Product Updates: IPA6

The upcoming release of IPA, IPA 6, includes Path Designer, a new pathway publishing tool that enables researchers to customize their networks and pathways to make them more biologically relevant for publications or presentations. IPA 6 also features several new content and analysis capabilities designed to address the data analysis, information search, and scientific communication challenges facing life scientists today. Many of the enhancements implemented in IPA 6 were requested directly by our customers – so keep your suggestions coming by contacting Customer Support at support@ingenuity.com or by attending one of our upcoming User Group Meetings in Cambridge, MA, or Cannes, France. Here are some highlights from the upcoming release of IPA 6:

• Path Designer, the easy-to-use pathway design and publishing tool in IPA: Transform your “ball and stick” networks and pathways in IPA into publication quality pathway graphics rich with color, customized text and fonts, biological icons, organelles, and custom backdrops. Path Designer pathways are fully interactive and supported by the high quality content stored in IPA. This easy-to-use graphics package ensures that your entire workflow – from data analysis to publication and communication of results to colleagues – can be completed within IPA.
  
  
• Alternate p-value calculations to narrow in on most significant Functional Analysis results: Users now have the option of using an additional algorithm for identifying the most significant results in IPA’s Functional, Canonical Pathway, My Pathway and List analyses. This calculation returns adjusted p-values based on the Benjamini Hochberg method of accounting for multiple testing, and enables you to control the noise in certain analysis results and focus in on the most significant biological functions associated with your genes of interest.
  
  
• Transcript expression profiles from the NCI-60 Cancer Cell Panel: We have dramatically enhanced our Tissue Expression Body Atlas, a collection of positive gene expression calls for over 30 normal tissues that is accessible through IPA’s Overlay menu, and IPA-Biomarker analysis, by including positive gene expression calls for the NCI-60 panel of cell lines. This collection of cell lines has become a key resource in Oncology and Drug Discovery research, and we are pleased to enable you to now quickly understand which genes in your IPA results, lists, or pathways are expressed in these cell lines.
  
  
• Content additions boost gene to disease knowledge, drug metabolism coverage, and pathway library: As with each IPA release, IPA 6 contains significant additions to several areas of content, including new Canonical Pathways describing toxicological responses, actin motility, and the balance between pro-apoptotic and anti-apoptotic events. We’ve also added several thousand relationships between clinical candidates and the diseases and indications they treat, as well as additional content on drug protein adducts, drug metabolism, women’s health topics, Alzheimer’s disease, biopolar disorder, hypereosinophilia, and obesity.

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2008 Ingenuity User Group Meetings

Register now for the 2008 Ingenuity User Group meetings:

» Sign up now
» Click to learn more about workshops

April 1-2, in Cambridge, MA
April 24-25 in Cannes, France

The Ingenuity User Group Meetings provide a valuable forum for IPA users to learn more about IPA and contribute to its ongoing development. This year, guests in Cannes and Cambridge will network with colleagues and Ingenuity scientists to learn best practices and new capabilities in IPA, as well as hear distinguished industry and academic speakers discuss how IPA is being applied in their research.

This year we are also repeating our immensely successful workshop format. The workshops will provide an opportunity for IPA users to spend quality time with Ingenuity specialists to discuss workflows, data analysis, or any other aspect of IPA analysis and content searching. Laptops will be available with Internet connections to allow users to discuss functionality or review analyses live. Workshop topics include:

• Data Analysis
• Toxicology
• Biomarker Discovery
• Search and Explore functionality

Ingenuity’s user group meetings are a complete experience including meals, refreshments, and evening social events. Last year’s wine tastings were enjoyed by all who participated, and the events planned for Cannes and Cambridge will be equally special. Don’t miss your opportunity to learn more about how IPA can help your research.

» Sign up now!

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Quick Tip: Path Designer

Are you currently using additional software packages to create images from your IPA network or custom pathway for a poster, presentation, or publication? With the upcoming release of IPA 6, you will be able to complete this workflow from within IPA.

IPA’s Path Designer tool is an excellent way to create graphically rich images for publication and clear communication of results to colleagues. This tool will be located under the Path Designer button available on any Network, Pathway, or Neighborhood in IPA (see screenshots below).

Clicking this button will open your pathway in a Path Designer workspace so that you can optimize the shapes, colors, and line styles, and add backgrounds and free text to create a custom image.

The Shapes tool allows you to select shape styles, change the fill color or gradient, or relabel molecules with your preferred common name. The Organelle tool allows you to add organelles to your image, and move molecules into their specific subcellular compartments. The Text tool allows you to label your images with relevant contextual details. Choose a suitable background (or upload a custom background) using the Background tool to finish your image. When complete, use one of IPA’s export options (export image, print, or send as an interactive email to your colleagues) to save and use your image outside of IPA.

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Feature Highlight: Tissue and Cell Line Expression Atlas

Do you need to rapidly identify the genes in a pathway or network that are expressed in a particular tissue or cell line? Use the Tissue and Cell Line Expression Atlas, which contains positive expression calls (an indication that a gene is present at the transcript level) in over 30 normal tissues and now, with the release of IPA 6, for the NCI-60 panel of cancer cell lines as well. You can access this expression information through multiple features in IPA including the Overlay menu in My Pathways and Path Designer, and also as a filter in IPA-Biomarker™.

As demonstrated in the figure below, the Tissue and Cell Line Atlas enables you to quickly identify the genes in any pathway or network that are expressed in a particular tissue or NCI-60 cell line. In the pathway below, which contains genes implicated in cell death pathways in melanoma and the drugs that affect their activity, the Cell Line Atlas quickly identified (in red) genes expressed in melanoma cell lines, which enables researchers to narrow in on cell lines that might be appropriate for subsequent assays.

