Pistoia Alliance Sequence Services and Eagle Genomics

Case Study
Pistoia Alliance Sequence Services and Eagle Genomics
Pistoia Alliance
Sequence Services and
Eagle Genomics
Recent successes enjoyed by specialist R&D software companies like
Eagle Genomics Ltd. (Eagle) are due in part to the active pursuit of open
innovation. Eagle’s involvement with Pistoia Alliance Sequence Services is
a clear example, and testament to how the Alliance’s mandate has been
achieved. The relationship resulted in new software and services that fit a
shared need in pre-competitive life sciences R&D IT and led to the creation
of a completely new type of product.
Data explosion
“The most
important thing
about open
innovation is
shared need
expressed in a
detailed way and
distributed openly.
This is what the
Pistoia Alliance
does very well.”
Over the last decade there has been
an explosion of genomics-related
technologies applied in commercial
settings. The Pistoia Alliance Sequence
Services project sought to ease the
process of adopting and incorporating
these new technologies into R&D
informatics processes, with a particular
focus on Next-Generation Sequencing
(NGS) platforms.
NGS can still in many cases be described
as disruptive innovation; continuously
creating new markets, challenges, and
opportunities that did not exist before.
The bioinformatics pipelines and software
systems required to manage NGS data are
important to get right, but differences in
implementation of these backend services
generally do not give a major competitive
advantage to any single company.
It made sense to develop a common
platform that would allow everyone to
manage and work with NGS and other
genomics-related data in the same way,
and so Sequence Services was conceived
to provide just that. This activity was
clearly pre-competitive and matched well
with the mandate of the Pistoia Alliance
to lower barriers to innovation in life
sciences R&D.
Will Spooner,
Chief Science Officer,
Eagle Genomics Ltd.
www.pistoiaalliance.org
@pistoiaalliance
© Pistoia Alliance 2015
Case Study
Pistoia Alliance Sequence Services and Eagle Genomics
Solutions through partnership
The Sequence Services project ran in
two phases with a Request For Proposal
(RFP) issued for each. Several companies
responded to the RFPs and the best
responses were awarded funds to support
the development of a proof-of-concept
solution. Eagle successfully participated
in both phases, working in partnership
with Cognizant Technology Solutions for
phase 1, and with Cycle Computing LLC
for phase 2.
Phase 1 set out to deploy and integrate
a simple set of common bioinformatics
tools protected by commercial-grade
security mechanisms such as singlesign-on technology. Phase 2 was
a much more complete consensus
specification developed by a wider range
of life sciences companies. Many of the
components specified were public or
open source and the challenge was to
Pistoia Alliance
Sequence Services
Phase 1 envisaged
a secure access
arrangement for a
genome browser and
a small number of
supporting tools and
datasets.
Eagle, in partnership with Cognizant in
phase 1 and Cycle Computing in phase 2,
put together a cloud-based solution that
satisfied the Sequence Services brief. The
funding made available from the Pistoia
Alliance helped support development
but the end result was still fundamentally
a proof of concept not yet ready for
production deployment. Eagle needed to
turn that proof of concept into a fullyfledged commercial product. To enable
this, Eagle went to the market and raised
US$1m investment capital to support
further development, resulting in the
release of the information management
platform eaglecore in September 2014.
Securely Hosted Sequence Services
Data secured at rest, services hardened
against unauthorised access
Industrial
Partners
Public
Domain
updates
Ensembl
Company
Confidential
Data
Role & Field
based security
PlasMapper
Example of
hosted open
source software
Academic
Partners
IT Service Providers
Phase 2 expanded this
concept to include
almost any selection
of tool or data to be
deployed within a
flexible, extensible
framework.
www.pistoiaalliance.org
seamlessly integrate these tools and
datasets, provide access to them via
command line interfaces, and enable
them to be included in user-defined high
throughput data processing pipelines.
