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IPA 5.0 won
the “Best
in Show” award for Life Science
Software & Informatics at CHI’s
recent Bio-IT World Conference and Expo.
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We would like to thank you, our users
and conference attendees, for showing
your enthusiastic support of our product
and contributing to this success. The
criteria for the award included technical
merit, functionality, and innovation,
and we are pleased that IPA continues
to bring these values to you. |
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Publications
using IPA: A closer look at infectious diseases
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| We continue to be delighted with the ongoing
publication of a wide variety of important,
peer-reviewed research that has been accelerated
through the use of IPA. Since our last Insider
issue, over 50 new articles have been published
that cite the use of IPA, bringing the total
to over 300 articles. A full bibliography is
available here,
searchable by research area. We want to highlight
two recent articles which illustrate how IPA
was used to generate important insights on infectious
disease.
A research team led by John Kash and Michael
Katze of the University of Washington analyzed
gene expression data in IPA and concluded
that infection with the 1918 influenza virus
resulted in significant activation of pro-inflammatory
and cell death responses, and that activation
of these pathways may be major contributors
to the severe immunopathology seen in mice
infected with the 1918 virus. A comparison
analysis run in IPA went on to reveal that
the biological responses most significantly
induced by infection with non-lethal strains
of the virus included cell-cycle and glutathione
metabolism pathways, both of which may contribute
to the less severe immunopathology seen in
mice infected those strains. Published in
the October 5, 2006 issue of Nature, the study
was considered the #24 science story of
the year by Discover magazine. Read more
here.
In the February 14th Journal of Virology,
Dr. Norbert Herzog and his colleagues describe
using a newly developed protein-scanning chip
and IPA to examine the activation and deactivation
of more than a thousand proteins in cells
from guinea pigs infected with two different
strains of Pichinde virus. To better understand
their results, the investigators analyzed
their experimental data in IPA. “Applying
IPA, which includes all sorts of cellular
pathways that would normally not occur to
us — pathways discovered by people studying
endocrinology, cancer, cystic fibrosis and
so on — we find that things suddenly
begin to make sense,” said UTMB professor
Norbert Herzog, one of the paper’s senior
authors. “Cell signaling networks are
like spider webs—pulling on one strand
causes all the strands to move, and the Ingenuity
system helped us see and comprehend connections
we would have missed otherwise.” Read
more here.
Other recent papers using IPA to understand
infectious disease:
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Top
Trends: Toxicology and Biomarkers
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| Bernadette Toner, editor for BioInform, recently
commented that toxicology was the new magic
word among pathway vendors. While spending time
at the Molecular Medicine Tri-Conference in
San Francisco, she spoke to Megan Laurance,
product research scientist at Ingenuity Systems,
about the upcoming release of IPA 5.0 which,
according to Toner “includes two capabilities
expected to be of great interest to drug-discovery
researchers: biomarker analysis and molecular
toxicology analysis.”
What do we think are some of the
top trends in molecular toxicology?
Tell us what you think.
- Rank compounds for relative safety
- Compare target to competitor molecules
- Develop early screens for potential latent
adverse effects
- Use toxicology as a starting point for
mechanistic analysis
One of the hottest buzzwords today is biomarker,
driven largely by the FDA’s recent announcement
of the Critical Path Initiative. Use of biomarkers
has been embraced by both the biotechnology
and pharmaceutical communities.
What do we think the top needs in
biomarker research are? Tell
us what you think.
- Define clinical needs for biomarkers
- Establish standard paradigm for biomarker
development
- Combine data from multiple biomarkers
using statistical methods
- Compare biomarkers from different sources
- Decide when marker is ready for testing
in the clinic
- Implement reference standards for assays
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Feature
Highlight: Emailing Interactive Pathways
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Ingenuity understands that collaboration
is a critical part of any research process.
To facilitate this goal, IPA 5.0 now allows
you to export fully interactive pathways,
with access to underlying information, and
insert them into emails or presentations.
It is a simple way to quickly share insights,
results, and information with colleagues,
no matter where they are.
Here’s how:
- Create your network
- Simply right click and select “Send
by e-mail”. You will then be prompted
for the email address, which you just type
in. You have the option to send the current
view or the entire pathway.
- That is it! If your colleagues have IPA,
they can instantly view and interact with
the network. If they are not an IPA user,
they will be prompted to sign up for a trial.
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IPA
Training Resources & Tips
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IPA Quick Tips
Need some help getting started with
your IPA account?
- In IPA, go to Help, Help Manual, Tutorials
to see a list of all tutorials and step-by-step
instructions on IPA.
- Attend one of our on-line training sessions.
Registration for training sessions is free
and available from www.ingenuity.com.
- View the on-line recorded training sessions:
In IPA, go to Help, Help Manual, Help Resources,
“View our pre-recorded training videos.”
Want to create your own biological
model within IPA?
