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HUBbub 2011 Speakers

Michael McLennan

Michael McLennan

Opening Remarks

Tuesday 4/5/11 8:30am - 9:00am

HUBzero Roadmap

Wednesday 4/6/11 11:00am - 12:00pm

Breakout Session #3: Creating and Deploying Scientific Tools

Tuesday 4/5/11, 2:30 - 5:30pm and Wednesday 4/6/11, 1:30 - 4:30pm

Michael McLennan is a senior research scientist at Purdue University’s Rosen Center for Advanced Computing, where he is Director of the HUBzero Platform for Scientific Collaboration. He received a Ph.D. in 1990 from Purdue University, supported as an SRC Graduate Fellow, for his dissertation on dissipative quantum mechanical electron transport in semiconductor heterostructure devices. He spent 14 years working in industry at Bell Labs and Cadence Design Systems, developing software for computer-aided design of integrated circuits. He created [incr Tcl], an object-oriented extension of the Tcl scripting language, which has been used by thousands of developers worldwide on projects ranging from the TiVo digital video recorder to the Mars Pathfinder. He coauthored two books, Effective Tcl/Tk Programming (Addison-Wesley, 1997) and Tcl/Tk Tools (O’Reilly Media, 1997). His latest project is the Rappture Toolkit, which accelerates the process of creating scientific tools for simulation and modeling.

Gabrielle Allen

Gabrielle Allen

Cyberinfrastructure for Computation and Data-enabled Science & Engineering

Tuesday 4/5/11 9:00am - 9:30am

Gabrielle Allen is a Program Director at the National Science Foundation in the Office of Cyberinfrastructure. She is also an Associate Professor in Computer Science at Louisiana State University, and a faculty member at the Center for Computation & Technology.

Gabrielle received a PhD in computational astrophysics from Cardiff University in 1993. Before moving from Europe to Louisiana State University in 2003, Gabrielle was the lead of the computer science area of the Max Planck Institute for Gravitational Physics (AEI) in Potsdam, Germany where she researched and developed techniques for high performance and grid computing. At the AEI, Gabrielle was the lead of the Cactus Code project and a PI for the European GridLab project. At LSU, Gabrielle played a major role in establishing the Center for Computation and Technology, led the cyberinfrastucture component of the statewide NSF research infrastructure improvement award, and continued to led the Cactus Code project. She has been deeply involved in a number of large, collaborative projects integrating computer science, scientific computing and the computational sciences across diverse fields including petroleum engineering, coastal modeling, computational fluid dynamics, numerical relativity, computational chemistry and computational biology.

Daniel Atkins

Daniel Atkins

Cyberinfrastructure for HPC: High Performance Collaboration

Tuesday 4/5/11 9:30am - 10:00am

Daniel E. Atkins is a Professor of Electrical and Computer Engineering in the College of Engineering at the University of Michigan (UM), Ann Arbor. He is also a Professor of Information, and the W. K. Kellogg Professor of Community Informatics in the School of Information. He currently serves as the Associate Vice-President for Research Cyberinfrastructure and Chair of the UM IT Governance Council. From June 2006 to June 2008 served as the inaugural Director of the Office of Cyberinfrastructure at the U.S. National Science Foundation.

Atkins began his research career in the field of computer architecture and did pioneering work in parallel computer architecture and high-speed computer arithmetic that is widely used in modern processor chips. He played significant roles in the design and implementation of seven general-purpose or special-purpose computers, including early work with processing CAT scan data with the Mayo Clinic. In the second decade of his research career, his focus shifted to research and teaching in the socio-technical, interdisciplinary field of distributed knowledge communities, with a specific focus on collaboratories -- laboratories without walls -- and digital libraries. He has directed several pioneering digital library and science collaboratory research projects funded by the NSF including the Upper-Atmospheric Research Collaboratory and the Space Physics and Aeronomy Research Collaboratory. These collaborations led to the formation of the ongoing Collaboratory for Research on Electronic Work. He also had significant roles in developing the NSF Digital Library Initiative, NSF FASTLANE, and the Mellon Foundation JSTOR project now in use in academic libraries worldwide.

He continues conceptual work in the area of distributed knowledge communities, currently with a focus on the future of research and learning in the digital age. Infrastructural aspects of this work are now embedded in the CIRRUS Project (Computing and Information Resources for Research as a Utility Service) that he has recently established at the UM.

He served as Associate Dean for Research and later as Dean of the UM College of Engineering. During this period he provided leadership for the early transition from time-sharing to networked workstation computing and its transformative adoption for science and engineering research and learning.

He was the founding Dean of the UM School of Information. This School has been a force for creating a growing international Information School (I-School) movement. During and after this deanship he formed and directed an Alliance for Community Technology (ACT) sponsored by the W.K. Kellogg Foundation to support the innovative use of information technology in civil society. ACT supported the formation of a Community Information Corp at SI, creation of a virtual library federation for the U.S. Native American tribal colleges, acceleration of the adoption of open source software in the nonprofit sector, and technical assistance to a variety of community technology centers in developing countries. Atkins served as a consultant to the W. K. Kellogg Foundation on the innovative use of information and communication technology for enriching education opportunities for at-risk youth in the U.S. and for both rural communities and higher education in southern Africa.

He served as Chair of a National Science Foundation Panel that in February 2002 issued the landmark Report of a Blue Ribbon Advisory Panel on Cyberinfrastructure recommending a major program to revolutionize science and engineering research and education. The report has helped catalyzed new priorities, the Office of Cyberinfrastructure at the NSF, and strategic e-science programs in many other countries.

Atkins also serves regularly on panels of the National Academies exploring issues such as scholarship in the digital age, the future of scholarly communication, the impact of information technology on the future of higher education, and research data policy. He is co-author of Higher Education in the Digital Age: Technology Issues and Strategies for American Colleges and Universities.

He has served as a consultant and invited speaker to industry, foundations, educational institutions, and government worldwide. Examples include the NSF, NIH, Intel, Mayo Clinic, Kellogg Foundation, Hewlett Foundation, MacArthur Foundation, Coalition for Networked Information, Internet2, the MIT Libraries, NPOWER, Los Alamos National Laboratory, the National Library of Medicine, National Archives and Records Administration, the OECC, European Commission, and the UK Research Councils. His recent report, A Review of the Open Educational Resources (OER) Movement: Achievements, Challenges, and Opportunities, with J. S. Brown and A. L. Hammond, is now helping to shape international investment in the next phase of the open courseware movement. Recently Atkins served as Chair of an international panel to review the UK Research Councils e-Science Programmes, as a member of a task force to draft the Obama Administration’s National Educational Technology Plan 2010, and as an expert witness to the FCC National Broadband Plan. He is currently serving as Chair of a Scientific Advisory Committee for Digital Media and Learning for the MacArthur Foundation.

Atkins is the recipient of several major awards including two UM Distinguished Service Awards, the 1993 Nina W. Mathesson Award for outstanding contributions to medical informatics, the 1998 Computerworld Smithsonian Award for innovation in use of the web for science, and the 2008 Paul Evan Peters Award for notable, lasting achievements in the creation and innovative use of information resources and services that advance scholarship and intellectual productivity through communication networks. He is a recipient of an NSF Service Commendation, and in May 2009 he was recognized with a University of Illinois College of Engineering Distinguished Alumni Award for his influence on high-performance computer architecture, pioneering work in the development of schools of information, and leadership in improving the U.S. cyberinfrastructure.