Life Science
Companies
@pistoiaalliance
© Pistoia Alliance 2015
Case Study
Pistoia Alliance Sequence Services and Eagle Genomics
Market access
“The Pistoia Alliance
gives you invaluable
information
and a detailed
understanding
of how R&D IT
thinking runs
in commercial
life science
organizations.”
By becoming involved with the Pistoia
Alliance and the Sequence Services
project, Eagle received significant support
in assessing potential markets and
developing a product proposal. Eagle was
able to reach a wider international market
and access key requirements information
that would otherwise have been much
more difficult to obtain, turning a
potentially slow and difficult process into
one of considerable advantage.
The Pistoia Alliance provided access to
the correct stakeholders and a reasonably
complete set of pre-defined requirements
explaining exactly what was needed. It
would have been extremely difficult for
Eagle to gather the depth of information
by themselves at that early stage of
product development. In a fast-moving
market affected by a major disruptive
innovation such as NGS, it is essential as
a small business to get this initial analysis
correct and build the correct solution the
first time.
The support from the Pistoia Alliance
Sequence Services project for the
development of the proofs of concept and
the opportunity to demonstrate them to a
qualified audience substantially de-risked
the project and encouraged Eagle to take
the challenge on. The Pistoia Alliance
enabled Eagle to take a huge step in the
right direction.
Will Spooner,
Chief Science Officer,
Eagle Genomics Ltd.
Eagle's core software product, eaglecore, is a centralised platform
for the management of genomic and large-scale research data
Eagle's information management platform, eaglecore,
showing example of advanced search functionality.
www.pistoiaalliance.org
@pistoiaalliance
Eagle's information management platform, eaglecore,
displaying an example of the intuitive screen layout of
study information.
© Pistoia Alliance 2015
Case Study
Pistoia Alliance Sequence Services and Eagle Genomics
“Just being part of
the Pistoia Alliance,
talking to people
within it, knowing
what’s going on,
enables Eagle to
identify common
problems and
propose solutions
that make sense.”
Abel Ureta-Vidal,
CEO, Eagle Genomics Ltd.
A new product is born
Today, Eagle are still using a lot of the
concepts and software components that
were initially developed as part of their
Sequence Services proof of concept.
The novel open source integration
techniques have supported the
establishment of a custom Ensembl
installation service, with bespoke Ensembl
instances integrated with each customer’s
infrastructure and data. Eagle also still use
the same basic technologies from their
Sequence Services solution to deploy
high throughput data processing pipelines
on a variety of cluster types and HPC
infrastructures.
However, the most important outcome of
Sequence Services for Eagle was a much
better understanding of the information
management challenges that are
prevalent in NGS and genomics in general,
and that this was the main priority for
many of its customers. Refactoring the
system using a ground-up approach to
adopt secure information management
best practices and principles throughout,
the eaglecore information management
platform was created.
Making use of existing community
standards wherever possible, such as
ISA, and with extensive use of ontologies
and controlled vocabularies, eaglecore
enables experimentalists to manage,
locate and work with data from across the
organization.
The realization of eaglecore as a direct
outcome of the Pistoia Alliance Sequence
Services project has transformed
Eagle’s business. It has allowed it to
raise investment and move from a pure
consultancy model to a blend of software
sales and professional services backed
with its own IP, and to double its revenue
and employ twice as many staff. Eagle
now services customers in a variety
of sectors including pharmaceutical
research, crop science, and consumer
goods.
More information
http://www.pistoiaalliance.org/projects/sequence-services/
[email protected]
http://www.eaglegenomics.com/eaglecore/
Pistoia Alliance: Lowering barriers to R&D innovation
Pistoia Alliance is a global, not-for-profit
alliance of life science companies, vendors,
publishers, and academic groups that work
together to lower barriers to innovation in R&D.
www.pistoiaalliance.org
@pistoiaalliance
Our members collaborate as equals on open
projects that generate significant value for the
worldwide life sciences community.
© Pistoia Alliance 2015