BIOINFORMATICS & BIOSTATISTICS (Under Construction)|
Informatics - Jack London, PhD, KCC, TJU.
The KCC Informatics Shared Resource (ISR) provides informatics support for the cancer center's basic, clinical, and translational research. This shared resource provides services for management and processing of data and information, including creating research software, data file management, hardware and software acquisition, and computer-related consultation. The ISR supports cancer center research by developing web-based database applications for clinical trials, biospecimen research repositories, and various research projects. It provides management of very large genomic experimental data sets, acquisition of hardware, development of software tools to facilitate inter- and intra-institutional collaborative research programs, and assistance with design proposals for research-related computing. ISR staff consults with investigators to recommend hardware and software, ranging from the desktop units to high performance computing clusters. Recognizing the importance for interoperability of independently developed informatics systems as crucial to the furtherance of cancer research through the sharing of research data and resources, the ISR has been an active participant in the NCI's cancer Biomedical Informatics Grid (caBIG™) since the initiative's inception.
The ISR is dedicated to using open source solutions when possible. The shared hardware includes 10 servers (8 Linux/Apache/PostgreSQL, 2 Microsoft Windows / IIS / MSSQL), and over a terabyte of network file storage. This networked storage is backed-up to tape daily. KCC faculty and staff are encouraged to use the network accessible shared disks for storing documents and data, since the ISR backup procedures limit their risk of losing file updates to a maximum of 1 day. Furthermore, this shared mass storage relieves individual investigators with very large disk storage needs of the expense, both in dollars and time, of maintaining large disk "farms." The ISR utilizes high-speed RAID storage systems, which provide fail-over capability from redundant drives. Another benefit of maintaining network file storage for KCC members is that it permits controlled access data and document sharing. The ISR encompasses 1,010 sft in 3 rooms. A computing machinery room containing the host computers and associated operating equipment occupies 120 sft.
Clinical Trials Applications: The ISR developed and maintains web-based database applications for clinical trials research. These applications include: The Clinical Trial Information Repository application, which has databases for clinical trial information and patients registered on these trials. This system is integrated with the TJU's Office of Human Research clinical research database. The automated electronic Serious Adverse Event Reporting system (eSAEy) incorporates NCI Cancer Therapy Evaluation Program Toxicity Criteria and electronic signatures for reporting adverse events that occur during KCC clinical research trials. This system is integrated with the Clinical Trial Information Repository and the TJU's Office of Human Research adverse event reporting database. The study calendar system, TreatmentCal, allows tracking of patients enrolled on KCC studies. Multilevel security is provided by "username/password" authentication with Web browser level log-ins, and authorization at the application and database table permission level. The transmission of confidential information, such as patient data, is protected via 128-bit encryption. These are compliant with HIPAA restrictions on the dissemination of Protected Health Information, and the electronic signature function adheres to the provisions of the FDA's 21CFR Part 11.
Biostatistics - Terry Hyslop, PhD, KCC, TJU.
The Biostatistics Shared Resource (BSR) supports KCC investigators in the design, conduct and analysis of cancer-related clinical, translational and scientific investigations. It also reviews cancer-related clinical trial proposals for the Cancer Clinical Research Review Committee (CCRRC). BSR is staffed by 5 PhD-level faculty biostatisticians and 3 MS-level biostatisticians. BSR provides consultation and expertise regarding study design (including validity of the overall design, feasibility of meeting objectives, sample size, study duration, and planned data analysis), recommendations for staffing (data management and analysis support), data analysis, preparation of reports and assistance with manuscript writing, and development of new biostatistical methods. The general goals of BSR are to ensure that study designs, monitoring, and analyses use state-of-the-art methods, and to help developmental studies supported by the Center successfully achieve peer reviewed funding. TJU's Strategic Plan commits resources to ensure continued investment into BSR, including development in key areas such as clinical trials design, bioinformatics, and analysis of high-throughput data.
Bioinformatics - Cathy Wu, PhD, CBCB/DBI, UD.
The mission of the Center for Bioinformatics and Computational Biology (CBCB) Core Facility is to: "Provide scientific expertise and core infrastructure support in Bioinformatics and Computational Biology for the Delaware research and education community". Drawing on the combined resources of the CBCB, the Delaware Biotechnology Institute (DBI), and the Protein Information Resource (PIR), the core facility offers services, collaborations, and computational resources for bioinformatic analysis at all levels of project development and execution, from "proposal to publication". The varied experience of the five Ph.D.-level staff members, provides expertise in numerous areas of biological analysis (genomics, metagenomics, amplicon libraries, phylogenetics, data visualization) and computing (databases, network administration, workflows, distributed computing, computer hardware). A full-time I.T. Associate provides desktop computer support and expertise in web site design and development. The core can also facilitate collaborations, connecting researchers with experts from our pool of over 40 CBCB-affiliated faculty members from five colleges within the University of Delaware, as well as from external networks in which CBCB participates including the Northeast Cyber-infrastructure and Bioinformatics Consortia (NECC and NEBC), the Delaware Health Science Alliance (DHSA), and the Delaware Valley Institute for Clinical and Translational Science (DVICTS). The facility also plays an integral role in data processing, storage, and distribution for next-generation sequencing platforms supported by the UD Sequencing and Genotyping Center and houses the CBCB Data Center, a computational and informational hub for NECC partner institutions. Computational resources include: High Performance Compute Clusters:123 Sunfire and 4 Dell compute nodes providea combined 334processor cores. Included are several nodes for memory intensive computing with 48 GB to 128 GB of RAM per machine.Common applications of the compute clusters include sequence homology searches (BLAST); sequence alignment, assembly, and clustering;biostatistical analysis (R, Matlab); and molecular modeling (Gaussian, GAMESS) Database Server Cluster: A cluster of 6 Sunfireservers act as a repository of experimental data in relational databases. Both MySQL and Oracle database systems are available, allowing researchers to organize, store, and evaluate their data. 3-D Visualization Studio: An immersive 3D graphics room with a 7'x15' rear-projection screen, delivering rear-projected, edge-blended images with total resolution of 2240 x 1024 pixels.
Outcomes research - William Weintraub, MD, CCHS.
The shared resource at the Christiana Center for Outcomes Research (CCOR) involves a multidisciplinary research group with expertise and provision of services in clinical medicine, epidemiology, biostatistics, and informatics, created in December 2005 to foster epidemiological and outcomes research within CCHS. Although the group is newly formed, CCOR scientists have broad research experience in creating, running, and analyzing data from registries, running clinical trials, health status assessment, and cost-effectiveness analysis. There are ongoing research programs in cardiovascular medicine, nephrology, endocrinology, pulmonary medicine, nutrition, radiology, and family medicine. CCOR also maintains ties with multiple leading institutions for outcomes research, including Harvard, Yale, Duke, McMaster, and the Mid-America Heart Institute.