Dr. Atkins received his BSEE from Bucknell University and his MS and PhD in EECS from the University of Illinois.

Ann Christine Catlin

Ann Christine Catlin

Database Technology at the HUB: Interactive DataViews for Community Shared Data

Tuesday 4/5/11 10:30am - 11:00am

Ann Christine Catlin is a research scientist in the Rosen Center for Advanced Computing at Purdue University. She received a B.S. in Mathematics from Seton Hill University and an M.S. in Mathematics from Notre Dame University. She has worked for companies both large (AT&T Information Systems) and small (Applied Data Research), and worked as a research scientist in the Computer Science Department at Purdue University before moving to the Rosen Center. Catlin worked on the design and development of problem-solving environments for partial differential equation-based applications on multi-computer platforms, and co-authored more than 30 peer-reviewed publications over a ten year period about her research. She created a knowledge-based shipboard troubleshooting system for the U.S. Navy, and for this effort she won the School of Science Merit award for Extraordinary Achievement in 2004 and the Techpoint Mira Award in 2005. Catlin’s work at the Rosen Center has focused on designing and developing research environments based on HUBzerotm technology. She participated in work on pharmaHUB, and currently works on projects for NEEShub, thermalHUB and the health-exchange HUB. She is leading the design and implementation of cceHUB, an infrastructure for collaborative research that supports the cancer care engineering projects.


A new "database" resource has been developed to serve the data sharing needs of hub communities. This resource was designed and implemented at cceHUB for the Cancer Care Engineering project, and is now operating across six hubs, offering sixteen community databases. The support infrastructure consists of a MySQL database together with Joomla! components that provide interfaces for data contribution and data exploration. For simple data models, database tables are created automatically by a spreadsheet parser. More complex data models require manual creation of data tables that describe elements and relationships.

Data is contributed to hub databases either via a spreadsheet parser operating on a standardized data format or through a sequence of web-forms representing the application data flow. Web-forms are managed by the “com_form” component which provides automatic form generation and processing. A simple data definition file is created for each form, using a toolkit of constructs for form design. Completed forms are submitted in XML format to back-end Java parsers for data validation, processing and insertion.

A powerful "com_dataview" component operates on hub database tables to provide spreadsheet-based data browse, filter, search, sort and download, with features such as linking to documents/images, viewing of photo galleries, and launching of hub tools - even dynamic plots and integrated Google maps. The core dataview code uses javascript and open source software (jquery, jqplot, datatables, explorercanvas). A simple data definition file is created for each view, identifying the columns and their features.

A few community databases were created in a single day, while other databases have been continuously revised and advanced for nearly two years. The current database creation process requires some manual interaction, but development efforts are underway to automate the entire process from beginning to end.

cceHUB: An Environment for Collaborative Cancer Care Research

Wednesday 4/6/11 4:00pm - 4:30pm, Breakout Session #1, Using HUBzero to Support Scientific Projects


cceHUB supports collaboration and community resource sharing for Cancer Care Engineering, a research project that links clinical teams at IU Simon Cancer Center with science laboratories and statisticians at Purdue and Indiana Universities. The cceHUB environment encompasses major elements of the cancer research workflow: (1) blood sample tracking and patient data collection, (2) annotation, upload and storage for instrument-generated datasets, (3) discovery pipelines and modeling tools for data analysis and synthesis, and (4) data views to browse, search, sort, filter, link and explore community-shared data. cceHUB is an entirely unique research environment, as it directly connects data, tools and the analysis process. cceHUB created a new hub-based data technology for sample tracking and analysis. Tracking follows samples from collection at the hospital through transfer, storage and distribution to laboratories. Protocols for sample handling can be uniquely configured for each study, and web-forms for sample tracking are auto-generated. A key feature of sample tracking is the association of datasets generated by laboratory instruments directly to samples used in the analysis. This guarantees the permanent electronic linkage of analysis results to the original samples. Massive laboratory datasets (e.g., mass spectrometry for proteomics) are uploaded to repositories with annotations and provenance metadata, where they are available for exploration, analysis, and integrative modeling. Knowledge associated with laboratory workflows is built into the database and directly controls how laboratory data is uploaded and stored. Patient data encompasses clinical information and demographics; web-forms are auto-generated from data elements and data flows defined by the clinical team, and are access-controlled for data contribution. Patient identifiers are carried throughout the research workflow, so that laboratory analysis and modeling tools can use patient information for phenotyping. A major component of cceHUB data technology is its data viewer, which is used to explore clinical data, laboratory data collections, and results collections from tool-generated analysis. cceHUB has been in operation for nearly two years, collecting and exploring clinical data for hundreds of patients; uploading and annotating thousands of laboratory datasets; and integrating a dozen valuable modeling codes for integrative analysis. The small group of CCE researchers depends on the data sharing capability of cceHUB, where some modeling codes have run for many thousands of hours and several of the clinical data views have been accessed tens of thousands of times.

Gerhard Klimeck

Gerhard Klimeck

Exploring the Impact of on Research and Education

Tuesday 4/5/11 11:00am - 11:30am

Gerhard Klimeck is the Director of the Network for Computational Nanotechnology at Purdue University and a Professor of Electrical and Computer Engineering. He guides the technical developments and strategies of which served over 170,000 users worldwide with on-line simulation, tutorials, and seminars in the last 12 months. He was the Technical Group Supervisor of the High Performance Computing Group and a Principal Scientist at the NASA Jet Propulsion Laboratory. Previously he was a member of technical staff at the Central Research Lab of Texas Instruments where he served as manager and principal architect of the Nanoelectronic Modeling (NEMO 1-D) program. NEMO 1-D was the first quantitative simulation tool for resonant tunneling diodes and 1D heterostructures. At JPL and Purdue Gerhard developed the Nanoelectronic Modeling tool (NEMO 3-D ) for multimillion atom simulations. NEMO 3-D has been used to quantitatively model optical properties of self-assembled quantum dots, disordered Si/SiGe systems, and single impurities in Silicon. Both tools are based on the representation of the nanoelectronic device with atomistic empirical tight-binding. Quantitative device modeling was demonstrated without any material parameter adjustments, just by entry of geometrical structure parameters. At Purdue his group is developing a new simulation engine that combines the NEMO 1-D and NEMO 3-D capabilities into a new code entitled OMEN. Prof. Klimeck’s research interest is in the modeling of nanoelectronic devices, parallel cluster computing, and genetic algorithms. Dr. Klimeck received his Ph.D. in 1994 on Quantum Transport from Purdue University and his German electrical engineering degree in 1990 from Ruhr-University Bochum. Dr. Klimeck’s work is documented in over 130 peer-reviewed journal and 125 proceedings publications and over 130 invited and 280 contributed conference presentations. He is a senior member of IEEE and member of APS, HKN and TBP. NEMO 1-D was recently demonstrated to scale to 23,000 parallel processors, NEMO 3-D was demonstrated to scale to 8,192 processors, and OMEN was demonstrated to scale to 222.720 processors.


