Download - IndianaCTSI HUB

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8 Δεκ 2013 (πριν από 3 χρόνια και 6 μήνες)

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Indiana
CTSI

ACCELERATING CLINICAL AND

TRANSLATIONAL RESEARCH

Update: the Indiana CTSI HUB Cyberinfrastructure

William K. Barnett (
barnettw@iu.edu
) , Indiana University and IU School of Medicine

Michael McLennan (
mmclenna@purdue.edu
), Purdue University

The Indiana CTSI HUB (
http://indianactsi.org
) is a modular Web 2.0 portal for translational activities at the Indiana CTSI. A recent NIH ARRA CTSA Supplement Award has p
rov
ided funding for
the Indiana CTSI to further develop its HUB cyberinfrastructure. This poster shows the evolving HUB architecture.
ASPECTS IN DOTTED LINE BOXES ARE UNDER DEVELOPMENT

INFRASTRUCTURE (enabling technologies)

FOUNDATIONS (key underlying frameworks and institutional efforts)

Joomla! Is an standards
-
based
content management system
framework that supports a wide array
of community contributions (
3,640
as
of 10/15/2009). The Joomla!
framework utilizes the Model View
Controller design that divides the
code into three distinct sections. The
Model is the interface between the
rest of the code and the places where
the information is stored. The core
Joomla! code can be extended with
Plugins that slightly alter the
functionality of part of the website
without altering the code base,
Modules that display small areas of
content, or Components that control
the main functional points of a
website.

PROPOSAL MANAGEMENT SYSTEM

Internal grant review was an early priority for
the Indiana CTSI. In order to rapidly develop
an online solution, we used Public Knowledge
Project’s
Open Journal System
, an open
-
source solution for online management of
academic journals. The journal review process
mapped easily to the internal grant application
review process. We customized the system to
suit our specific needs, such as restricted
login. In the first year of use, applications
increased from 33 to 104, despite an
additional requirement of multi
-
institutional
partnership.

A
Competition
Is Posted

Investigators
Submit
Proposals

Competition
Chairperson
Assigns
Reviewers

Reviewers
Submit
Reviews

Committee
Chooses
Awardees

Investigators
Notified of
Results

BUILT
-
IN HUB SERVICES

All HUBs provide a ready
-
to
-
use environment with a set of tools
for virtual organization collaboration:


CONTENT TAGGING:
User
-
submitted multimedia resources can be tagged.


RATINGS AND CITATIONS:
Contributions can be ranked and the HUB
automatically generates citations in BibTex and EndNote formats.


FEEDBACK AND TROUBLE TICKETING
: The HUB has built
-
in feedback to the
site administrators that tracks issues and complaints.


NEWS AND EVENTS:
Public forums for information dissemination.


INTEGRATED SEARCH:
Results are organized by content category.


WIKIS AND BLOGS
: For topical sharing and collective editing.


METRICS:
Interfaces for access to Web site activity across the HUB.


INFORMATION MANAGEMENT

All content in the Indiana CTSI HUB is managed as part of MySQL
databases so it can easily be tagged, updated, and reported on.


Like many web sites today, the Indiana CTSI HUB is completely
dynamic and populated by the data stored across dozens of tables in
the underlying MySQL database. Each registered user, for example,
has an entry in the “members” table with a unique identifier. The
activities of each member
--
including the resources uploaded, the
questions asked, the reviews posted, and the tools accessed
--
appear
as entries in various tables, with each entry bearing the member’s
unique identifier. All web pages are generated on
-
the
-
fly using the
freshest data in the database, and impact metrics (such as the total
number of viewers for a seminar) can be extracted from the database.

Surveys of researchers have discovered a pervasive
challenge: an online environment where groups can
privately collaborate around a research project or grant
proposal, including the sharing of ePHI data according to
HIPAA guidelines. Industry solutions such as Sharepoint
do not allow collaboration across institutions. The strategy
of this solution is to deploy a group
management/authorization umbrella and install or develop
Joomla! Components that allow file sharing, group
emailing, forums, and Wikis. This project will build on Sean
Mooney’s successful
Laboratree
prototype
(
http://laboratree.org
) to build multi
-
institutional
collaboration environments, and will use Indiana
University’s substantial HIPAA aligned research
cyberinfrastructure to manage private data.


While there are numerous web sites and services
that provide information about health care
innovations and disclosures
, there is no parallel
listing of companies and their contacts. The Indiana
CTSI HUB is developing such a service.


The Indiana CTSI is working with the CTSA IP project
(
http://www.rochesterctsa.org/ip/
) and the
Pharmaceutical Assets Portal

(
http://ctsapharmaportal.org
).


Locally, we are partnering with the Indiana University
Technology Research Corporation (the IU Tech
Transfer office), Biocrossroads, and Cook, Inc.


We are currently in the requirements gathering phase
of this project.

PRIVATE GROUP

COLLABORATION

INDUSTRY PARTNER

DISCOVERY TOOL

RAPPTURE TOOLKIT

“Rappture

is a toolkit supporting
R
apid
app
lication infrastruc
ture
, making it
quick and easy to develop powerful scientific applications. At its core,
Rappture is a C++ toolkit, but it has additional language bindings that let it
be used in C, Fortran, MATLAB, Octave, Perl, Python, and Tcl applications. It
combines numerical building blocks, such as Poisson equation solvers and
iterative matrix solvers, along with a powerful infrastructure for handling user
interfaces. Once you describe the input/output for your simulator, Rappture
handles the rest, generating a graphical interface automatically based on
your description. The Rappture toolkit provides the basic infrastructure for a
large class of scientific applications, letting scientists focus on their core
algorithm when developing new simulators. Rappture makes it easy to put a
friendly, interactive interface on existing legacy applications, without having
to rewrite the code.”
1


It has the ability to automatically utilize
supercomputers and grids, like the TeraGrid, to accomplish compute
-

or
data
-
intensive tasks.


