skills/claude-scientific-skills
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scientific-integrations/benchling-integration/SKILL.md
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@@ -7,7 +7,7 @@ description: "Benchling R&D platform integration. Access registry (DNA, proteins
## Overview
Integrate with Benchling's cloud platform for life sciences R&D, enabling programmatic access to registry entities, inventory management, electronic lab notebooks, and workflow automation. This skill provides comprehensive guidance for using both the Python SDK and REST API to interact with Benchling data.
Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, proteins), inventory, electronic lab notebooks, and workflows programmatically via Python SDK and REST API.
## When to Use This Skill

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scientific-integrations/dnanexus-integration/SKILL.md
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@@ -7,25 +7,18 @@ description: "DNAnexus cloud genomics platform. Build apps/applets, manage data
## Overview
DNAnexus is a cloud-based platform for biomedical data analysis, particularly genomics. This skill provides comprehensive guidance for interacting with DNAnexus through:
- Building and deploying apps and applets (Python/Bash)
- Managing data objects (files, records, databases)
- Running analyses and workflows
- Using the dxpy Python SDK
- Configuring app metadata and dependencies
DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
## When to Use This Skill
This skill should be used when working with:
- **App Development**: Creating, building, or modifying DNAnexus apps/applets
- **Data Management**: Uploading, downloading, searching, or organizing files and records
- **Job Execution**: Running analyses, monitoring jobs, creating workflows
- **Python SDK**: Writing scripts using dxpy to interact with the platform
- **Configuration**: Setting up dxapp.json, managing dependencies, using Docker
- **Genomics Workflows**: Processing FASTQ, BAM, VCF, or other bioinformatics files
- **Platform Operations**: Managing projects, permissions, or platform resources
This skill should be used when:
- Creating, building, or modifying DNAnexus apps/applets
- Uploading, downloading, searching, or organizing files and records
- Running analyses, monitoring jobs, creating workflows
- Writing scripts using dxpy to interact with the platform
- Setting up dxapp.json, managing dependencies, using Docker
- Processing FASTQ, BAM, VCF, or other bioinformatics files
- Managing projects, permissions, or platform resources
## Core Capabilities

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scientific-integrations/labarchive-integration/SKILL.md
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---
name: labarchive-integration
description: "LabArchives ELN API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows."
description: "Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows."
---
# LabArchives Integration
## Overview
Provide comprehensive tools and workflows for interacting with the LabArchives Electronic Lab Notebook (ELN) REST API. LabArchives is a widely-used electronic lab notebook platform for research documentation, data management, and collaboration in academic and industrial laboratories.
LabArchives is an electronic lab notebook platform for research documentation and data management. Access notebooks, manage entries and attachments, generate reports, and integrate with third-party tools programmatically via REST API.
This skill enables programmatic access to LabArchives notebooks, including user authentication, notebook operations, entry management, report generation, and third-party integrations.
## When to Use This Skill
This skill should be used when:
- Working with LabArchives REST API for notebook automation
- Backing up notebooks programmatically
- Creating or managing notebook entries and attachments
- Generating site reports and analytics
- Integrating LabArchives with third-party tools (Protocols.io, Jupyter, REDCap)
- Automating data upload to electronic lab notebooks
- Managing user access and permissions programmatically
## Core Capabilities

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scientific-integrations/latchbio-integration/SKILL.md
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@@ -7,7 +7,7 @@ description: "Latch platform for bioinformatics workflows. Build pipelines with
## Overview
The Latch SDK is a Python framework for building and deploying bioinformatics workflows as serverless pipelines with automatic UI generation. Built on Flyte, Latch provides containerization, type safety, scalable cloud infrastructure, and a comprehensive data management system. This skill provides guidance for creating workflows, managing data, configuring resources, and using verified pre-built pipelines.
Latch is a Python framework for building and deploying bioinformatics workflows as serverless pipelines. Built on Flyte, create workflows with @workflow/@task decorators, manage cloud data with LatchFile/LatchDir, configure resources, and integrate Nextflow/Snakemake pipelines.
## Core Capabilities

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scientific-integrations/omero-integration/SKILL.md
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---
name: omero-integration
description: "OMERO microscopy data management. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows."
description: "Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows."
---
# OMERO Integration
## Overview
OMERO is an open-source client-server platform for managing, visualizing, and analyzing microscopy images and associated metadata. This skill provides comprehensive guidance for using OMERO's Python API (omero-py) to programmatically interact with OMERO servers for data retrieval, analysis, and management.
OMERO is an open-source platform for managing, visualizing, and analyzing microscopy images and metadata. Access images via Python API, retrieve datasets, analyze pixels, manage ROIs and annotations, for high-content screening and microscopy workflows.
## When to Use This Skill
This skill should be used when:
- Working with OMERO Python API (omero-py) to access microscopy data
- Retrieving images, datasets, projects, or screening data programmatically
- Analyzing pixel data and creating derived images
- Creating or managing ROIs (regions of interest) on microscopy images
- Adding annotations, tags, or metadata to OMERO objects
- Storing measurement results in OMERO tables
- Creating server-side scripts for batch processing
- Performing high-content screening analysis
## Core Capabilities

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scientific-integrations/opentrons-integration/SKILL.md
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---
name: opentrons-integration
description: "Opentrons lab automation. Write Protocol API v2 protocols for Flex/OT-2 robots, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows."
description: "Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows."
---
# Opentrons Integration
## Overview
Opentrons provides a Python-based automation platform for laboratory protocols using Flex and OT-2 robots. This skill enables creation and management of Python Protocol API v2 protocols for automated liquid handling, hardware module control, and complex laboratory workflows.
Opentrons is a Python-based lab automation platform for Flex and OT-2 robots. Write Protocol API v2 protocols for liquid handling, control hardware modules (heater-shaker, thermocycler), manage labware, for automated pipetting workflows.
## When to Use This Skill
This skill should be used when:
- Writing Opentrons Protocol API v2 protocols in Python
- Automating liquid handling workflows on Flex or OT-2 robots
- Controlling hardware modules (temperature, magnetic, heater-shaker, thermocycler)
- Setting up labware configurations and deck layouts
- Implementing complex pipetting operations (serial dilutions, plate replication, PCR setup)
- Managing tip usage and optimizing protocol efficiency
- Working with multi-channel pipettes for 96-well plate operations
- Simulating and testing protocols before robot execution
## Core Capabilities