Authors: Gerhard Klimeck, George B. Adams III, Krishna P. C. Madhavan, Nathan Denny, Michael G. Zentner, Swaroop Shivarajapura, Lynn K. Zentner, Diane L. Beaudoin, and Mehdi Salmani-Jelodar Network for Computational Nanotechnology, Purdue University

As the first and largest HUB utilizing the HUBzero infrastructure, provides a prime example of how HUBs function as virtual organizations, with the potential to accelerate scientific research and enrich education. With over 170,000 users in the last 12 months and over 2,300 resources including nearly 200 simulation tools, has established itself as the world’s largest Nanotechnology User Facility. Critical attributes for the success of such science gateways are open access, ease of use, utterly dependable operation, and diverse, high-quality content. Through, these attributes are realized, resulting in significant global knowledge transfer among researchers and from research to education. The impact and success of a science gateway can be measured and evaluated utilizing a variety of usage statistics, usage patterns, and analysis of citation data. An algorithm-based analysis reveals patterns in classroom usage and citation analysis illustrates multi-directional dissemination of research within the community. These success criteria apply not only to, but can be extended to other science gateways and other HUBs using HUBzero technology.

Timothy Sands

Timothy Sands

What Next for Public Research Universities?

Tuesday 4/5/11 11:30am - Noon; Tuesday 4/5/11

Timothy D. Sands became Executive Vice President for Academic Affairs and Provost of Purdue University on April 1, 2010. He earned a bachelor's degree with highest honors in engineering physics and a master's degree and doctorate in materials science from the University of California, Berkeley.

As executive vice president and provost, Dr. Sands will be responsible for all of Purdue’s colleges and schools, the regional campuses and related academic activities in coordination with the Office of the President.

Dr. Sands joined the Purdue faculty in 2002 as the Basil S. Turner Professor of Engineering in the schools of materials engineering and electrical and computer engineering. From 1993-2002, Sands was a professor of materials science and engineering at the University of California-Berkeley and before that, he performed and directed research at Bellcore.

Sands has published more than 200 papers and has been granted 15 patents in electronic and optoelectronic materials and devices. His present research efforts are directed toward the development of novel nanocomposite materials for environmentally friendly and cost-effective solid-state lighting, direct conversion of heat to electrical power and thermoelectric refrigeration. He is a fellow of IEEE and the Materials Research Society.


The Morrill Act of 1862 outlined a framework for the creation of state public universities designed for the express purposes of promoting economic development through applied research and supporting our democracy by educating the citizenry. In the past three decades, the impact of these institutions has expanded beyond state borders, and their funding portfolios have become diversified. At the same time, less resilient components of the states’ obligations have grown, and taxpayers have gradually disinvested from their public and state land-grant research universities. The Great Recession has accelerated this trend, presenting both an immense challenge and an unprecedented opportunity. It is clearly time for fundamental change in both the funding model and in the delivery model for synergistic teaching and learning, research and engagement at public research institutions. HUBzero™ may be one of the enabling platforms that brings the dual role of promoting democracy and economic development into a modern context that recognizes both the constraints of a new funding model and an evolving global reach for our public research universities.

Anna Alber

Anna Alber

Integrating Modeling Tools with a Shared Data Architecture on the HUBzero Platform

Tuesday 4/5/11 1:30pm - 1:50pm

Anna Alber is a Research Programmer at the University of Notre Dame Center for Research Computing. She is a member of Cyberinfrastructure Group where she is involved in web application development, HUBzero administration and computational tool development. She has MS in Physics and worked both in academia and industry.


Authors: Anna Alber and Timothy Wright

The HUBzero platform does a good job of bringing users and modeling tools together. However, hubs are generally intended to deploy tools of modest means, with input and output data not readily shared across user accounts. In answer to this issue, we have extended HUBzero along two fronts: first, to run the sophisticated openModeller desktop tool, and, second, to provide seamless access to external Network File System (NFS) drive space where hub users may store and manage input and output data. We designed our solution so that data may be shared or kept private with no significant administrative overhead. As a result our test hub allows scientists to converge in one place where they can run the openModeller tool and choose to share or keep private their input/output data files. Moreover, our approach to openModeller applies equally well to any sophisticated modeling tool that can be operated on a hub. For particularly large modeling efforts it makes sense to move our openModeller jobs off of HUBzero; to this end, we have begun a separate project that will embed an interface into HUBzero. This new interface will permit users to submit openModeller jobs to a remote server, which also share's the hub's NFS space.

Jason Lambert

Jason Lambert

Enhancing Hub Technology for Education, Outreach and Training Efforts

Tuesday 4/5/11 1:50pm - 2:10pm

Jason Lambert is the web systems software engineer at NEESComm located in the Purdue Research Discovery Park where he builds cyber-infrastructure for education, outreach and training efforts. He has been given the mandate of making education and training accessible, integrated and engaging by integrating existing and new technology into the hub architecture. Jason received his Masters in Computer Graphics Technology from Purdue University where he also worked in research groups including virtual worlds for engineering education and carbon emission visualization.


The George E. Brown Network for Earthquake Engineering Simulations (NEES) has many stakeholders for the education, outreach and training (EOT) program with various needs. The EOT development team has customized the core hub code with additional modules to support continuing education for students, faculty and practicing professionals. Several third party modules have been seamlessly integrated into NEEShub to host courses with assessment, deliver live presentations to a mass audience and share educational content all within a single sign-on environment.

For example, a lightweight course management system called Moodle, is a free and low-barrier-to-entry method for hosting learning modules. This popular alternative to the more expensive Blackboard system contains the same basic administrative methods and delivery systems. Its potential is now extended with modules to link with traditional hub resources which provides a "contribute once, reuse many times" environment for instructors and professional organizations wishing to provide learning modules linked with assessments.

The NEES development team has established a new "Learning Object" resource type, and increased the fidelity of editing in the associated contribution steps. This allows educators to create rich content pages within the hub, and easily embed information from other sources, such as images, videos and other course content.

The NEEShub can provide freely hosted live content using a flash based media server to stream content to and from any browser. This content can be a simple webcam stream, or a more sophisticated webcast, comprised of desktop presentations, video and Q&A sessions with attendees. We are exploring the feasibility of this system as a low cost alternative to provide webinars for professional development and teleprescence methods during large scale testing operations.

This presentation will show these highlighted NEES EOT customizations, their uses, and how each was seamlessly integrated into the hub architecture.

Chris Smoak

Groups, More than Just Collaboration

Tuesday 4/5/11 2:10pm - 2:30pm

Christopher Smoak is a web application programmer on the HUBzero Team from Saratoga Springs, NY. He graduated from Purdue University in May 2010 with a Bachelors in Computer Graphics Technology and a certificate of Entrepreneurship. He discovered his passion for web design and development in January of 2008 after taking on his first freelance client. Since then Christopher has completed many web design/development projects ranging from a funeral home website to a fully working e-commerce apparel store. He worked for Purdue Convocations, during his undergrad at Purdue as their web guru, where he was able to refine his skills. Now working for HUBzero, he has been able to expand his skill set ten fold, and he continues to learn everyday by reading related books and online blogs, in order to keep up with the ever changing web.


