Pipeline Studio
Real-world examples of scientific agents leveraging the AROS Federation to solve complex biological workflows.
Workflows
This document provides detailed examples of common mass spectrometry analysis workflows using matchms....
Transformations Workflows
This reference documents pymatgen's transformation framework and provides recipes for common materials science workflows....
Brainstorming Workflow
Transform user-proposed ideas into clear, discussable directions—clarifying first, then diverging, and finally converging into actionable next steps....
Dual Agent Workflow Details
canonicallocation: "01.SharedAssets/KIs/agenticmanuscriptpublishing"...
Standard Workflow
Complete step-by-step guide for analyzing Neuropixels recordings from raw data to curated units....
Kakenhi Management Pipeline Spec
Universal — applicable to any JSPS KAKENHI researcher, any research field, any grant category...
Pipelines And Composition
Pipelines chain multiple processing steps into a single estimator, preventing data leakage and simplifying code. They enable reproducible workflows an...
Workflows
This reference provides standard workflows and patterns for building, validating, and analyzing Bayesian models in PyMC....
Workflows
This document provides detailed step-by-step workflows for common COBRApy tasks in metabolic modeling....
Simulation Workflow
Follow these steps to run a fluidsim simulation:...
Pipeline Registry
This file serves as the canonical registry for all pipelines maintained within the AROS Pipeline Factory. Agents should parse this table to discover a...
Kakenhi Management Pipeline Spec
Universal — applicable to any JSPS KAKENHI researcher, any research field, any grant category...
Antigravity Workflow Authoring Skill
name: antigravity-workflow-authoring...
Visual Review Workflow
Visual review is a critical quality assurance step for presentations, allowing you to identify and fix layout issues, text overflow, element overlap, ...
Kakenhi Pipeline
The KAKENHI Pipeline is a specialized workflow for managing JSPS KAKENHI grant reports and applications....
Manuscript Write Pipeline
The Manuscript Write Pipeline is a dual-agent autonomous system for authoring scientific papers....
Grant Write Pipeline
The Universal Scientific Grant Writing Pipeline is a funder-agnostic proposal generator designed to orchestrate the entire lifecycle of a grant applic...
Cross Pipeline Compatibility Protocol
Status: ACTIVE — LAW 0 in `AGENTS.md`...
Pipeline Registry Migration
On 2026-05-11, the AROS Pipeline Factory migrated from the generic `00.RawData/INDEX.csv` (a biological assay tracking format inherited from the stand...
Analysis Pipeline Patterns
Cultured MSCs often show higher gene detectability. Stricter thresholds are recommended to ensure high-quality separation....
Bulk Workflows
Argument specifications for `cacheresultshistory` and common multi-step batch...
Workflows Examples
This document provides practical workflows and usage examples for common DiffDock tasks....
Report Export Pipeline
The recommended final output is:...
Common Workflows
This document provides practical examples of common bioinformatics workflows using pysam, demonstrating how to combine different file types and operat...
Workflows
Extended workflow examples demonstrating how to combine multiple gget modules for common bioinformatics tasks....
Standard Workflow
This document outlines the standard workflow for analyzing single-cell RNA-seq data using scanpy....
Workflows
This document provides complete, end-to-end examples of common workflows using ESM3 and ESM C. Each workflow includes setup, execution, and analysis c...
Workflows
This document covers common workflows, best practices, and advanced usage patterns for scvi-tools....
Workflow Recipes
Common multi-step patterns combining Parallel's Search, Extract, and Deep Research APIs for scientific writing tasks....
Workflows
This document provides complete workflows for common tasks using the ETE Toolkit....
Workflows
This document provides complete workflow examples for common deepTools analyses....
Pipelines
Pipelines provide the simplest way to use pre-trained models for inference. They abstract away tokenization, model loading, and post-processing, offer...
Workflow Types
1. Property Prediction Workflows...
Workflow Creation
The Latch SDK enables defining serverless bioinformatics workflows using Python decorators and deploying them with automatic containerization and UI g...
Verified Workflows
Latch Verified Workflows are production-ready, pre-built bioinformatics pipelines developed and maintained by Latch engineers. These workflows are use...
Workflows
Follow these checklists for complex, multi-step queries to ensure accurate...
Workflows
This document provides detailed workflows for common DeepChem use cases....
Svg Pipeline
These tools cover post-processing, SVG validation, speaker notes, and PPTX export....
Workflows
This document provides comprehensive workflows, best practices, and common use cases for using SHAP in various model interpretation scenarios....
Scanpy Workflow
Complete workflow for going from a Scanpy AnnData object to CellphoneDB results....
Export Pipeline
Use markdown as the single editable source of truth. Generate distribution formats from that source rather than maintaining separate copies by hand....
Research Pipeline
The main class for orchestrating research workflows....
Common Workflows
This document provides examples of common workflows and use cases for working with NCBI Gene database....
Workflow Guide
This document provides detailed step-by-step workflows for common PyDESeq2 analysis patterns....
Workflow Patterns
This document describes detailed multi-step workflows for common bioinformatics tasks using BioServices....
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