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Product Updates: IPA Summer Release coming soon! |
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Early this summer, Ingenuity will be releasing the latest version of IPA. In addition to the major feature changes (listed below), other enhancements include improved usability in areas such as Path Designer , list comparison, and overall performance. Major new features include:
- Support of Affymetrix Exon Arrays (for gene expression use cases)
IPA now supports the upload of transcript IDs from all probes that map to genes.
- Support of new species with EntrezGene IDs
Researchers will now be able to analyze data from nine new species through direct mapping to the human, rat, or mouse orthologs.
- Compare Feature
Researchers can easily identify unique, common, or combined sets of molecules in lists, pathways, biomarkers, and analyses.
- New Content
The summer release of IPA includes content updates for: drug information (such as manufacturer, trial sponsor, and link to NCT website), protein-protein interactions, new canonical pathways, and more.
- Reference Management
Export your references directly into Endnote, BibTeX, or PlainText formats.
» Click here to learn more about these new features.
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Quick Tips |
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Q: How can I build my own pathway from a list of genes without uploading my dataset?
If you want to build your own pathways using a list of genes, you can create a list in IPA without having to upload your dataset. On the quick start screen in IPA, under Analyze/Core, click on Analyze a dataset. On the create core analysis window click on UPLOAD button. Browse your computer for the dataset file and click on open. This will bring up the dataset upload page.
Click on Dataset Summary tab and then on Show Details
This will bring up the Mapped and Unmapped tabs. Click on the Mapped tab and then do Ctrl A on your keyboard to select all the molecules. Click on Add To List button and choose new list.
In this way you can create a list in IPA without uploading your dataset or running an analysis.
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Feature Highlight |
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Feature Highlight: Compare Feature
The new compare feature (available in the summer release of IPA) is a simple tool that helps you identify commonalities and/or differences across different lists, pathways, biomarkers, or analyses. This feature can help you understand early versus late drug response patterns, as well as annotate and export lists of molecules with biological content.
You can use this feature directly from the quick start window (see below), or directly from your lists, pathways, analyses, biomarker filters, canonical pathways, or Tox lists.
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Ingenuity Whitepapers |
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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 |
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Focus: Neurological Disease and Disorders
Each year, millions of individuals are affected by neurological diseases and disorders such as schizophrenia, bipolar disorder, and Alzheimer's disease. These disorders have been extensively studied by researchers from multiple angles - including attempts to develop new drugs targets as well as to identify and understand the disorder's underlying mechanism of action. In the past few months, researchers worldwide have used IPA as part of their research and discovery workflows to identify structural variants that contribute to schizophrenia, to understand the differential gene expression between neurological disorders, and to identify potential biomarkers in the blood.
Below we've highlighted a sample of some of the more recent IPA publications in this area. For a complete list of neuroscience-related publications citing IPA, please go to http://www.ingenuity.com/library/search-pub.html, and select "Neuroscience" from the "Research Area/Field of Interest" search field.
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Ingenuity Events |
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Report from our User Group Meetings
See what attendees had to say!
"Thank you for being so open to suggestions from users, it inspires loyalty to IPA and increases user confidence in being able to use the product, as well as confidence in the product."
"I especially appreciated the scribes at the breakout sessions who clearly were interested in getting down user suggestions."
The most valuable part of the meeting was:
- "Breakout sessions - it was really interesting to share experiences between users"
- "To see in which context Ingenuity has been used"
- "The interactive parts and discussions with Ingenuity and users. I had a chance to influence the future of IPA as well as understanding how other people are using IPA and how they would like to be able to work in the future."
- "Kindness of IPA team to take time listening to every possible question I had."
- "As a relatively new user, I enjoyed the workshop on core analysis, especially for informing us on the tools."
Feature Awareness Alert
Below are some feature requests we've received that are actually already a part of IPA functionality. How many do you already know about?
| WHAT YOU WANT TO DO |
WHERE TO GO IN IPA |
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Graphic representation of functional clustering of data |
Overlay function |
| Analyze time course data |
Use Comparison and Overlay Expression bar charts; each time point is a separate observation |
| Easier visualization of expression overlay using different background colors |
Newly added via Path Designer functionality |
| Visualization of gene expression in tissues |
Use Overlay Tissue Expression |
| Run comparison analyses from different datasets |
Use Comparison Analysis Feature and select "datasets" |
| Add links to publications that support toxicology functions, biomarker filtering |
Select function on molecule of choice to view molecule summary > gene view > categorized literature > findings. |
| Button to remove unconnected nodes/edges |
Use delete button -"x" |
| See overlays, union, unique, or comparison between lists/pathways |
Use List Comparison feature |
| Add algorithm for multiple testing correction |
Newly added to IPA 6 |
Questions? Contact Customer Support at 650.381.5111 or support@ingenuity.com
How Are Attendees Using IPA?