Groups are one one of the most important and easiest ways for hub users to collaborate within their projects. Groups not only wanted a way to have discussions, and have their own private resources, and even share a blog, but they also wanted a way to showcase their group to the outside community.

The New HUBzero groups do just that. They have all the same features as before, but now with a whole slew of new ones. The main one being group pages, which is a way for groups to customize the public facing side of their group. Group Managers can embed content on these pages, with the same wiki-syntax used throughout the rest of the hub. Each group can have any number of these pages. Also on these group pages managers can choose to load custom modules or smaller content blocks on the side of the content.

Among the other new features to groups is the ability to have a group identity, refined access controls which can be set per group, a group calendar, improvements to the inviting process, and of course a complete redesign to the group interface.

Katy Borner

Katy Borner

Atlas of Science: Envisioning Scholarly Data

Wednesday 4/6/11 8:30am - 9:00am

Katy Borner is the Victor H. Yngve Professor of Information Science at the School of Library and Information Science, Adjunct Professor in the School of Informatics and Computing, Adjunct Professor at the Department of Statistics in the College of Arts and Sciences, Core Faculty of Cognitive Science, Research Affiliate of the Biocomplexity Institute, Fellow of the Center for Research on Learning and Technology, Member of the Advanced Visualization Laboratory, and Founding Director of the Cyberinfrastructure for Network Science Center at Indiana University. She is a curator of the Places & Spaces: Mapping Science exhibit

Her research focuses on the development of data analysis and visualization techniques for information access, understanding, and management. She is particularly interested in the study of the structure and evolution of scientific disciplines; the analysis and visualization of online activity; and the development of cyberinfrastructures for large scale scientific collaboration and computation.

She is the co-editor of the Springer book on ‘Visual Interfaces to Digital Libraries’ and of a special issue of PNAS 101 (Suppl. 1) on 'Mapping Knowledge Domains' published in April 2004. She also co-edited a special issue on ‘Collaborative Information Visualization Environments’ in PRESENCE: Teleoperators and Virtual Environments, MIT Press (Feb. 2005), ‘Information Visualization Interfaces for Retrieval and Analysis’ in the Journal of Digital Libraries (March 2005), and ‘Mapping Humanity’s Knowledge’ in Environment and Planning B (Sept 2007). Her new book ‘Atlas of Science: Guiding the Navigation and Management of Scholarly Knowledge’ published by MIT Press will become available in 2010.

She and her colleagues at the Cyberinfrastructure for Network Science Center serve the:

She is the recipient of many fellowships and awards, including Outstanding Junior Faculty Award, Pervasive Technology Laboratories Fellows

hip, SBC Fellow, NSF CAREER Award, and Trustees Teaching Award. She is currently PI or Co-PI in funded research: Collaborative Research: Social Networking Tools to Enable Collaboration in the Tobacco Surveillance, Epidemiology, and Evaluation Network (NSF), Modeling the Structure and Evolution of Scholarly Knowledge (James S. McDonnell Foundation), CAREER: Visualizing Knowledge Domains (NSF), Mapping Indiana's Intellectual Space (21st Century Grant), Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research (NSF), Towards a Macroscope for Science Policy Decision Making (NSF), and Creative Metaphors to Stimulate New Approaches to Visualizing, Understanding, and Rethinking Large Repositories of Scholarly Data (NSF).

For more information on her research agenda, teaching, and other activities, visit: and


Cartographic maps have guided our explorations for centuries, allowing us to navigate the world. Science maps have the potential to guide our search for knowledge in the same way, allowing us to visualize scientific results. Science maps help us navigate, understand, and communicate the dynamic and changing structure of science and technology—help us make sense of the avalanche of data generated by scientific research today. Atlas of Science (, based on the popular exhibit, "Places & Spaces: Mapping Science" (, describes and displays successful mapping techniques. Not even the most brilliant minds can keep up with today's deluge of scientific results. Science maps show us the landscape of what we know.

Jean-Claude Bradley

Jean-Claude Bradley

Open Notebook Science: Does Transparency Work?

Wednesday 4/6/11, 9:00 - 9:30am

Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College of Arts and Sciences at Drexel University. He leads the UsefulChem project, a synthetic organic chemistry initiative started in the summer of 2005 to make the scientific process as transparent as possible by publishing all research work in real time to a collection of public blogs, wikis and other web pages. Jean-Claude coined the term Open Notebook Science to distinguish this approach from other more restricted forms of Open Science. In 2008 he created the Open Notebook Science Solubility Challenge to crowdsource the measurement of non-aqueous solubility. Sponsored by Submeta, Sigma-Aldrich, Nature and the Royal Society of Chemistry, the ONS Challenge has resulted in the publication of a book combining the results of 10 student award winners from the US and the UK. Jean-Claude teaches undergraduate organic chemistry courses with most content freely available on public blogs, wikis, games, Second Life and audio and video podcasts. He has a Ph.D. in organic chemistry and has published articles and obtained patents in the areas of synthetic and mechanistic chemistry, gene therapy, nanotechnology and scientific knowledge management.


This presentation will first describe Open Notebook Science, the practice of making the laboratory notebook and all associated raw data available to the public in real time. Examples of current applications in organic chemistry - solubility and chemical reactions - will be detailed. Key details of the current technical implementation will be described and possible applicability to nanotechnology projects will be explored. Finally, the implications for Intellectual Property protection, claims of priority, subsequent publication in peer reviewed journals and the eventual automation of the scientific process will be explored.

Sangtae Kim

Sang Kim

Cyberinfrastructure for Regenerative Personalized Medicine: The Vision and Challenges

Wednesday 4/6/11, 9:30am - 10:00am

Sangtae “Sang” Kim is the executive director of the new, private not-for-profit Morgridge Institute for Research (MIR) in Madison, Wisconsin. In this position, he is empowered to build a world-class interdisciplinary institute designed to advance biomedical research to new heights by placing special emphasis on the enabling role of cyberinfrastructure.

Prior to the Morgridge appointment, Sang brings experiences from three sectors: academia (distinguished professorships at University of Wisconsin and Purdue University), industry (VP of R&D IT at Parke-Davis Pharmaceutical Research and Lilly Research Laboratories) and government (inaugural Division Director for cyberinfrastructure programs at NSF).

On the research side, his current work in pharmaceutical informatics at MIR explores the intersection of cyberinfrastructure and drug discovery and development including the role of collaborative work flow tools.


Successive waves of advances in the biological sciences: genomic, proteomics and systems biology, have brought us to an unprecedented level of understanding of multi-scale (molecular to cellular) processes in living systems. Regenerative medicine fits into this framework by connecting new insights on stem cells (how they differentiate into the many cell types in the entire organism) to regenerative biology (multi-scale transport processes in tissue engineering). The ultimate vision is personalized medicine, namely therapeutic treatments for an individual based on reprogrammed cells from that same individual. Cyberinfrastructure is central to the realization of this vision. Within the next few years, we will transition from a few dozen stem cell lines to over a hundred thousand induced pluripotent (iPS) cell lines; the healthcare IT ecosystem that is already rife with “medical errors” as a leading source of adverse events will face unprecedented challenges in the personalized logistics of iPS cell banking. A collaborative cyberinfrastructure project between MIR and WiCell that explores strategies for meeting this challenge will be presented.

