93 skills · sorted by relevance
Search biomedical literature in PubMed, build queries with standardized subject terms and filters, and retrieve abstracts and publication details. Record search methods for repeatable reviews and use NCBI APIs to monitor literature.
Search biomedical papers, regulatory documents, clinical trials, and protein records through GXL Paperclip. Extract comparable information across documents, inspect figures, and organize findings with citations linked to the source lines that support them.
Build PyTorch machine learning workflows for molecules, proteins, and biomedical relationships. Get guidance on datasets, model selection, training, and evaluation for property prediction, protein modeling, molecule generation, and planning synthesis routes from target molecules.
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
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HuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes, diseases, chemicals), relation extraction, QA, text classification, abstract summarization. Covers loading, biomedical tokenization, inference pipelines, fine-tuning. Alternatives: spaCy en_core_sci_lg (rule-based NER), Stanza (biomedical models), NLTK.
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Think and work like an expert Biomedical Imaging Scientist. Use when a task calls for Biomedical Imaging Scientist judgment. Reasons from contrast mechanisms, the resolution-SNR-scan-time triangle, and measurement reliability through DICOM/BIDS pipelines, QIBA profiles, phantom QC (ACR, NEMA IQ, Catphan), and blinded central reads (RECIST, RANO, PERCIST) while treating motion, partial volume effects, and cross-scanner harmonization drift as first-class failure modes.
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Think and work like an expert Biomedical Engineer. Use when a task calls for Biomedical Engineer judgment. Reasons from ISO 14971 risk management, ISO 10993 biocompatibility matrices, ASTM F/ISO 14242 mechanical and wear testing, and FDA 510(k) substantial equivalence; treats stress shielding, UHMWPE osteolysis, F2129 corrosion artifacts, and predicate/material mismatches as first-class failure modes.
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Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
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Expert-level biomedical imaging covering X-ray, CT, MRI, ultrasound, nuclear medicine, optical imaging, and image processing for clinical and research applications.
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Look up biomedical relationships in ARAX using explicit entity types and tightly bounded paths. Inspect direct links or paths through one intermediate entity, along with returned publications and source records, to identify candidates for further research.
Organize MRI, EEG, and other biomedical research data using BIDS, a shared standard for filenames, folders, and metadata. Query datasets, check compliance, convert DICOM files, and prepare metadata or processed outputs for analysis and sharing.
Generates structured biomedical outlines for review articles, discussion sections, and thesis proposals. Use when a user provides biomedical keywords, results/discussion text, or a proposal title plus background and needs a directly usable academic writing scaffold.
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Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.
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Apply the bioengineering, mechanobiology, and lymphatic transport reasoning of J. Brandon Dixon, professor of mechanical and biomedical engineering at Georgia Institute of Technology. Reach for this skill whenever analyzing lymphatic biomechanics, active vessel contractility versus passive drainage, peristaltic fluid transport, microfluidic organ-on-a-chip design, preclinical lymphedema models, non-invasive functional imaging, targeted nanomedicine delivery, or automated disease staging. Use this skill to critique bioengineering assumptions, guide quantitative protocol design, evaluate biomechanical pump failure, and formulate interdisciplinary biomedical solutions.
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Discover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics, multi-omics, pathway, metagenomics, database queries, visualization, workflows): search the index, locate the best-matching skill, fetch its SKILL.md, and follow it.
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Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.
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Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.
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Use when a task needs the judgment of a biomedical/bioengineering engineer — running a design control phase (inputs, outputs, verification, validation) for a medical device, scoring a Design FMEA and deciding whether a failure mode needs mitigation, planning a human factors/usability validation study, building a design traceability matrix, or writing a design verification or risk-mitigation report. Distinct from a regulatory-affairs-specialist (owns the submission/clearance process, not the engineering itself) and from a clinical-data-manager/biostatistician (trial data and analysis, not device design).
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NLM PubTator3 实体级关系挖掘 — 检索"疾病-药物-基因-化学品-突变"在生物医学文献中的标注与关系。当用户问"哪些研究讨论了 BTK 抑制剂与肺曲霉病"、"基因 X 与疾病 Y 的关联"、"药物-基因相互作用"、"找含某突变的文献"、"PubTator / 实体标注 / NER / annotation / biomedical entity / 疾病基因关联 / 药物-基因 / 化学品-疾病 / 突变检索"时使用。无需 API key。**实体级 · 关系挖掘**定位 — 不做文献综合检索(用 pubmed-eutils / europepmc-search)、不做全文(用 BioC)、不做试验(用 ct-v2)。
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Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, integrate into your AI projects.
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Plan literature searches, screen academic and technical sources, and combine findings into a cited review. Records search methods and exclusions, compares conflicting evidence, identifies research gaps, and checks references so readers can trace the review's claims.
Finds papers, preprints, citation links, and openly available full text through 18 scholarly APIs. Selects databases for the task and returns relevant records with search parameters, identifiers, and access dates so the retrieval can be repeated.
Guides PyTorch model training and fine-tuning, from choosing architectures to configuring optimizers and learning rates. Provides troubleshooting steps for unstable loss and memory shortages, plus methods for improving GPU throughput and comparing experiments.
Search multiple academic databases, screen studies against documented criteria, and compare findings by theme. Produce literature reviews in Markdown and PDF with study quality assessments, verified citation details, and diagrams explaining the review process or findings.