Shoko-official/Claude-Science-System-Prompts
Plugin Claude Code
Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Anthropic's hosted PubMed server: lets the agent search biomedical literature and read abstracts and citations from PubMed. Remote server at pubmed.mcp.claude.com.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
BioRender's hosted server: lets the agent create and edit scientific figures and diagrams in BioRender. Remote server at mcp.services.biorender.com.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
One of Anthropic's hosted health and life-sciences servers (bioRxiv/medRxiv preprints, ClinicalTrials.gov, ChEMBL and others): lets the agent search and read that source directly. Remote server at hcls.mcp.claude.com.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Consensus's hosted MCP server: lets the agent search peer-reviewed research and get evidence-based answers with citations. Remote server at mcp.consensus.app.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
One of Anthropic's hosted health and life-sciences servers (bioRxiv/medRxiv preprints, ClinicalTrials.gov, ChEMBL and others): lets the agent search and read that source directly. Remote server at hcls.mcp.claude.com.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
One of Anthropic's hosted health and life-sciences servers (bioRxiv/medRxiv preprints, ClinicalTrials.gov, ChEMBL and others): lets the agent search and read that source directly. Remote server at hcls.mcp.claude.com.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Sage Bionetworks' Synapse server: lets the agent find and read datasets, files and projects on the Synapse research data platform. Remote server at mcp.synapse.org.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Wiley Scholar Gateway: lets the agent search and read Wiley's scholarly journals and books. Remote server at connector.scholargateway.ai.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Owkin's hosted server: lets the agent query Owkin's biomedical and multi-omics knowledge. Remote server at mcp.k.owkin.com.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Open Targets' hosted server: lets the agent query target–disease associations, drugs and genetics evidence. Remote server at mcp.platform.opentargets.org.
Shoko-official/Claude-Science-System-Prompts
MCP server Claude CodeCodexCursor +2
Benchling's MCP server: lets the agent read and update entities, entries and results in a Benchling R&D workspace.
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project.
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developing FDA submission documentation for…
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Conduct rigorous, reproducible multi-step scientific work with literature, databases, local files, Python, R, shell, artifacts, reviewers, and approved compute. Use for evidence synthesis, data or statistical analysis, machine learning, simulation, study design, scientific figures or manuscripts, reproduction audits…
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis…
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate…
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics…
Shoko-official/Claude-Science-System-Prompts
Skill Claude CodeCodex
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.