Derrick Kearney

HUBcheck - check the hub

Wednesday 4/6/11, 10:30am - 10:45am

Derrick Kearney is a software engineer for HUBzero and Purdue University.


HUBcheck is a testing infrastructure developed to help identify incorrect setup and missing components of the HUBzero Platform. It supports test cases written in Tcl, Perl, and Python. In the future, other languages, like Ruby and Shell, will also be supported. Currently there are over 200 working tests in the test suite with more than 50 ideas in progress. The tests cover some of the most frequently forgotten areas of the the HUBzero Platform like filexfer installation, workspace package setup, workspace network access, website redirection between http and https sites, use setup, window manager setup, and user account setup. This talk introduces the motivations behind hubcheck, current capabilities of the system, and future work towards improving the test suite.

Michael Zentner

Nathan Denny

Nathan Denny

Applications for Interactive Behavior Exploration

Wednesday 4/6/11, 10:45am - 11:00am

Michael Zentner is a Senior Research Scientist at the Rosen Center for Advanced Computing (RCAC) at Purdue University working on visualization and data analysis. Prior to joining Purdue, he was founder/senior team member of several information technology companies, where he created innovative solutions for extracting patterns from data, collaboration, and constrained optimization. Dr. Zentner has consulted with many Fortune 500 companies to apply these technologies for solving business problems including operations scheduling, strategic capital investment, process improvement, and new product innovation and creation.

Nathan T. Denny (Software Engineeer, Rosen Center for Advanced Computing, Purdue University) received his Master of Science in Computer Science from Southern Illinois University in 1998 and his Bachelors of Science in Computer Science and Mathematics from Southern Illinois University in 1997. He has a diverse background and has published in fields such as design for testability (DFT) of very large scale integrated circuits (VLSI), information re-use in case-based reasoning, Internet spam control, automation in agricultural irrigation, peer-to-peer networking, knowledge management in global software development, intelligent human-machine interfaces, and simulations in social sciences. He currently works with the HubZero group at the Rosen Center for Advanced Computing where he contributes to statistics, datagraphics, and visualization.


Authors: Michael Zentner, Nathan Denny, Gerhard Klimeck, Ken Musselman, George Bunch Adams III

In the Spring of 2010 we became engaged with nanoHUB to help develop an understanding of the user activity on the site. After attempting several techniques for classifying user behaviors, it became apparent that a better understanding of this behavior from bulk characterizations down to the level of individual users was necessary. This work resulted in the development of custom visualization software and the application of commercial software that has been licensed for use in conjunction with the HUBs. Through using these software tools, we were able to understand nanoHUB user behavior at its lowest level, and subsequently successfully develop automatic user characterization methods based on those findings. These tools are now also being applied in However, in catalyzeCare the tools are not used for user behavior analysis. Rather, they are used by researchers to develop an understanding of hospital patient behavior and in particular regarding patients who visit a hospital multiple times, termed "readmissions." In this talk we discuss these tools and demonstrate their use in nanoHUB and catalyzeCare.

George Adams

George Adams

HUBzero Roadmap and Community Feedback

Wednesday 4/6/11 11:00am - Noon

George B. Adams III is an Executive Consultant of the HUBzero Project. He is also the Deputy Director of the Network for Computational Nanotechnology (NCN). He earned the BSEE degree from Virginia Polytechnic Institute and State University in 1978 and the MSEE and PhD degrees in 1980 and 1984 from Purdue University. In 1983 he joined the Research Institute for Advanced Computer Science at the NASA Ames Research Center as one of the initial five staff members and worked in high-performance computing for scientific applications. He was a member of the founding Executive Committee for Supercomputing ’88 (now known as the SC’XX conference series). In 1987 he joined the faculty of the School of Electrical Engineering, Purdue University. In 2000, he joined the planning team for what became the Birck Nanotechnology Center (BNC) facility in Purdue’s Discovery Park, widely considered the preeminent university nanoscale research facility. He became Research Development Manager for BNC in 2004 and Special Projects Manager for Discovery Park in 2006. Dr. Adams has written over 50 papers and book chapters, held one US patent, and received three national awards for his distance education classes.

Gerry McCartney

Gerry McCartney

Research Support at Purdue University

Wednesday, 4/6/11 Noon - 12:15pm

Gerry McCartney was appointed Purdue's vice president for information technology and CIO in July 2007. He was named the Olga Oesterle England Professor of Information Technology in June 2009. From 1993-2004, McCartney was associate dean and chief information officer at the University of Pennsylvania's Wharton School.

As Purdue CIO, McCartney oversees Information Technology for the University and directs all the central computing (research, academic and administrative) as well as the networking and telecommunications systems on the West Lafayette campus. Purdue’s IT organization has 930 staff members and an annual budget of more than $78 million.

William Barnett

Bill Barnett

Breakout Session #1 Chair: Using HUBzero to Support Scientific Projects

Tuesday 4/5/11, 2:30 - 5:30pm and Wednesday 4/6/11, 1:30 - 4:30pm

William K. Barnett oversees life sciences and biomedical research technologies at Indiana University and the Indiana University School of Medicine (IUSM). As the Senior Manager of Life Sciences, Bill oversees the development and implementation of research technology programs for biological research including high performance computing (HPC) applications, analytical pipelines, and genomics research. As the Director of the Advanced IT Core at the IUSM, Bill oversees the development and management of biomedical applications, including HPC and applications development in support of health care research. As the Director of Information Architectures for the Indiana CTSI, he oversees the development of collaborative technologies for the Indiana Clinical and Translational Sciences Institute. As Associate Director of the Center for Applied Cybersecurity Research, Bill also oversees privacy programs for research technologies, including HIPAA alignment of academic computing systems at Indiana University.

Wednesday 4/6/11 2:30pm - 3:00pm, Breakout Session #1, Using HUBzero to Support Scientific Projects


The Indiana CTSI HUB represents a somewhat unique use case in HUBzero deployments. An institutional virtual organization, it represents an attempt to link Indiana University, Indiana University School of Medicine, Purdue University, and the University of Notre Dame in a statewide effort to advance translational medical research. This translation involves connecting basic and clinical researchers and their efforts as well as collaboration with hospitals, industry, and the public. Dr. Barnett will discuss how the Indiana CTSI HUB came to be, what kinds of translational research challenges it seeks to solve, and how it has gone about approaching these challenges.

Steve Wereley

Steve Werely

Kristina Bross

Using HUBzero to Distribute and Enable Analysis of Deepwater Horizon Oil Spill Videos

Tuesday 4/5/11 2:30pm - 3:00pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Professor Wereley has bachelor degrees in Physics (Lawrence University, 1990) and Mechanical Engineering (Washington University, St. Louis, 1990) followed by masters and doctoral degrees from Northwestern University (1992 and 1997). He is currently Professor of Mechanical Engineering at Purdue University where he has been working since 1999 and a Fellow at the Center of Smart Interfaces, Technische Universität Darmstadt (Germany). Professor Wereley served as an Alexander von Humboldt Fellow at Technische Universität Darmstadt (2007) and Universität der Bundeswehr (2009). His current research interests focus on fluid flows in microscopic domains, commonly known as microfluidics. Professor Wereley is the co-author of the monographs Fundamentals and Applications of Microfluidics (Artech House, 2002 and 2006) and Particle Image Velocimetry: A Practical Guide (Springer, 2007). The latter book led to his involvement with the oil spill.