Photos from the European Meeting:
The 2008 European User Group Meeting was held in Cannes, France |
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CEO Jake Leschly speaks with Rasoul Nourizadeh from the Norwegian School of Veterinary Science at the rooftop reception. |
Keynote Speaker Mike Trower from GSK's Research Informatics group presenting on Improving Target Validation in IPA |
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Lunch at the Chez Panisse in Cannes |
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Ingenuity News |
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FDA Collaboration with Ingenuity Featured in Bio-IT
John Russell of Bio-IT recently spoke with Frederico Goodsaid of the FDA at the 2008 Molecular Medicine Tri-Conference about the FDA's increasing use of pathways tools in the Voluntary Exploratory Data Submissions program. Goodsaid discussed the challenges the FDA faces when turning lists of differentially expressed genes into knowledge that answers key biological questions. His belief that pathway tools are an important part of the solution is reflected in the FDA's recent collaboration with Ingenuity. According to the article, "Goodsaid noted this as the driving rationale behind the agency's recent CRADA with Ingenuity Systems. Initial goals to adapt Ingenuity's platform to support the VXDS program, deploy IPA and provide training, and build an API for integration with NCTR's ArrayTrack application are completed."
"Now the two are working on building an IPA-based solution for regulatory review of biomarker, pharmacogenomic, and toxicogenomic data. Content is being expanded as well. 'The idea is to expand the content of the tool to make sure it covers the drug, chemical, and biomarker universe that we're interested in,' indicated Goodsaid."
» Read the full article
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Path Designer wins Best in Show at Molecular Medicine!
Thank you for voting Path Designer as best new product at Molecular Medicine!
Ingenuity would like to thank the scientific community for its support of Path Designer, the new tool in IPA that helps you to create customized, publication-quality graphics to more clearly communicate your experimental findings and scientific hypotheses. With Path Designer, graphics remain interactive, so new information can be added and the original knowledge used to build the pathway remains accessible."
"We are delighted to have won this award," stated Brigitte Ganter, Director of Product Management at Ingenuity Systems. "IPA's development has always been customer-centric, and we developed Path Designer in response to our to customers' need to effectively communicate their scientific findings in a visually compelling and meaningful manner. We are honored to receive this community-chosen award and appreciate the strong support from the IPA user community in designing the product."
» Download the Path Designer white paper
» Click to read the full press release |
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Introducing the new Ingenuity Scientific Seminar Series
This new scientific webinar series from Ingenuity focuses on using IPA to answer specific research questions.
Past Topics:
- May 7 - Lipoplysacharide Toxicity in Rat Liver
Here we show how IPA can help determine the mechanism of action and hepatotoxicity in rat treated with LPS, as well as investigate the effects of lipopolysaccharide on global liver gene expression.
- May 21 - Metabolic Changes in Acetaminophen Treated Mice
Acetominophen is known to cause hepatotoxicity in large doses. This case study shows how to use a combination of the IPA-Metabolomics Analysis with IPA-Core and Tox analyses to learn about both the changes in metabolites and expressed genes.
The below upcoming topics and dates are subject to change. Please check www.ingenuity.com for the latest schedule.
- June 4 - Large Scale Data Analysis
- June 18 - Post-translational Modification Analysis Using IPA
- July 2 - Biomarker Analysis: Patient Subtyping
- July 16 - Proteomics Analysis using IPA
- August 6 - siRNA Genome Wide
- August 20 - microRNA Analysis Using IPA
- September 3 - SNP Analysis Using IPA
- September 17 - CHIP on CHIP Analysis Using IPA
PDF Resources to Download
Ingenuity has compiled a new series of downloadable resources to help you with your IPA experience. Please click on any of the below titles to learn more.
INGENUITY PRODUCTS AND SERVICES |
| IPA Integration Module |
Enable direct links between internal applications/content or third party applications (Spotfire, Rosetta, etc) and IPA for more powerful workflows. |
| Ingenuity WebASK |
Learn how to ask sophisticated biological questions with Ingenuity's query tool. |
| Ingenuity Single Sign On integration package |
Learn the benefits of accessing IPA directly through your existing enterprise infrastructure. |
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Ingenuity is Hiring! |
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Do you know someone who would be interested?
Our technologies help life science researchers more effectively search, explore, visualize, and analyze biological and chemical findings related to genes, proteins, and small molecules (e.g. drugs). Our solutions are created by biologists and developers who combine innovative semantic search, ontology, and software development technologies with life science research expertise. Some current positions include:
- Biomedical NLP Engineer
- Field Application Scientist
- Senior Interaction Designer
- Senior Unix Applications Administrator
- Senior Vertical Search Architect
» Click here to browse all of our current openings
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Copyright
2007 %%Member_Busname%% %%Member_Addr%%, %%Member_City%%,
%%Member_State%% %%Member_PostalCode%%, %%Member_Country%%
www.ingenuity.com | North American Sales: (1) 650.381.5056
| European Sales: +44 798 887 6927
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