Ingenuity Systems - AbsoluteAstronomy.com

Ingenuity Systems, Inc is a company based in Redwood City, California, that provides software to help life science researchers explore, interpret, and analyze complex biological systems. Its first product, IPA, was introduced in 2003, and is used to help researchers analyze 'omics data and model biological systems. The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems biology

Systems biology

Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...

researchers and bioinformaticians

Bioinformatics

Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

in drug discovery and institutional research. Ingenuity Answers, the newest addition to Ingenuity's product line, was introduced in 2009. The company also offers analysis services and enterprise services.

Technology

All Ingenuity products use the Ingenuity Knowledge Base, which contains biological and chemical interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These modeled relationships include contextual details, link to the original article, and are manually reviewed for accuracy. Each relationship originates from reported experimental facts from primary literature sources, including peer-reviewed journal articles, review articles and textbooks. In addition to findings from the literature, the Ingenuity Knowledge Base contains findings and annotations from other sources, including EntrezGene

Entrez

The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...

, RefSeq

RefSeq

The Reference Sequence database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. This database is built by National Center for Biotechnology Information , and, unlike GenBank, provides only single record for each natural...

, OMIM, GWAS database, Gene Ontology

Gene Ontology

The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...

, Tissue Expression Body Atlas, NCI-60 Cell Line Expression Atlas, KEGG Metabolic pathway information, LIGAND enzyme/substrate reactions, protein-protein interactions (from BIND, DIP, MINT, MIPS

Munich Information Center for Protein Sequences

The Munich Information Center for Protein Sequences is a research center hosted at the Institute for Bioinformatics at Neuherberg, Germany with a focus on genome oriented bioinformatics, in particular on the systematic analysis of genome information including the development and application of...

, BIOGRID

BioGRID

The Biological General Repository for Interaction Datasets is a curated biological database of protein-protein and genetic interactions created in 2003 The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions...

, INTACT, and Cognia), and microRNA-mRNA target interactions (from ARGONAUTE 2, TARBASE). The knowledge acquisition and extraction process is protected by multiple US Patents .

IPA

IPA is broadly adopted in the life science community and has been cited in thousands of peer-reviewed journal articles. IPA can be used with or without data. IPA helps researchers analyze data derived from expression and SNP microarrays, proteomics experiments

Proteomics

Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...

, and small-scale experiments that generate gene lists, in order to gain insight into molecular and chemical interactions, cellular phenotypes, and disease processes within a system. IPA also lets researchers search for information on genes, proteins, chemicals, drugs, and reagent

Reagent

A reagent is a "substance or compound that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs." Although the terms reactant and reagent are often used interchangeably, a reactant is less specifically a "substance that is consumed in the course of...

s. Resulting information can be used to build biological models, design experiments, or get up to speed in an area of research.

Ingenuity iReport

Ingenuity iReport is the fastest way to understand the meaning of expression data. It combines biological and statistical analysis for a rapid and accurate analysis of what genes are significantly differentially expressed in a dataset, and summarizes the affected biology. iReport includes novel interactive & visual tools that help researchers quickly identify the most interesting subset of genes for follow-up.

E-Commerce

Ingenuity offers search and visualization tools that can be deployed on life science e-commerce websites to enable customers to use information about biological and chemical systems to better design their experiments and select their reagents. Ingenuity has two prominent partnerships. Sigma-Aldrich

Sigma-Aldrich

Sigma-Aldrich Corporation , is a life science and high technology company with over 7,600 employees and operations in 40 countries. Its chemical and biochemical products and kits are used in scientific research, biotechnology, pharmaceutical development, the diagnosis of disease, and as key...

leverages Ingenuity technology in their Your Favorite Gene – Powered by Ingenuity application, and BD Biosciences

Becton Dickinson

Becton, Dickinson and Company , is an American medical technology company that manufactures and sells medical devices, instrument systems and reagents. Founded in 1897 and headquartered in Franklin Lakes, New Jersey, BD does business in nearly 50 countries and has 28,803 employees worldwide. In...

leverages Ingenuity technology in their BD Cell Pathways application.

Analysis services

Ingenuity offers scientific services that accesses the capabilities of the software and knowledge base. Services include data analysis and interpretation, model building for target ID and validation, biomarker identification and prioritization, toxicity assessments, and help with result presentation.

Investors

Accel Partners, Three Arch Partners, Bay City Capital, Morgan Stanley Capital Partners, Oracle Venture Fund, Millenium Pharmaceuticals, Affymetrix Corporation

Affymetrix

Affymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...

Timeline

2003 - Ingenuity first offers Ingenuity Knowledge Base

2004 - Stanford University licenses IPA

2004 - Independent analysis finds significant ROI for pharmaceutical companies using IPA

2005 - US Food and Drug Administration adopts IPA to review pharmacogenomics submissions

2006 - Ingenuity enters into partnerships with Asuragen, Spotfire, Agilent, Genedata, and Inforsense

2007 - Ingenuity introduces toxicology and biomarker capabilities within IPA 5.0

2007 - IPA 5.0 wins Best in Show - Best New Product at Bio-IT World

2007 - Ingenuity and FDA enter three year collaboration to enhance regulatory review process

2008 - IPA's newest feature, Path Designer, wins Best New Product at Molecular Medicine

2009 - Sigma Aldrich launches Your Favorite Gene - Powered by Ingenuity
2009 - BD Biosciences launches BD Cell Pathways, powered by Ingenuity

2011 - Ingenuity announces early access to Ingenuity iReport