Kristina Bross is Associate Professor of English and American Studies at Purdue University. She received her Ph.D. from the University of Chicago in 1997. She has received both a National Endowment for the Humanities and a Fulbright fellowship as well as the Murphy Award for Excellence in Undergraduate Education at Purdue. A member of the executive committee for the Society of Early Americanists, she will become the vice-president in June, 2011. Author of books and journal articles on early American literature and culture, her interests in the history of violence and catastrophe in America led to the construction of an American Studies undergraduate class, "Oil and Water: Literature, Science, and Disaster." In this course, students take an interdisciplinary approach to the study of Hurricane Katrina and the Deepwater Horizon oil spill, including close consideration of fiction, poetry, and visual art created in response to these two Gulf of Mexico disasters.


Authors: Steve Wereley, Kristina Bross, Derrick Kearney, Christopher Smoak, Michael Zentner

Last summer the Gulf of Mexico was subject to the worst ever oil spill in US history. In order to plug the damaged well, a fleet of Remote Operated Vehicles (ROVs) was brought in. Each of these vehicles is operated via video camera. All of the ROV footage was offered to Purdue by Rep Markey and Sen Boxer. Purdue's ITaP team developed a hub to stream these videos to the general public to make them widely available. The general public, media, and scientific communities have found them useful and have visited the hub. In order to help users interpret and work with the videos several tools have been developed. These include a journal tool to log comments on each of the videos, where interesting events occur, etc., as well as photogrammetry tool that allows users to determine the size of features seen in the videos by scaling according to some feature of known size. The photogrammetry tool also allows users to mark points in one frame and track the motion of fluid features across several frames. Both of these tools are being used in the English/American Studies class, Oil and Water.

Lynn Zentner

Lynn Zentner

Success Criteria for Establishing a Thriving HUBzero Based Site: A Model for Science 2.0

Tuesday 4/5/11 3:00pm - 3:30pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Dr. Lynn K. Zentner joined the Network for Computational Nanotechnology (NCN) in August 2010 and currently serves as NCN Technical Director. She was previously a visiting professor in the Mechanical Engineering Technology Department at Purdue. Dr. Zentner received a Ph.D. in Mechanical Engineering from Purdue University in 1993 and has been involved in modeling and simulation research since 1986.


Authors: Lynn Zentner, Gerhard Klimeck, Krishna P. C. Madhavan, George Bunch Adams III

Science gateways utilizing HUBzero technology provide the means for rapid dissemination and use of research results by a global research and education community, extending resources that used to be available to an elite few to a broader and more diverse community. Users may range from educators and their students to the computational research community, experimentalists, and a wide variety of users in related and peripheral fields. This community requires reliable, easy to use tools with a transparent infrastructure providing necessary computational muscle. The developers that supply these tools require ease of deployment and mechanisms to support their contributions as well as incentives to contribute these resources to the community at large. A mature, tested infrastructure is necessary to meet these requirements consistently and dependably. Funding agencies require demonstration of the impact of the gateway through clear metrics. Meeting these multiple and sometimes conflicting requirements calls for a creative and thoughtful approach to building and maintaining a science gateway, which will be discussed in this presentation.

Linas Mockus

Linas Mockus

Research Collaboration and Knowledge Sharing in the Pharmaceutical Domain

Tuesday 4/5/11 3:30pm - 4:00pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Dr. Mockus is currently Sr. Research Scientist at Purdue University where he is actively supporting QbD projects. From 2004 to 2008 he was with Allergan as Sr. Project Engineer and from 1997 he was with Pfizer as Sr. Development Engineer. He earned his Ph.D. in Chemical Engineering from Purdue University as well as equivalent degree in Computer Science from Moscow Institute of Physics and Technology.


Authors: Linas Mockus, Jose Lainez, Gintaras Reklaitis, Carl Wassgren, Kristine Alston, Ann Catlin

Nowadays, scientific collaborations are considerably growing and all forms of cyber-infrastructure are often used to tackle a single complex problem. To sustain and exploit this movement, the establishment of long-term community-wide hubs has been envisaged. Here, a Hub deployed to support knowledge sharing and scientific collaboration for pharmaceutical science and engineering, the, is presented.

As an example of global scientific collaboration a database of excipient properties which is implemented on pharmaHUB will be discussed. Excipients are the non-pharmacologically active portion of the dosage form and are used in virtually all drug products. An excipient may fulfill various functional purposes depending on its use in a formulation and manufacturing process. The chemical and physical properties of excipients are critical to manufacturing, stability, and performance of drug products. However, not all the critical properties have been identified and specified in the compendial standards.

Generally, excipients are derived from natural products, synthetically modified natural products, or completely synthetic, and they are available from a multitude of sources. As a result, their properties may vary from lot-to-lot, vendor-to-vendor, and occasionally even within a lot. It is variations like these that are often at the root of production problems and failures that emerge unpredictably during the life cycle of a drug product.

The objective of database is to provide manufacturers and regulators better information concerning excipient property variation. A variety of property measurements, such as particle size distribution, powder flowability, and compact elastic modulus, will be collected from several independent laboratories for a range of excipients and lots. The web interface used to view the data is flexible and can be used to search for particular excipients, properties, or property ranges, compare selected excipients, and plot histograms and scatter plots of the data.

Lan Zhao

Lan Zhao

DRINET Hub for Drought Information Synthesis, Modeling and Applications

Tuesday 4/5/11 4:00pm - 4:30pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Lan Zhao is a research scientist at Rosen Center for Advanced Computing (RCAC) in Purdue University. Her interests include infrastructure for scientific data storage, retrieval, provenance, and processing, integration and sharing of heterogeneous data sets and models, and composition of data-driven scientific workflows using service-oriented technologies.


Authors: Lan Zhao, Carol Song

An interdisciplinary team of researchers is building the DRINET hub to support regional scale drought information dissemination and synthesis, and sharing of datasets, models and tools in an NSF-funded data interoperability project. The DRINET project engages diverse stakeholders, from hydrologists, agriculture experts, climatologists, to farmers and educators, to collect, publish drought related information and build community acceptance of local and regional data collection/compilation processes and data formats. To-date, many gaps hamper efforts at forecasting droughts and mitigating their impact. This project is fostering increased communication and cross-synthesis of data for diverse applications, and providing a solid basis for study of improved drought risk assessment and trigger indicators. Further, it will serve the purpose of an educational tool, and draw on visualization capabilities to better explain, for example, the role of precipitation and stream flow patterns on droughts.

