Microsoft Server Product Portfolio
Customer Solution Case Study
Epilepsy Study Chooses Microsoft for EDC,
Global Collaboration, and Data Management
Overview
Country or Region: United States
Industry: Healthcare—Life sciences
Customer Profile
The University of California at San
Francisco is dedicated to advanced
biomedical research, graduate-level
education in the life sciences and health
professions, and excellence in patient
care. It has 10,000 employees.
Business Situation
The university needed an unusually large
and sophisticated technology platform to
support hundreds of researchers in 20
centers around the world, while
minimizing the burden on the informatics
staff.
Solution
Project directors chose to base their
public Web site, intranet portal,
applications, and databases on Microsoft
technologies from end to end.
Benefits
 Cuts development time by 50 percent
 Provides exceptional ease of use
 Delivers near 100 percent uptime,
minimizing support needs
“This is such an advance for the field of clinical research
informatics that we’re looking at making components
of the architecture available to others in the research
community.”
Gerry Nesbitt, Director of Bioinformatics, the Epilepsy Phenome/Genome Project,
University of California at San Francisco
Unlocking the genetic secrets to epilepsy might provide the key
not only to better treatments but also to prevention. To pursue
that possibility, researchers at the University of California at San
Francisco and at New York University are heading up the
Epilepsy Phenome/Genome Project, which spans hundreds of
researchers at 20 centers worldwide. Their challenges in
collecting, processing, storing, accessing, and analyzing massive
amounts of data, and in collaborating with colleagues around
the globe, are enormous. To gain the patient-tracking, electronic
data capture (EDC), global collaboration, and data management
capabilities that they need, the researchers chose Microsoft
technologies. The resulting solution meets their needs for
reliable and efficient data collection, low-cost support and
training, faster application enhancement, faster knowledge
discovery, and improved productivity.
“We chose Microsoft
technologies over LAMP
because we needed 100
percent reliability and
scalability, and we had
very little time to get the
solution into production.”
Gerry Nesbitt, Director of Bioinformatics,
the Epilepsy Phenome/Genome Project,
University of California at San Francisco
Situation
Epilepsy. It’s a word no one wants to hear,
but too many people hear it nonetheless.
The disease afflicts more than 50 million
people worldwide, according to the World
Health Organization (WHO). Epilepsy can
strike the young as well as the old.
Symptoms can range from brief staring
spells to full-blown seizures. There are
treatments but no known cure. Although
some patients respond well to the first antiepilepsy drug they take, others experience
intractable forms of the disease that do not
respond well to medications. They may
require massively invasive surgery, such as
the removal of part of the brain, to achieve
a level of relief.
In 2007, two of the largest centers for
epilepsy research in the United States—the
University of California at San Francisco in
the west and New York University in the
east—decided to team up to study one of
the least understood aspects of epilepsy: its
genetic basis. The National Institutes of
Health granted U.S.$15 million for the
research.
The researchers at the University of
California at San Francisco and New York
University formed the Epilepsy
Phenome/Genome Project (EPGP) as the
centerpiece for what became an
international, multi-institutional, multiyear,
collaborative research effort. That effort
grew to include 20 academic research
centers worldwide, making it one of the
largest such studies ever conducted. The
broad scope of the project—which
encompassed thousands of data points for
each of thousands of research subjects—
was necessary to give researchers a study
population large enough that they could
identify and link genetic information to
phenotypic data.
It wasn’t only the research population that
needed to be large. The researchers quickly
realized that they needed an informatics
infrastructure and an application
architecture that were as large and
sophisticated as the questions they were
studying. One reason was the large
volumes of data that researchers would
need to store and access. Another was that
the researchers—who, after all, were
experts in biology, not computer science—
needed the ability to work easily with and
analyze that computerized data.
In addition, the large numbers of
geographically dispersed researchers
meant that the project’s five-person
informatics staff couldn’t possibly provide
in-depth technical support; the project
therefore needed applications that were as
easy for the researchers to learn and use on
their own as they were easy for the
informatics staff to deploy, administer, and
support.
That the group of researchers was large
and dispersed also indicated the need for
collaboration and workflow tools so that
researchers halfway around the world could
work together as though they were down
the hall from one another. Reliability was
another requirement because project
leaders knew that they couldn’t afford to
lose or compromise any of the research
data.