The Indiana CTSI is
partnering with the National Center for
Biomedical Ontology to implement their Annotator web
service.
Dr. Nigham Shah
will work with HUB programmers
and School of Medicine Knowledge Informaticians to
implement this web service on the Indiana CTSI HUB. This
work will make the data management system for the Indiana
CTSI HUB, and applications on the HUB, web services
compliant and programmed to utilize web services to access
the NCBO Annotator service. We are partnering with
Dr.
Ying Ding
of the School of Library and Information Sciences
at Indiana U. to develop tools so ontological terms can be
presented on the HUB as semantic tags so that they can be
easily discovered by searching and browsing the Indiana
CTSI HUB.
http://bioontology.org/wiki/index.php/Annotator_Web_service
)


ONTOLOGICAL TEXT ANNOTATION

FEDERATED IDENTITY MANAGEMENT

The Indiana CTSI HUB supports federated identities, meaning that for those
institutions we partner with, researchers will be able to use their institutional
credentials to log into our site for secure access to HUB services, and
Indiana CTSI members can do the same in reverse. This standard has been
adopted by the NIH for CTSAWeb. We can also authenticale members of
the public that have Google or Protect Network accounts.


Via InCommon, we have federated with:



Purdue, Stanford, Iowa, and the NIH

Via OpenID, we have federated with:



Google and Protect Network


INTERESTED IN FEDERATING WITH INDIANA? LET US KNOW!


Background powerpoint:
https://www.indianactsi.org/resources/186


We are investigating making the HUB an Open Social
Container and so we can populate it, and interact with,
social networking tools.


“Based on HTML and JavaScript, as well as the Google
Gadgets framework, OpenSocial includes four APIs for
social software applications to access data and core
functions on participating social networks. Each API
addresses a different aspect: one is the general JavaScript
API, one for People and Friends (people and relationship
information), one for Activities (publishing and accessing
user activity information), and one for Persistence (simple
key
-
value pair data for server
-
free stateful applications).”
2


OPEN SOCIAL CONTAINER

SOFTWARE SUSTAINABILITY

The Indiana CTSI HUB (
www.indianactsi.org
) uses the
HUBzero

platform,
developed at Purdue University. HUBzero has become a community source
consortium to license, distribute, maintain, and grow HUBs and HUB software to
sustainably support virtual research organizations. Founding
HUBzero
Consortium (
www.hubzero.org
)
members are Purdue U., Indiana U., U. of
Wisconsin, and Clemson U. HUBzero development was funded originally by the
National Science Foundation. The codebase and all contributed components will
be provided and maintained as free, open source products.


Other notable HUBs include:



NanoHUB (nanotechnology


the original HUB with 90,000 users),



cceHUB (cancer care engineering),



pharmaHUB (pharmaceutical product development and marketing),



thermalHUB (heat transfer research),



manufacturingHUB (academic/industry manufacturing partnerships)



centerforassistivetechnologyHUB (assistive technology community)

The VOSS (Virtual Organizations as Socio
-
technical
Systems) team at Purdue University and the University
of Michigan were funded by the NSF to study electronic
collaboration of researchers who are geographically
distributed but focused on the same intellectual
challenges. The goal of this research is to understand
the degree to which websites used as science
gateways, including the Indiana CTSI Hub, generate
new intellectual capital; the technical and social
features of the sites that support knowledge
generation; and the conditions needed to improve
design choices for the expansion and creation of
science gateways.


Contact: Dr. Michael Beyerlein

(
mbeyerle@purdue.edu
)

COLLABORATION RESEARCH

The Indiana CTSI will be partnering with
Dr.
Noshir Contracto
r, Northwestern University, to
undertake a pilot network analysis study of a
subset of HUB users and their existing and
potential interaction spheres. This pilot will be
based on the activities and networks of the most
recent round of successful Indiana CTSI translation
grant projects.


Using algorithms developed at Northwestern, the
goal of this pilot is to discover potential linkages
that will result in a
recommender system
to guide
potential future partnerships and activities.


NETWORK ANALYSIS

The
Network Workbench
tool supports large
-
scale network
analysis, modeling and visualization for biomedical, social
science, and physics research. Created jointly by a team
from Indiana University, Northeastern University, and the
University of Michigan led by
Dr. Katy Börner
, this tool has
the potential to support collaboration as a service that can
visualize complex relationships amongst researchers and
their interests, grants received, publications, and research
data such as annotations. By visualizing the complex
relationships among data, researchers can profitably
understand research trends, discover collaborators, and
develop proposals that advance translational medicine. As
part of this project, we will implement the Network
Workbench tool as a HUB component.


See: NWB Team. (2006). Network Workbench Tool. Indiana
University, Northeastern University, and University of
Michigan,
http://nwb.slis.indiana.edu

META SCIENCE VISUALIZATION

The HUB provides a central repository for the Indiana CTSI
Translational Technologies and Resources (TTR) Program.
Features developed to date include:



Listing of CTSI Cores and Resources for Indiana CTSI
institutions with links to educational resources and contacts



Search for services by core director defined keywords



On
-
line ordering (expandable prototype)



Investigator requests for TTR Liaison assistance



Designation of CTSI cores eligible for core pilot grants.



Comparison grid for similar cores



Survey tool for core director surveys


The HUB development has been essential in the TTR
progress for the following stated goals: #2) facilitate access
to novel resources for translational research projects; and
#3) provide education to CTSI investigators about novel
technologies.

Contact: Lilith Reeves (
lreeves@iupui.edu
)

ONLINE CORES

2
http://en.wikipedia.org/wiki/Opensocial


1

http://www.rapture.org