The DRINET hub is home to researchers, students to publish their own models and tools, datasets, analysis, visualization, training and educational materials for studying droughts. This presentation provides an overview of the datasets, tools and applications that have been built into the DRINET hub to support (1) dynamic data access/analysis using GIS (geographic information system) software; (2) self data publishing and sharing among stakeholders; (3) metadata standardization; (4) tools/applications for drought characterization, prediction and visualization; (5) education and community engagement. Emphasis will be placed on the technologies used to enable quick web application development in the hub environment as well as the integration of GIS and data management capabilities which currently lack native support from the HUBzero software stack. The presenters will also seek developer and end user input on how these components can be improved and shared with the community.

Alisa Neeman

Alisa Neeman

Collaborative Research in a Regional Grid -- Using HUBzero to Facilitate Collaboration

Tuesday 4/5/11 4:30pm - 5:00pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Alisa Neeman is a scientific programmer at University at Buffalo's Center for Computational Research (CCR). She works on the web portal, teaches, and helps students, researchers and industry clients use CCR's supercomputing resources. Prior to working for CCR, Dr. Neeman worked as a Graduate Student Researcher at Los Alamos National Laboratory and as an intern at IBM. Dr. Neeman received her Ph.D. in computer science from University of California, Santa Cruz in 2009. Her research interests include grid computing, storage systems and scientific visualization.


Authors: Alisa Neeman, Steven Gallo, Efstratios Efstathiadis

Research teams collaborating across institutional, geographical and cultural boundaries are increasingly common. Funding agencies including the National Science Foundation (NSF) and National Institutes of Health (NIH) strongly encourage virtual organization building and collaboration across institutions and disciplines. A set of software tools that enables scientists to efficiently share information and resources with distributed collaborators is key to facilitate collaboration of research teams across institutional and geographical boundaries. Utilizing HUBzero, we have implemented a regional infrastructure supporting the High Performance Computing Consortium (HPC2) initiative within New York State. This hub consists of a web- portal infrastructure that allows investigators and research groups to easily create and share research materials as well as computational and storage resources among their members. In this paper, we describe the process of launching the hub and providing access to a regional grid consisting of three supercomputing sites with heterogeneous computing platforms and security/access policies. We address issues of capacity and security that arose as we road-tested this evolving platform.

Nataliia Perova

Nataliia Perova

CLEERHub: Using an Online Collaborative Workspace as a Cognitive Tool

Tuesday 4/5/11 5:00pm - 5:30pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Natasha Perova is currently a PhD student in the School of Engineering Education at Purdue University. She previously worked at the Harvard Graduate School of Education as a research assistant focusing on students’ learning algebra and also taught an introductory physics course at Suffolk University, Boston, Massachusetts. Before that she worked as a graduate research assistant at the Center for Engineering Educational and Outreach at Tufts University, Medford, Massachusetts. Natasha received her M.S. in Mathematics, Science, Technology and Engineering education in 2008 and M.S. in Electrical Engineering in 2005 from Tufts University and B.S. in Electrical Engineering from Suffolk University.


Authors: Nataliia Perova, Qaiser Malik, Dr. Ruth Streveler

Our research looks at how to better support collaboration in Communities of Practice. In particular, we focus on using as an online platform for collaboration. To facilitate online group research collaboration, CLEERHub integrates Wiki documents for shared co-editing, Resources pages for listing relevant literature information and Discussion spaces for easier communication among group members.

In Fall 2010 we conducted a pilot study to test the feasibility of using the platform to support team collaboration. Participants in the study were students enrolled in a semester-long undergraduate course, Contemporary Science and Innovation, designed to introduce students to current scientific and engineering issues. We implemented a CLEERHub Usage Survey that was designed to collect students' feedback about their experiences using CLEERHub as an online space for their assigned team project. Our preliminary findings indicate that many of the students found the CLEERHub workspace useful for their project work. Some of the participants said that CLEERHub made sharing information, planning meetings, and organizing work tasks easier. One of the students said that CLEERHub was useful for doing a brainstorming for the project and allowed everyone to contribute. Another participant commented: ""CLEERHub was most useful for being able to share information online without having to get together outside of class time.""

For this presentation we will focus on how we can design the CLEERHub group workspace to better facilitate collaborative online efforts. Specifically, we will discuss features that would help to support group the problem-solving process during brainstorming and synthesis of ideas stages. We will also discuss possible ways HUBS could support the process of moving from idea to solution-space. We will explore how such an online collaborative environment could offer valuable insights into collaborative knowledge-building.

Michael Witt

Michael Witt

Aswathy Sivaram

Aswathy Sivaram

Exposing HUB Objects for Aggregation Using OAI-ORE and Linked Data

Wednesday 4/6/11 1:30pm - 2:00pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Michael Witt (website, is an assistant professor of library science and Interdisciplinary Research Librarian at Purdue University. His interests include research data curation and the development of new tools, protocols, and practices for librarians and the producers and users of digital information in non-traditional formats and platforms such as cyberinfrastructure. He is affiliated with the Distributed Data Curation Center (D2C2) of the Purdue University Libraries.

Aswathy Sivaram is a Masters candidate in the School of Civil Engineering at Purdue University. She is a Graduate Research Assistant, working with Dr. Michael Witt on exposing hub objects as resource maps. Her interests include designing and building low cost housing, geophysical modeling of soil, and programming.


Authors: Michael Witt, Aswathy Sivaram

The Open Archives Initiative Object Reuse and Exchange (ORE) defines a standard for the description and exchange of aggregations of Web resources. Work is currently underway to develop an OAI-ORE implementation for HUBzero as part of the Open Parks Grid, which is a hub launched by Clemson University in collaboration with the National Parks Service, Purdue University, and the Georgia, North and South Carolina State Parks to serve the parks professionals community. A brief tutorial on ORE will introduce its underlying technology (e.g., web architecture, Resource Description Framework, Linked Data), abstract data model, and how to express, serialize, and expose ORE resource maps. Our project design, implementation ideas, and project status will be presented. Two use-cases will be presented as examples and as applications that will be developed and released as free, open source software in the future. In the first use-case, ORE will be used to replicate the digital objects, metadata, and semantics of the Open Parks Grid to a Fedora preservation repository. In the second use-case, a new tool will be developed to enable HUB users to create their own custom collections of digital objects from the web and publish them on the HUB as ORE aggregations. A goal of sharing and discussing this project in its early stages is to identify and collaborate with other HUB developers who are interested in ORE and other Semantic Web technologies. This project is sponsored by the Institute of Museum and Library Services (IMLS LG-05-10-0117-10).

Bruce Barton

Bruce Barton

Adapting HUBzero for the Arts and Humanities

Wednesday 4/6/11 2:00pm - 2:30pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Bruce Barton is leading the effort in Project Bamboo to adapt HUBzero for use a Bamboo Work Space. He is a project manager and software developer in the Division of Information Technology at the University of Wisconsin-Madison.


Author: Bruce Barton

Project Bamboo is a multi-institutional effort to develop and deploy rich computing platforms and services for conducting collaborative research in the arts and humanities.

