1. Ingenuity Pathway Analysis Alex Pico

2. Description "IPA is a software application that enables researchers to analyze and understand the complex biological and chemical systems at the core of life science research. IPA integrates content from the world's largest and highest quality knowledge base of biological and chemical interactions, and employs powerful algorithms and an easy to use software interface to provide researchers with the insights and confidence to make better and faster decisions at every step of their research, from experimental planning to data interpretation."

3. Basics Target Audience: Industry researchers in drug discovery Primary use cases:  # Search and explore "the largest knowledge base of its kind with the most descriptive structure, highest degree of accuracy, and largest number of literature findings."  # Analyze and interpret data from expression and SNP arrays, proteomics and metabolomics experiments, and small-scale experiments that generate gene lists. Grow gene lists into pathways via the knowledge base using any combination of contextual, annotation, or relationship information. Identify ideal biomarkers. Map experimental data onto pathways (curated or home-grown). Use themed modules to study Metabolomics, Toxicity, or Biomarkers.  # Share and collaborate on analyses. Generate summary reports. Export results, tables of annotations, bibliographies and high-res images. Utilize API, or deploy locally. Last updated: version 5.5 (sometime in the last few months) Platform: Web browser or standalone app on Vista, XP, Mac Plugin Architecture: API to integrate into local software pipeline. Integrated with GeneSpring (Agilent), Resolver (Rosetta) and Spotfire

4. Features # The knowledge base is impressive in terms of both the model and content. This is the sort of thing we could never hope to compete with as a non-profit consortium. Though I can imagine an open, community-curated knowledge base that would, in the end, produce a superior product, this is probably not a task for Cytoscape. # Ingenuity is able to integrate a single knowledge base for gene ID aliases, chemicals, drugs and small molecules, interactions, curated pathways, literature- based relationships, and workflow-related annotations (e.g., biomarkers). This singular, controlled source allows them to reference across multiple data types and levels from different perspectives. While we may not be able to produce a knowledge base, we can (and do) integrate public databases. It might be worth thinking about how information from these sources can be integrated or cross-referenced within Cytoscape. It may be equally worthwhile thinking about when sources should be segregated or pruned to provide focus (e.g., biological semantics). # Beyond the knowledge base, Ingenuity's most valuable qualities are the polished, professional look and feel (including its new web interface) and its specialized workflows and modules. Having focused workflows and perspectives brings to bear specialized windows, menus, data types and integrated content that make the application very user-friendly and effective.