The Biomedical Informatics Key Function's ultimate goal is to establish and maintain an integrated informatics infrastructure that effectively supports clinical and translational research at the University of Iowa and across the national consortium. We offer useful and accessible knowledge resources for researchers in the form of a federated infrastructure (a broad selection of local and national databases combined into a single virtual framework). These interconnected resources are fully capable of capturing, archiving, and managing all the various technological forms and mediums involved with conducting biomedical research.
We employ a multi-layered, federated approach to system architecture, because we believe it promotes a collaborative environment, helps alleviate many key challenges involved with performing this kind of work, and allows us to readily adapt to constantly shifting representation, techniques, and technologies. Other goals include:
Currently, we're focusing on 3 major umbrella projects and numerous satellite projects designed to enhance ICTS investigators' research experiences:
Research Warehouse - Our Research Warehouse is designed to support a broad spectrum of investigative needs associated with conducting clinical and translational research. Specifically, the Research Warehouse provides researchers with a centrally located place to store large amounts of data and offers a means of organizing and coordinating that data within a single resource. Some examples of current sub-projects include: tracking, evaluating, archiving, and reporting on clinical and translational activities across campus; creating a central repository for storing imaging data; designing a centralized tissue sample repository, complete with managing and tracking capabilities, that will eventually integrate with the larger research data warehouse;collaborating with other centers and institutes on campus to share informatics resources rather than replicate them (e.g. Iowa Institute for Biomedical Imaging, Psychiatric Iowa Neuroimaging, Nanoscience and Nanotechnology Institute, just to name a few); designing a platform that pulls from various data sources around the UI campus providing up-to-date information and easier application development.
Data Mining, Analysis,and Visualization - We offer support services so researchers can maneuver the various tools and mechanisms involved with accessing and using the Research Warehouse. Current sub-projects include: providing a secure computing environment capable of supporting the computational demands of various tools; identifying and implementing data analysis tools designed specifically to serve ICTS researchers' needs; providing ICTS researchers with various desktop analysis tools (e.g., SAS statistical package); and, providing support services to investigators analyzing imaging data.
Collaboration and Awareness Services - These services foster collaboration and keep you effortlessly up-to-date about important funding and publication opportunities. We provide a rich array of web services supporting the various needs of researchers interacting with the ICTS. This includes information dissemination, collaboration brokering,and on-going interaction with the multiple ICTS key functions and regulatory units on campus. Some current sub-projects include: enhancing our new research networking application, Loki, for UI investigators; supporting an electronic CV system; creating secure wiki sites for investigative groups; advertising pilot grant opportunities to various audiences and electronically supporting grant preparation, review, and notification; building up our website as an informational and dynamic user tool; and, providing an online resource for grant and position applications.
The following functions are in place to help us reach our goals:
| Function/Program |
Name | Position | Phone | Address | |
|---|---|---|---|---|---|
| Biomedical Informatics | Alter, Duane | Systems Administrator | 319 353 6484 | 11500-4 PFP | |
| Connel, RJ | System Administrator | 319 467 5484 | 11500-4 PFP | ||
| Davis, Heather | Webmaster | 319 384 5409 | CC302-GH | ||
| Eichmann, Dave | Key Function Director | 319 384 5242 | W319-A GH | ||
| Finley, Brian | Applications Dev and Sup II | 319 467 5285 | CC302 GH | ||
| Harding, Adam | Info Tech Support Services I | 319 353 6310 | W281 GH | ||
| Klawitter, Bill | Database Admin/Application III | 319 467 5479 | 11500-13 PFP | ||
| Rogers, Ben | Systems Administrator | 319 353 8539 | 11500-14 PFP | ||
| Ryu, Gi-yung | Database Administrator | 319 467 5545 | 11500-07 PFP | ||
| Schappet, James | Applications Dev and Sup III | 319 384 7355 | 11500-05 PFP | ||
| Van Tol, Lucas | Info Tech Support Services I | 319 467 5285 | W281 GH | ||
| ICTS Graduate Students | Bui, Cuong Kien | Graduate Research Assistant | 319 384 5038 | CC302-GH | |
| Chin, Si-Chi | Graduate Research Assistant | 319 384 5244 | CC302-GH | ||
| Madlock-Brown, Charisse | Graduate Research Assistant | 319 384 5245 | CC302-GH | ||
| Papke, Todd | Graduate Research Assistant | 319 384 5243 | CC302-GH | ||
| Park DJ | Graduate Research Assistant | 319 384 5247 | CC302-GH | ||
| Windham, Jonathan | Graduate Research Assistant | 319 384 5246 | CC302-GH | ||
The following resource list provides information about our storage capacity, computing capabilities, and consulting services.