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Ingenuity Whitepapers: Simple Examples to Answer Your Questions

We have created a number of whitepapers to provide tangible examples of how IPA can be used to address a variety of research challenges. These whitepapers focus on features that are having a significant impact on life scientists’ workflows and experiences with IPA, and we have created these whitepapers to provide clear, concise information on how and when to apply these features to your own research. Click on the below links to download these valuable resources about IPA.

Search and Explore whitepaper: The search capability generates relevant lists of genes and chemicals associated with specific biological functions, pathways, or annotations. Unlike traditional solutions, the resulting lists can then be transformed into fully interactive, literature-supported graphical models of experimental systems using IPA Explore tools such as Grow, Connect, and Path Explorer. This whitepaper explores how the search function can be used to quickly identify genes and chemicals involved in tumor angiogenesis and rapidly flag the subset of druggable tumor angiogenesis genes. Pathway building tools are then applied to examine how tumor angiogenesis genes work together as a molecular module, to identify adjacent signaling and metabolic pathways, and to identify experimental tools and drugs that can be used to perturb those pathways.

API Integration Module whitepaper: This valuable module enables life science researchers to access the high quality, detail-rich biological and chemical knowledge in IPA directly from their internal websites and gene catalogues, as well as from internal research reports, e-mails and other shared documents that are part of their day to day research workflows. This easy-to-implement module increases the utility of internal web sites, search portals and research reports by providing easy links to the content and analysis capabilities in IPA.

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Publications

Focus: IPA Contributes to a Better Understanding of Host Response to Pathogens

The emergence of multi-drug resistant strains of bacteria and viruses is being met with the development of novel strategies for discovering new targets for therapeutic intervention – including methods for identifying and targeting the host cellular pathways that are essential to pathogen survival. As part of this new approach, infectious disease researchers are turning to large-scale technologies such as transcriptomics, proteomics, and metabolomics to understand the host-pathogen response at a system-wide level. Many of these researchers have quickly adopted IPA as part of this research strategy in order to rapidly understand the cellular networks and pathways that are activated in response to pathogen infection and which may hold the key to pathogen survival. Below we’ve highlighted a sample of some of the more recent IPA publications in this area. For a complete list of Infectious Disease publications citing IPA please go to http://www.ingenuity.com/library/search-pub.html, and select “Infectious Disease” from the “Research Area/Field of Interest” search field.

• Systems biology and the host response to viral infection - Nature Biotechnology, 2007 Dec; 25(12):1383-9
  
  
• Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1 - Nature, 2007 Nov 29; 450(7170):725-30
  
  
• Identification of differentially activated cell-signaling networks associated with pichinde virus pathogenesis by using systems kinomics - Journal of Virology. 2007 Feb; 81(4):1923-33

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IPA Certification Program

Would you like to be the IPA expert at your institution, or just gain more confidence using IPA? We have recently enrolled a tremendous number of people into our free online IPA Certification Program. These researchers are participating in a structured curriculum designed to provide comprehensive training for those who want an in-depth understanding of IPA content and capabilities and gain an edge in their research. Upon completion of the program, participants will receive official certification as an IPA Certified Analyst.

» Click here to learn more about the program, and to enroll.

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2008 Ingenuity Events

Ingenuity will be attending a number of conferences in the next few months. We will also be presenting at the ToxExpo in Seattle and at CHI’s Molecular Medicine conference in San Francisco. Attend our presentations and drop by our booth: we’d like to hear your feedback about IPA, or help you learn more about how IPA can contribute to your research.

ToxExpo 2008
Seattle, Washington
Visit Ingenuity Systems at Booth 2104
Dr. Brigitte Ganter, Ingenuity Systems, will present on Tuesday, March 18 at 2:45 pm March 17-19, 2008

CHI Molecular Medicine Tri-Conference
San Francisco, California
Visit Ingenuity Systems at Booth 301
Dr. Art Okamoto, Ingenuity Systems, will present on Thursday, March 27 at 10:15 am March 26-28, 2008

Ingenuity U.S. User Group Meeting
Cambridge, Massachusetts April 1-2, 2008

Primate Genomics and Human Disease
Seattle, Washington April 13-16, 2008

Ingenuity European User Group Meeting
Cannes, France April 24-25, 2008

»Click here for more 2008 events.

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Other News

• The Pritzker Neuropsychiatric Disorders Research Consortium Renews and Expands Access to Ingenuity Pathways Analysis To Aid Efforts to Identify Novel Treatment Targets
  
  
• Ingenuity Systems and FDA Enter 3-Year, $6 Million Collaboration to Enhance Regulatory Review Process
  
  
• Ingenuity Systems Launches New Metabolomics Solution Within IPA
  
  
• Ingenuity Systems Joins Biomarkers Consortium
  
  
• Sigma-Aldrich and Ingenuity Systems Announce Partnership to Create E-Commerce Search Solution Based on Biological Knowledge

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We're hiring!

Ingenuity systems is looking to add to its world-class team. Do you know someone who would be interested?

Our groundbreaking technologies help life science researchers more effectively search, explore, visualize, and analyze birological and chemical findings related to genes, proteins, and small molecules (e.g. drugs). Our solutions are created by biologists and deelopers who combine innovative semantic search, ontology, and software development technologies with life science research expertise. Biologists provide key insight and scientific integrity to out product and content development processes, while our software development, quality assurance, ad operations staff leverage cutting edge tools and technologies to develop and deploy products that effectively address our customers' needs. A wide range of sales, marketing, support, and administrative positions round out our team and ensure that our business operations are as efficient and well-run as our product offerings. In each of our locations, we hire talented, local people to assist in our goal of developing solutions that enable our customers to succeed. Do you have something to contribute?

» Click here to browse for current job openings

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