The project’s informatics staff, based out of
the University of California at San Francisco,
had a complex, multifaceted set of
requirements to meet—and not much time
in which to meet them. The staff had just
eight months before the project was slated
to enroll its first research subjects, and
informatics systems had to be live by then
to accept incoming data.
“Enterprise-class data
management was
essential, and SQL Server
provided that.”
Gerry Nesbitt, Director of Bioinformatics,
the Epilepsy Phenome/Genome Project,
University of California at San Francisco
Solution
The first step in developing the informatics
infrastructure was to identify the services
and functions that the solution would have
to support. Working closely with the
researchers, the informatics staff developed
a list of requirements that included
everything from collecting and managing
detailed phenotypic data,
electroencephalographs (EEGs), and
magnetic resonance images (MRIs) to
tracking the status of participants and their
blood specimens throughout the term of
the study.
Off-the-Shelf or Custom Development?
The next step was to decide how to
implement the needed functionality—that
is, whether to purchase and modify an offthe-shelf solution or to develop a custom
solution. The responsibility for that decision
fell to Gerry Nesbitt, the project’s Director
of Bioinformatics at the University of
California at San Francisco. He and his team
considered commercially available software
for clinical trial management, such as
Oracle Clinical and PhaseForward InForm,
and found them wanting. Some were too
expensive, others couldn’t accommodate
the electronic collection of large
phenotypic data sets, and most were not
scalable enough.
That left custom development. The most
common technology platform in academia
is the so-called LAMP stack—the Linux
operating system, Apache Web server,
MySQL database, and PHP programming
language—with Apple Macintosh
computers on the front end. But Nesbitt
and his colleagues made a different choice.
Choosing the Right Platform
“We chose Microsoft technologies over
LAMP because we needed 100 percent
reliability and scalability, and we had very
little time to get the solution into
production,” says Nesbitt. “Enterprise-class
data management was essential, and SQL
Server provided that. SQL Server also gave
us fully supported, out-of-the-box and
third-party options for reporting and
analysis. MySQL didn’t. Similarly, SharePoint
Server 2007 gave us the features, again
built-in, that we needed for both a public
Web site and an internal collaboration site.”
In addition to Microsoft SQL Server 2008
data management software and Microsoft
Office SharePoint Server 2007, the project’s
informatics solution was based on
Microsoft technologies, including the
Windows Server 2008 operating system,
Microsoft ASP.NET, the Microsoft Visual
Studio 2005 development system, and,
later, Visual Studio Team System 2008
Team Suite.
Applications and a Portal
The informatics team worked for eight
months, and its solution went live in
January 2008. That solution consisted of
applications accessed through a secure
intranet portal. All components of the
solution were Web based, which addressed
the requirement that the solution be easily
accessible both to global users and to
informatics maintenance and support
personnel.
Those components included the following:
 A public Web site to provide information
about the project and to solicit the
participation of volunteers as research
subjects.
 A private intranet portal for researchers,
which provided access to the
applications, to the study’s documents,
and to collaboration tools.
 Applications for tracking participant
activity, which made it possible for each
clinical site to track its participants’ visits,
manage events and issues, and complete
phenotypic data collection.
“By using Microsoft
technologies, we’ve
been able to give our
researchers and
coordinators a level
of informatics
sophistication rarely seen
on projects funded by
the National Institutes of
Health.”
Gerry Nesbitt, Director of Bioinformatics,
the Epilepsy Phenome/Genome Project,
University of California at San Francisco
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A specimen-tracking system to manage
the life cycle of blood specimens from
the moment a blood sample was drawn
to its arrival at the specimen repository.
A case-report form designer and datacollection tools.
Applications for EEG data collection and
reviews by neurophysiology experts.
Applications for MRI data collection and
reviews by imaging experts.
Secure file transfer for EEG and MRI files.
A central database repository providing
data storage, validation and integration,
and robust security.