View frequently asked questions and their answers
The ICTS provides a number of different storage services designed to fit all of your research needs. Please contact Ben Rogers for more information.
Desktop File Sharing (SMB or CIFS) - CIFS allows multiple users to share and store files on a network drive. This type of connection works with Linux, Macintosh, and Windows computers. At present this service is provided on a limited basis from wintermute.icts.uiowa.edu. Users must use their ICTS account to login. Future support is planned for HawkIDs. Please contact us for more information.
Network File System (NFS) - NFS allows multiple users to share and store files on a network drive. This type of connection works with Linux and Macintosh computers and requires a static ip address (an address that you have manually defined on your computer that does not change each time you connect to the network). At present this service is provided on request to users affiliated with ICTS. Please contact us for more information.
Rsync - Rsync is a program used to synchronize data between two locations. ICTS uses rsync tunneled through ssh to create a simple, but secure backup mechanism. The tools needed for this to work are built in on Linux and Macintosh computers. It is also possible to connect from a Windows machine but additional software installation is required. At present this service is provided on request to users affiliated with ICTS. Please contact us for more information.
ZFS - ZFS is a new type of filesystem created by Sun Microsystems that provides advanced data security and replication functionality. ICTS uses ZFS replication technology to provide efficient off site backups. This backup mechanism, tunneled through ssh is also available to the user community but is only recommended for advanced users. At present ICTS has only tested the Solaris and OpenSolaris operating systems with ZFS. Please contact us for more information.
The ICTS has combined together a large number of separate systems, forming a powerful cluster of Mac OS X and Linux systems. This cluster provides a valuable computational resource to researchers on the University of Iowa campus that increases processing times, data storage levels, and management capabilities. Priority on the cluster is given to researchers who are new to their field and those who are directly working with ICTS key functions. To request an account please contact Ben Rogers via email.
The ICTS currently has a developmental cluster, a.k.a., one really big computer with massive amounts of memory and fast processing reflexes, available for early adopters. The head node of this cluster is accessible at cluster.icts.uiowa.edu. The system uses the same ICTS ldap username and password as all other systems but does not currently share the same home account space (support for shared home accounts is under way). At present the cluster is still in shakedown mode so jobs may need to be interrupted on an occasional basis. The core of the system is composed of five 8 Core 2GHz Opteron systems with 16GB of ram for a total of 40 cores and 80GB of memory. The scheduler used on the system is Sun Grid Engine (man qsub will provide the basics of job submission).*
If you are interested in obtaining more information about the cluster, web based statistics are available at http://cluster.icts.uiowa.edu. Please contact Ben Rogers via email for more information.
Loki is a web-based networking application receiving praise from within the CSTA consortium. This application provides easy access to a vast array of investigators' research profiles, fueling collaborations both within and across disciplines and research interests. Fully integrated with PubMed, Loki automatically revises your publication lists on a daily basis, so you don't waste valuable time trying to do it yourself. Loki's search engine automatically supplies MeSH terms, and also allows you the opportunity to enter in your own unique key words and key word combos, leading to higher visibility and more powerful collaborations.
The ICTS uses Confluence, an easy-to-use commercial wiki, which was designed to ease and facilitate the collaborative process. Confluence allows individuals to converse freely while writing, editing, enhancing, sharing, and archiving documents that are all securely stored in one space. Confluence is searchable and has active development capabilities, plugin architecture (i.e., you can alter its design to fit your specific needs), and a large academic customer base. Capabilities include:
If you have questions or comments, please contact Heath Davis. Visit Confluence to learn more or you can read about users' experiences with the program.
Drupal, the content management system, is used to generate and distribute web content to the public, grassroots investigators, and lab groups. ICTS administration will serve as content editor, vetting content for public visibility. Please contact Heath Davis for further information.
We're currently using JIRA, an issue/request tracking system, for Biomedical Informatics and potentially other key functions (e.g., Biostatistics/Epidemiology/Research Design). JIRA acts like a customer support call center, allowing users to input work orders, and log and track problems, requests, and comments. Please contact Dave Eichmann for further information.
The ICTS' Regulatory Knowledge and Support Key Function has requirements relating to protocol review and tracking that dovetail into the administrative requirements from NIH for annual reporting. The CRU Informatics Working Group has a couple of systems that are available for use, including WebCAMP (a web-based system for administrative management), that specifically deal with protocol and review. We're currently discussing access to this package with Columbia U, the developing institution. Please contact Dave Eichmann for further information.
Standard web service framework that powers our website, wiki, and other services listed above. Please contact Ben Rogers for more information.
