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Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.
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Based on SOC occupation classification
| name | general-biorxiv-search |
| description | Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research. |
| category | general |
Search and retrieve preprint metadata (title, authors, abstract, DOI, category, etc.) from bioRxiv and medRxiv using the official REST API. Supports keyword filtering, subject category filtering, date-range search, and DOI lookup.
Search last 30 days for papers matching keywords in title/abstract.
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "protein folding" --max_results 5 --output protein_folding.json
Retrieve preprints posted in a specific date range, with optional keyword/category filter.
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "CRISPR" --start 2025-01-01 --end 2025-06-01 --max_results 10 --output crispr_2025.json
Filter by subject category (use shortcuts or full names).
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 14 --max_results 10
Supported Category Shortcuts:
biochemistry, bioinformatics, biophysicscancer โ cancer_biologycell-bio โ cell_biologydev-bio โ developmental_biologyecology, epidemiology, evolutiongenetics, genomics, immunologymicrobiology, molecular-bio โ molecular_biologyneuroscience, pharmacology, physiologyplant-bio โ plant_biologysynthetic-bio โ synthetic_biologysystems-bio โ systems_biologyUse --server medrxiv for medical preprints.
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "COVID vaccine efficacy" --server medrxiv --max_results 5 --output covid_vaccine.json
Retrieve metadata for a specific preprint by DOI.
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --doi 10.1101/2021.01.01.000000 --output paper.json
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py --category neuroscience --days 7 --max_results 5
# Env: base-agent
python .agents/skills/general-biorxiv-search/scripts/biorxiv_search.py "single cell sequencing" --category genomics --start 2024-01-01 --end 2024-12-31 --max_results 10 --output scrna_2024.json
--max_results.base-agent conda environment.requests.Author: mlederbauer Contact: GitHub @learningmatter-mit
Quantify prediction uncertainty of MACE MLIPs using committee (ensemble) models; flag high-uncertainty structures for DFT verification.
Compute phonon-limited carrier mobility and mode-resolved electron-phonon coupling in 2D materials from first principles with Quantum ESPRESSO and EPW.
GPU-accelerated batched inference for MACE, MatGL (TensorNet/M3GNet/CHGNet), and FairChem MLIPs using NValchemi, enabling parallel static, relax, and MD workflows across multiple structures simultaneously.
Extract structured synthesis procedures from a folder of PDFs using the LeMat-Synth GeneralSynthesisOntology schema, producing one JSON file per paper with per-material synthesis records.
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.
Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.