A data warehouse through which
researchers query the data using
Microsoft or third-party tools, including
Microsoft Office Excel spreadsheet
software, Office Access database
software, SQL Server Reporting Services,
Office PerformancePoint Server 2007 (a
part of Office SharePoint Server 2007),
and Visokio Omniscope.
coordinators a level of informatics
sophistication rarely seen on projects
funded by the National Institutes of
Health,” says Nesbitt. “We’re seeing more
reliable and efficient data collection, fewer
resources needed for support and training,
faster completion of application
enhancements, faster knowledge discovery,
and higher productivity overall.”
Cuts Development Time by 50 Percent
To build the large and sophisticated
informatics solution on an aggressive
project schedule, the developers turned to
an Agile development strategy, which they
implemented through the use of Visual
Studio 2005 and, later, Visual Studio Team
System 2008 Team Suite. Nesbitt estimates
that because the team used the Visual
Studio tools, development time was about
50 percent less than it would have been
using the alternatives he might have
chosen.
These applications are hosted in a West
Coast data center and mirrored for backup
and disaster recovery in an East Coast data
center. Each data center hosts a pair of
databases: one is a transactional database,
with which researchers interact through the
various applications for data collection,
tracking, and transmittal. The other is a
reporting database that provides the basis
for analysis, data visualization, and reports
in response to queries from the
researchers’ business intelligence tools.
“The Visual Studio tools allowed our team
to get a real jump-start on development,”
says Nesbitt. “We took advantage of the
tools’ strong interoperability with our
foundation applications, such as SQL
Server, and of their features for
collaboration among developers—such as
check-in and check-out of code and strict
version control. That helped us to achieve
smooth collaboration between our
domestic team and our outsourced
developers in Chennai, India.”
Benefits
For example, the Microsoft tools supported
a 24-hour development and quality
assurance (QA) cycle in which local
developers created code and performed
QA before the end of day, and then passed
their work on to the developers in Chennai
to address bugs and other issues. The
outsourced developers finished their work
just in time for Nesbitt’s local developers to
The massive research project was up and
running in just eight months and now gives
researchers easy and dependable access to
applications and data. In addition, it
minimizes the support burden on the lean
informatics staff.
“By using Microsoft technologies, we’ve
been able to give our researchers and
pick up again with the new code. That
shortened development considerably.
The Microsoft technologies also helped to
speed development by providing
components—such as business intelligence
in SQL Server and collaboration tools in
Office SharePoint Server—that eliminated
the need to build or buy this functionality
and then integrate it with the rest of the
system.
The informatics team used
Microsoft Office SharePoint
Server 2007 to create a public
Web site that doesn’t look like a
“typical SharePoint site.”
Master pages in SharePoint Server made it
easy for the developers to add logos,
colors, and typefaces into the public Web
site, and then to make the use of those
visual elements consistent throughout that
site. Nesbitt proudly notes that his team
got the public Web site and intranet portal
up and running in less than one week.
Further, the same capabilities that
supported the fast development of the
solution are now used by the project
developers to speed application
enhancements and extensions.
Provides Exceptional Ease of Use
The EPGP informatics applications had to
be as easy for researchers to use as they
were easy for the informatics team to
develop. The Microsoft technologies also
helped the informatics team to meet that
requirement, according to Nesbitt.
Researchers benefit from the use of Office
SharePoint Server for the intranet portal,
which provides a convenient, central place
to find all of the EPGP applications, all of
the research data and tools, and all of the
reports and other study documentation.
“Because the
applications are based
on Microsoft
technologies, we can
train new coordinators in
one hour, and they are
fully equipped with the
skills and confidence to
use the applications
immediately.”
Gerry Nesbitt, Director of Bioinformatics,
the Epilepsy Phenome/Genome Project,
University of California at San Francisco
The intranet portal also gives researchers a
broad choice of analysis tools. Researchers
can work through familiar tools, such as
Microsoft Office Excel; visual dashboards
based on Office PerformancePoint Server;
and research-specific, third-party tools,
such as Omniscope. Because the
informatics solution uses Web-based tools
for tracking participants and phenotypic
data collection, researchers and study
coordinators gain real-time access to
subject enrollment statistics, study metrics,
and research data.
