The University of Illinois and Mayo Clinic have partnered to support the installation of an instance of the Department of Energy (DOE) Systems Biology Knowledgebase, or “KBase” on the Illinois campus.
KBase is an open source software and data platform that integrates data, tools, and their associated interfaces into one unified environment rather than forcing users to access various sources and learn multiple systems—it’s basically a one-stop shop for all things systems biology. KBase enables researchers to collaboratively generate, test, and share new hypotheses about gene and protein functions; perform largescale analyses on scalable computing infrastructure; and model interactions in microbes, plants, and their communities. KBase employs a Narrative Interface as its graphical user interface, which keeps a record of the computational analyses that are designed and carried out by the researcher. These records, called Narratives, can be kept private or they can be shared and published. Shared Narratives enable collaborators or other researchers in the community to follow the steps and thought processes that were used in the analysis for anyone who might wish to repeat the experiment or to change the parameters and/or inputs to generate different or enhanced results.
KBase is not completely new to Illinois or Mayo Clinic researchers—many are already using the DOE instance. However, the instance of KBase deployed by the DOE is limited in that it only handles data from projects that are within the scope of the DOE’s mission (e.g., related to energy and the environment). The instance of KBase at Illinois will not have the same limitations on the type of data allowed, which will make KBase an excellent resource for researchers working with health related microbiome data. Researchers should note, however, that KBase is not HIPAA compliant and the version at Illinois will maintain the DOE’s restrictions for human subject data. In other words, uploading of human data or personally identifiable information will be prohibited.
Due to the impact that KBase is anticipated to have as a resource for health-focused research, Illinois and Mayo Clinic have both invested equally in the installation of KBase on the Illinois campus. This includes both the purchasing of new hardware and support for personnel to perform the software installation. Various colleges and units at Illinois have helped to support the installation, including the Office of the Vice Chancellor for Research, the Mayo Clinic and Illinois Alliance for Technology-Based Healthcare, and the Colleges of ACES, Engineering, Liberal Arts and Sciences, Applied Health Sciences and Veterinary Medicine.
The KBase system is housed at the Carl R. Woese Institute for Genomic Biology (IGB). System maintenance and user support will be provided by the HPCBio group in the Roy J. Carver Biotechnology Center and the Computer and Network Resource Group (CNRG) at IGB.
KBase is free to use for Illinois and Mayo Clinic researchers until July 1, 2018. After 2018, fees for use may be applied in order to keep the system up to date and replace hardware as needed. As of this article, the IGB CNRG staff is working on installation of specific modules. The software should be ready to use by the fall 2016 semester. Stay tuned for updates from the Mayo Clinic and Illinois Alliance on utilizing this exciting new research tool.