Two HUBzero Consortium members, the University of Wisconsin-Madison and Indiana University, are extending HUBzero functionality for humanities research. We are integrating a CMIS client for use in browsing and retrieving materials housed in remote digital repositories such a HathiTrust and the Perseus Project. We are incorporating the open source Fedora repository to provide humanists with a rich infrastructure for storing local copies of digital objects, such as texts and images, and related metadata, and for representing the relationships between objects. We are building RESTful web services clients for HUBzero that will enable scholars to apply sophisticated textual analysis tools such as those delivered by the University of Chicago's ARTFL project to the objects they have curated. We are building techniques that will enable scholars to use the HUBzero workspace environment to apply locally hosted analytical tools to digital objects and to develop visualizations of their experimental results. We plan to incorporate an OpenSocial container into HUBzero so that tools implemented as OpenSocial gadgets such as Oxford University's Virtual Research Environment for the Study of Documents and Manuscripts can be integrated into the user's experience of the HUBzero research platform.

In this talk I will describe our plans, what we have achieved to date, and the kinds of research HUBzero, adapted for the humanities, will be able to support.

Project Bamboo is made possible through the generous support of the Andrew W. Mellon Foundation and the contributions of ten partner institutions, including the University of Wisconsin-Madison and Indiana University.

Pamela Morris

Pamela Morris

Amira Zamin

Amira Zamin

CatalyzeCare: Transforming Healthcare Delivery Through Communities

Wednesday 4/6/11 3:00pm - 3:30pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Pamela is currently a Ph.D. student in Communication at Purdue University. Her interests are collaborative computing and technology adoption in organizations. She is currently a graduate research assistant with the Regenstrief Institute for Healthcare Engineering (see and a TA for a variety of courses in the Department of Communication. She has also been a graduate research assistant on the Department of Organizational Leadership and Supervision's Hub Collaboration Research Team and taught Meeting Management for that department. Pamela studied computer science and worked at IBM for 12 years before coming to Purdue. Pamela is a certified Project Manager and aspires to work with technology when she completes her degree.

Amira Zamin serves as the communications specialist for the Regenstrief Center for Healthcare Engineering (RCHE). Her background includes marketing communications for higher education and healthcare. Amira earned her BA and MA at the University of Iowa.


Authors: Pamela Morris, Amira Zamin

The purpose of CatalyzeCare is to provide a cyberinfrastructure for online collaboration that aims to improve and transform healthcare delivery. The site, funded by the Regenstrief Center for Healthcare Engineering, seeks to initially provide a free and open place for researchers to share data sets and collaborate on the development and piloting of tools for modeling and data visualization. Outcomes of such projects can then be disseminated via CatalyzeCare to appropriate audiences including other researchers, practitioners, and patients.

Finally, CatalyzeCare aims to assist projects that will clearly lead to impacts on healthcare delivery. A key to fulfilling these goals is the establishment of communities centered on an interest area or research project team. Such teams cross the boundaries of universities and disciplines and may include practitioners and patients in addition to researchers. Often the project's community is the sole way to access data or activate tools relevant to that community. Sub-communities are used to partition parts of a project as well. Our talk will tour two of our active communities who share data and private tools. We'll explain how these communities are being used to provide unique opportunities for research, dissemination, and impact using a model of sharing and cooperation that is not centered in academia and thus differs somewhat from other HUBs.

Erin Twamley

Erin Twamley

Collaborating on Health Care Quality Improvement: from Theory to Practice

Wednesday 4/6/11 3:30pm - 4:00pm, Breakout Session #1, Using HUBzero to Support Scientific Projects

Erin Twamley is a Research Analyst at Optimal Solutions Group, LLC (Optimal) a small public policy research firm and research affiliate of the University of Maryland at College Park. Ms. Twamley has experience in conducting education and workforce development research. She has facilitated the design and development of web-based tools including the Service Obligation Tracking System ( for the U.S. Department of Education. Ms. Twamley is co-leading the design, customization and implementation of HUBzero platform for a quality improvement collaboration. She has evaluated program implementations and collaborations for the District of Columbia Government and conducted systematic literature reviews for the National Institutes of Health. Additional areas of research interest include examining racial disparities in criminal conviction rates and sentencing, and the gender achievement gap in Science Technology Engineering and Mathematics (STEM) fields. Ms. Twamley graduated with honors from Macalester College (St. Paul, MN) with a B.A. in Psychology and Political Science. She is a member of the Project Management Institute, The National Honor Society in Psychology, and The Society for the Psychological Study of Social Issues.


Authors: Dr. Mark Turner, Erin Twamley

Optimal currently evaluates Medicare Advantage plans' quality improvement plans on behalf of the Centers for Medicare and Medicaid Services (CMS). CMS requires Medicare Advantage Organizations (MAOs) to implement ongoing quality improvement programs that include a chronic care improvement program (CCIP) and an annual quality improvement project (QIP). Optimal's current approach to evaluating CCIP and QIP is to collect information on the plans' quality improvement projects, evaluate the programs' ability to demonstrate improvement, and provide technical assistance to plans. Optimal has automated the review process to achieve greater efficiency and accuracy using the internal tracking database to collect and process technical assistance requests from MAOs, third-party vendors, and HEDIS auditors. Optimal provides CMS with monthly and ad hoc updates on the challenges and issues the MAOs are facing as well as Optimal's suggested responses to address them.

A critical next step for Hubzero is to expand the hubs outside of the scientific community, in particular to establish and promote quality improvement in health care practices, beginning with the Transforming Health Care Delivery Hub.

For example, the Transforming Health Care Delivery HUB would be accessible to not only the scientific community (e.g. health policy and health care practitioners), but also Medicare Advantage plans that are obligated to implement quality improvement initiatives that are methodologically sound.

This presentation would include a theoretical case study examining how collaboration and research within MAO communities could be used to further enhance collaboration, innovation, and health care outcomes.

Sam Wilson

Sam Wilson

Configuring and Managing Your Hub

Tuesday 4/5/11 2:30pm - 5:30pm, Breakout Session #2, Configuring and Managing Your Hub Part 1

Wednesday 4/6/11 2:30 - 3:30, Breakout Session #4, Installing the HUBzero Software

Sam is a Hub Liaison for HUBzero. He enjoys helping hub managers understand how hubs work, and how they can properly configure and manage their hub. Prior to joining the HUBzero team, Sam worked with the Networks and Security division of Information Technology at Purdue (ITaP). While there, he worked to develop improved methods for telecommunications data access, including an iPhone web app for ITaP employees to access data in the field. Sam received his BS in Management with a focus in Management Information Systems from Purdue University.

Nikki Huang

Configuring and Managing Your Hub

Wednesday 4/6/11 1:30pm - 4:30pm, Breakout Session #2, Configuring and Managing Your Hub Part 2

Nikki is a Hub Liaison for HUBzero. She is skilled in creating documentation, providing training, and helping hub managers get started with their new hub. Prior to joining the HUBzero team, Nikki was an undergraduate trainer and technology consultant for Undergraduate Training at Purdue (UT@P). She specialized in multimedia editing and online collaboration tools. She received her Bachelor's degree in Mass Communication from Purdue University.

Steve Snyder

Steve Snyder

Configuring and Managing Your Hub

Wednesday 4/6/11 2:30 - 3:30, Breakout Session #4, Enhancing Web Functionality Through Template Overrides

Steve Snyder is web application programmer with the HUBzero team at Purdue, specializing in search and related functions.

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