- Use the My Pathways feature in IPA. See
our quick start tutorial on My Pathways
to get started. Go to Help, Help Manual,
PDF Files to Download, My Pathways.
Want to search the Ingenuity Pathways
Knowledge Base for information on a particular
function, disease, gene, or drug?
- Use Basic or Advanced search. Use our
quick start tutorial on either topic to
get started. Go to Help, Help Manual, PDF
Files to Download, Basic Search or Advanced
Search.
Want to learn more about the new features
in IPA 5.0?
- IPA's Help section has been updated with
step-by-step tutorials and detailed descriptions
of each feature.
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Events
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European User Group Meeting: Report From
Basel
The European User Group Meeting in Basel
was an informative and fun way for IPA users
to network with colleagues and see how other
researchers are using IPA’s powerful
capabilities.
"There were great presentations from
our customers, and it was interesting to see
how IPA was utilized in multiple research
areas.” stated Art Okamoto, Senior Product
Manager at Ingenuity. “It was also extremely
useful to see firsthand how the community
actually uses IPA. It’s another extremely
valuable way to understand their needs and
challenges and translate that into clear product
development.”
“I thought it was a valuable venue,
as it allowed our European users to network
and discuss the issues that are important
in their community,” noted Brigitte
Ganter, another Senior Product Manager at
Ingenuity. “Lots of clever ideas and
suggestions were brought forward that we plan
to include in our product process. These meeting
are great opportunities to exchange thoughts
with our users.”
Many of the new improvements in the recently
released IPA 5.0 were first suggested by customers
at past user group meetings, including:
- Searching on mixed identifiers
- Visualizing inhibitors or pharmacological
agents on networks
- Enabling of full "network" functionality
in canonical pathways
- Customizing colors on bar charts
- Supporting more than ten timepoints in
comparison analyses
See below for pictures from our user group
meeting in Basel.
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| Estelle Marrer and Andre Cordier from
Novartis |
Seeing how colleagues use IPA |
Getting personal attention in the IPA
Workshop |
Sign up for the U.S User Group Meeting Now!
Sign
up now for our U.S. User Group meeting
in beautiful San Francisco, California! It
is a unique opportunity to get hands on training,
network with colleagues, and learn about new
ways you can apply IPA to your research projects.
This year’s meeting features a distinguished
series of speakers and a timely selection
of topics, including:
- Beth Basham, Ph.D., Schering-Plough
Biopharma
Analysis of Transcriptional Regulation using
Transfac, the UCSC Genome and Ingenuity
IPA
- James Greg Falls, Ph.D.,
GlaxoSmithKline
Insight into Peroxisome Proliferator Activated
Receptor (PPAR) Agonism Using Ingenuity
Pathway Analysis
- Dejan Juric, M.D., Massachusetts
General Hospital, Harvard Medical School
Knowledge-Based Interaction Networks in
Cancer Drug Resistance and Oncogene-Driven
Transformation
- Edward “Ward” Kadel,
Research Associate, Pharmacodynamic Biomarkers,
Oncology, Genentech
Ingenuity Pathways Analysis 5.0 –
A Pharmacodynamic Biomarker Perspective
- Eric Muise, M.Sc., Research
Associate, Merck
Microarray Profiling Demonstrates Important
Similarities, and Differences, Between the
Liver and Adipose Tissue Signatures of Adiponectin
and PPARg Agonists
- Jose Pardina, Ph.D.,
Principal Research Scientist, Centocor Discovery
Research
Leveraging Pathway Analysis to Engineer
Mammalian Cell Lines With Increased Protein
Production Capacity
- Rob Sladek, Ph.D., McGill
University
A High Density Genome-Wide Association Study
Identifies Novel Susceptibility Genes For
Type 2 Diabetes Mellitus And Reveals New
Mechanisms For Glucose Intolerance
- Wenzhong Xiao, Ph.D.,
Stanford University
Knowledge-based Network Analysis of Inflammation
and the Host Response to Injury
- Ramon Felciano, Ph.D.,
CTO and VP Research, Ingenuity Systems
Leveraging the Ingenuity Knowledge Platform
for Life Sciences Research
- Art Okamoto, Ph.D.,
Senior Product Manager, Ingenuity Systems
Application of New Solutions in IPA 5.0
For a detailed agenda, please
click here. Or, sign
up now.
Meet Ingenuity: Upcoming Events
We love to meet our customers! Ingenuity
is proud to have a strong history of incorporating
customer comments and requests into the development
of our products. We are also committed to
answering your questions and providing you
with the most up-to-date information on our
products and services.
Please come by any of the following events
to learn more about us, make a suggestion,
or just say hi:
- Ingenuity Systems U.S. User Group
Meeting (click
here to register)
San Francisco, CA
June 4-5, 2007
- Beyond Genome
San Francisco, CA
Visit Ingenuity Systems at Booth 203
June 20-22, 2007
- Japanese User Group Meeting
Tokyo, Japan
August 28-29, 2007
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