Researchers also find that their work is
expedited—and that the impact of having
colleagues spread among various research
centers is mitigated—by collaboration
tools, especially those available in Office
SharePoint Server. For example, they use
discussion boards for ongoing virtual
conversations, while wikis provide a way to
share best practices—such as how to boost
subject recruitment—among study
coordinators.
Even nonresearch functions are made
easier for project researchers through the
use of Microsoft technologies. The public
Web site, for example, is maintained not by
dedicated informatics staff, but rather by
two researchers whose work on the site is
one of their many duties. That work is
made easier both by the publishing tools in
Office SharePoint Server and by the
software’s workflow tools, from which
Nesbitt and his colleagues created an
automated workflow that routes proposed
content to authors, editors, and reviewers
for approval prior to posting.
And researchers aren’t the only ones who
can work effectively because of the
Microsoft technology underlying the
solution. The easy-to-use applications and
tools make it possible for study
coordinators to complete their tasks
quickly, contributing to the widespread
acceptance of those applications, higher
productivity among coordinators, and
reduced turnover in staff.
“The applications had to be especially easy
to use for two reasons,” says Nesbitt. “First,
anything that distracts our researchers from
doing their real work is a problem. Second,
research projects generally have a high
turnover of study coordinators—which
requires us to continually train new
coordinators. Because the applications are
based on Microsoft technologies, we can
train new coordinators in one hour, and
they are fully equipped with the skills and
confidence to use the applications
immediately.”
Delivers Near 100 Percent Uptime,
Minimizing Support Needs
In choosing a technology set for their
applications, Nesbitt and his colleagues
were also looking for a platform that would
minimize ongoing support demands. The
Microsoft technologies meet that
requirement, too, and do so in a variety of
ways.
First, the project solution is fully scalable,
able to support the hundreds of broadly
dispersed, simultaneous users who
contribute to the project. Should the
population of researchers ever grow
beyond the limits of the current
architecture, the informatics team can add
Web and database computers costeffectively, using commodity hardware. In
addition, because all the informatics
applications are Web based, the Epilepsy
Phenome/Genome Project spends less on
deployment than it would to deploy
traditional client-server applications and
also saves on the maintenance costs of
keeping servers and workstations updated
and trouble-free.
The system is also highly reliable. Built-in
validation rules and checks in the
applications and databases help to ensure
that the collected data is correct, that it is
verifiable, and that it follows the study’s
protocols. Should problems occur with the
databases, SQL Server data mirroring
between the East and West Coast data
centers helps ensure that data is available
for backup or data recovery.
Not that Nesbitt is anticipating such
problems—to date, the system has
experienced negligible unscheduled
downtime, providing the equivalent of near
100 percent uptime. Even scheduled
downtime for maintenance is just two to
three hours a month, 50 percent of the
downtime that Nesbitt says he would have
seen with other platforms.
All this means that researchers can use the
applications and data as they need to,
without having to consider limits to system
availability. Nor does the IT staff need to
devote significant resources to system
support. Help-desk calls are running at the
rate of one or two a day—a very small
number for an endeavor the size of the
Epilepsy Phenome/Genome Project,
according to Nesbitt.
“Using Microsoft technologies, we’ve built a
major platform that delivers enterpriselevel scalability and reliability, along with
the functionality and ease of use that our
researchers need, all of which is supported
by an informatics administrative and
development staff of five,” says Nesbitt.
“This is such an advance for the field of
clinical research informatics that we’re
looking at making components of the
architecture available to others in the
research community.”
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For more information about the
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call (415) 476-9000 or visit the Web site
at:
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Software and Services
 Microsoft Visual Studio
Microsoft Server Product Portfolio
− Microsoft Visual Studio Team System
− Microsoft SQL Server 2008 Enterprise
2008 Team Suite
− Windows Server 2008 Enterprise
 Technologies
 Microsoft Office
− Microsoft ASP.NET
− Microsoft Office Access 2007
− Microsoft SQL Server 2008 Reporting
− Microsoft Office Excel 2007
Services
− Microsoft Office PerformancePoint
Server 2007
− Microsoft Office SharePoint Server
2007
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This case study is for informational purposes only.
MICROSOFT MAKES NO WARRANTIES, EXPRESS OR
IMPLIED, IN THIS SUMMARY.
Document published May 2010