Biomedical Engineering Reference
In-Depth Information
are important for successful collaborations. Tools for document sharing, project
repositories, tools for process tracking and instant notifi cation, instant messag-
ing, free video and voice calling, and so on, exist in open source or otherwise
(http://en.wikipedia.org/wiki/List_of_collaborative_software), but there exists
no platform that can provide all of these functionalities on a single platform
for drug discovery. This means that researchers are bound to use these applica-
tions independently. Moreover, there are no existing technologies to track
intellectual contributions of researchers across different applications. Hence
it was felt necessary to develop applications and integrate them in a manner
that allows for seamless online collaborations and track contributions. The
OSDD portal congregates the best - of - breed open - source applications to
achieve the functionalities of a virtual collaboration platform for drug discov-
ery. It makes full use of existing open-source tools that promote effective
collaborations.
A major challenge while designing the portal was to implement a SSO
across applications, which required customizing their authentication system as
well as interfacing their database with the portal data store. This architecture,
although challenging to implement, ensures scalability for integrating data and
tools from any resource.
The OSDD portal provides a robust scalable platform for collaborations
and managing drug discovery projects. In OSDD, large complex problems are
broken down into simpler tasks that can be implemented with the help of
community members. An excellent example to highlight this approach is the
development of TBrowse with OSDD community members. TBrowse is an
integrative genomics map of
Mycobacterium tuberculosis
and attempts to
connect nearly a million data points from various databases, including compu-
tational predictions and data from the literature [9]. Also, it is well known that
the process of drug discovery is highly complex and challenging. Integrating
projects, resources, and intellect becomes the key to facilitating collaborations
for solving challenging problems. Such collaborations need compute infra-
structure for their speedy implementation.
SysBorg (Systems Biology of the Organism) is the core component of the
OSDD portal (http://sysborg2.osdd.net). This component is comprised of sub-
components, namely, open ideas, open project space, open laboratory note-
book, resources, and document repository. Any project starts with an idea
which is translated into a project with well-defi ned deliverables with specifi c
timelines. The OSDD portal provides space for posting ideas and developing
projects on these ideas. There is also provision to develop subprojects on exist-
ing projects. The project space has a predefi ned template and the participating
members of the project automatically become part of the community for that
subproject. In addition to community members, other members are also
welcome to comment and provide their inputs on the project, thus improving
the work design and providing crucial inputs.
Sharing negative results is a big challenge in research as most often these
are not published and remain with individual researchers or groups. In OSDD,
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