Update: the Indiana CTSI HUB Cyberinfrastructure

1. Committee Chooses Awardees Investigators Submit Proposals A Competition Is Posted Reviewers Submit Reviews Investigators Notified of Results Competition Chairperson Assigns Reviewers 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 provided 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 SERVICES (partial listing of tools and components) PRIVATE GROUP COLLABORATION BUILT-IN HUB SERVICES INDUSTRY PARTNER DISCOVERY TOOL PROPOSAL MANAGEMENT SYSTEM ONLINE CORES 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. • 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) 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. 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. 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. INFRASTRUCTURE (enabling technologies) OPEN SOCIAL CONTAINER ONTOLOGICAL TEXT ANNOTATION RAPPTURE TOOLKIT META SCIENCE VISUALIZATION 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 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 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) “Rappture is a toolkit supporting Rapid application infrastructure, 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. 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 2 http://en.wikipedia.org/wiki/Opensocial 1http://www.rapture.org FOUNDATIONS (key underlying frameworks and institutional efforts) SOFTWARE SUSTAINABILITY 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. INFORMATION MANAGEMENT NETWORK ANALYSIS COLLABORATION RESEARCH • 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) 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. The Indiana CTSI will be partnering with Dr. Noshir Contractor, 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.