SLURM jobs — check status, retrieve output, filter candidates

phonon

Compute phonon properties and assess dynamic stability using ML potentials via phonopy

structure-enumeration

Generate candidate crystal structures by element substitution in prototype structures

alphafold

Use 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).

boltz

Use when predicting biomolecular structures (proteins, RNA, DNA, ligands) with the open-source Boltz diffusion model as an alternative to AlphaFold3.

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.

disease-research

Generate comprehensive disease research reports using 100+ ToolUniverse tools. The agent creates a detailed markdown report file and progressively updates it with findings from 10 research dimensions, with full source citations. Use when users ask about…

drug-research

Generates 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…

autoresearch

Autonomous 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.

bioreason-pro

Multimodal reasoning LLM for protein function prediction integrating protein embeddings with biological context to generate structured reasoning traces and functional annotations.

doc-to-lora

A method to instantly internalize document contexts into language models using LoRA without fine-tuning.

dreams

Agentic materials discovery and DFT simulation framework using ASE, Quantum ESPRESSO, and Claude LLMs via LangGraph.

softjax

Soft differentiable drop-in replacements for non-differentiable JAX functions (abs, relu, sort, argmax, comparison, logical operators, etc.) with adjustable softening strength.

symtorch

Approximate deep learning model components with symbolic equations using PySR

text-to-lora

Generate task-specific LoRA adapters from natural language descriptions using a trained T2L model for instant transformer adaptation.

youtu-agent

Flexible, high-performance framework for building, running, and evaluating autonomous agents with automated generation, experience learning, and RL training capabilities.

scienceclaw-investigate

Run a multi-agent autonomous scientific investigation on any topic. Spawns specialized AI agents that use 300+ scientific tools (PubMed, BLAST, UniProt, PubChem, TDC, RDKit, etc.) to investigate and post findings to Infinite.

scienceclaw-local-files

Investigate local files (PDFs, FASTA, CSV, TSV, JSON, TXT) using ScienceClaw's multi-agent science engine. Accepts files shared in chat or paths on disk, extracts content, and runs a full scientific investigation.

scienceclaw-query

Run a scientific investigation on any topic and return findings directly to chat — without posting to Infinite. Use this for quick research, previews, or when the user says "don't post" or "just show me".

scienceclaw-status

Check the status of a ScienceClaw agent — journal stats, recent investigations, knowledge graph size, and activity summary.

scienceclaw-watch

Run a live multi-agent scientific collaboration session and return a full summary when complete. Multiple specialised agents work in parallel, challenge each other's findings, and generate figures. Results and figures are saved to disk and a summary is…

adaptyv

Cloud 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…

adverse-event-detection

ToolUniverse workflow — Adverse Event Detection

aeon

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed…

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.

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for…

antibody-engineering

ToolUniverse workflow — Antibody Engineering

arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and…

arxiv

Search ArXiv for scientific preprints in biology, chemistry, and related fields

ase

Atomic 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…