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Infrastructure Development in Computational Biology and Bioinformatics (CBB)

The goal of CBB is to continue strengthening the optimal use of computational resources and information technology (IT) by RCMI researchers at Tuskegee University (TU) to address health disparities in underserved communities. The CBB multidisciplinary faculty and staff at Tuskegee University's Center for Computational Epidemiology, Bioinformatics & Risk Analysis (CCEBRA) and its counterpart, Biomedical Information Management Systems (BIMS) provide services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at TU. Of central importance is the fact that the CCEBRA research team is supported by BIMS strong IT team. The BIMS team provides all IT needs of the RCMI researchers at TU including the RCMI web page at TU, development of online application and different database management. The team also provides technical support and training for both hardware and software as well as troubleshooting.

Overarching aims:
  1. Sponsor bioinformatics and related workshops to train scientists, graduate-students and undergraduate-students to become competent in the use of computational biology and bioinformtics resources that are available at the CBR at TU. This includes accessing, searching and extracting data from national and international bioinformatics databases, genomics facilities and sequencing facilities.
  2. Increase the CBB resources selectively to create sustainable research capacity and  state-of-the-art  professional development support for RCMI scientists and other researchers;
  3. Promote collaborative research among RCMI scientists at TU as well as at other institutions. Active collaboration with the RCMI-Translational Research Network (RTRN) is most important in this arena.   This includes providing a common data management and application development framework, with a robust services-oriented-infrastructure that standardizes  and  streamlines  the  RCMI's  researcher  community  collaborations;  and
  4. Create a Telehealth/ Telemedicine infrastructure at CBR to address health disparities in the BBC of Alabama.  

Services:

CBB has been providing services in three major areas: 

  1. Bioinformatics service delivery capacity;
  2. Statistical analysis support; and
  3. IT support.  

Specifically, services being provided by CBB to TU researchers include:

  1. Software related: 
    • Data Modeling
    • Development environment (Test, Develop, production environment)
    • DNA and RNA Sequence Analysis
  2. Provide biostatistics consultation to RCMI researchers
    • Develop and provide high-level bioinformatics capabilities and services, including the storage, management, curation, integration and collaborative annotation of -omic data, generated by TU researchers;
    • Ensure best practice in bioinformatics and statistical analysis of all research data, and the transfer of technology and skills into the application of research in the area of health disparities;
    • Establish  and  consolidate  links  with  RTRN/RCMI  institutions  and  with  other  major bioinformatics centers and programs; and
    • Leverage TeraGrid resources: This team will train faculty and staff so they can tap into the ample resources of TeraGrid. TeraGrid is an open scientific discovery infrastructure that combines leadership and enterprise-class resources at eight partner sites to create an integrated, persistent computational resource. TeraGrid integrates high-performance computers, data resources and tools for high-end experimental facilities around the country.   These integrated resources include more than 102 teraflops (i.e., 1012 or trillions) of computing capabilities and more than 15 petabytes (quadrillions of bytes) of online and archival data storage, with rapid access and retrieval over high-performance networks. Through the TeraGrid, researchers can access  over 100  discipline-specific  databases.  With  this  combination  of  resources,  the TeraGrid is the world's largest, most comprehensive distributed cyber-infrastructure for open scientific research.
  3. Database  development:
    • Outcome  assessments  tool  development  from  the  database development to the analysis
    • Back-end interfacing to data processing systems and displays
    • Privacy protection and security assessment
  4. Web based software tools:
    • Web interface
    • Website development, hosting and maintenance
    • Search engine development and management
    • Webpage studentstatistics
  5. Workflow technology:
    • Network security and monitoring
    • Systems design and development
    • Testing and deployment of collaborative technologies
  6. Training and workshops
    • Seminar and Workshop Series
    • Participate in Bioinformatics webinar series in collaboration with RCMI Translational Research Network (RTRN) Bioinformatics working group
    • Consultant epidemiologic services to investigators in the areas of Cancer, HIV/AIDS, and other infectious diseases
  7. Videoconferencing:
    • Two pilot Internet Telemedicine/Telehealth centers have been set up
      • The first center is with Montgomery Aids Outreach Inc., where two Apple laptop computers were provided for use in providing services to their clients (like: education, counseling) and to facilitate remote meetings connecting their main office to their branch offices which are located in different counties  and are apart more than 45 minutes. The second center is based in Macon County and we have provided one Apple laptop computer; b) Currently we host the TU's teleconference for the Morehouse/TU/University of Alabama at Birmingham cancer research project held twice a month
  8. Other basic services
    • Consultation regarding software, hardware and accessories
    • Quality control of the core lab computers
    • Troubleshooting of networks, PC's, Mac's, and servers
  9. Facilitate advice, lead, coordinate and manage bioinformatics capabilities at TU in the area of  the Genomics, Proteomics and Metabolomics (-omics) platforms;
    • Genomics processes include: 
      • Assembly
      • Annotation
      • Mapping
      • Searching non-coding RNA
      • Disease association
      • Comparative genomics
      • New tools for alignment
      • Phylogenetic
      • Visualization
    • Transcriptomics processes include:
      • Similarity searching and clustering
      • Alternative splicing
      • Annotation
      • Gene expression and statistical analysis
      • Small RNA gene identification
      • Visualization
    • Proteomics processes include:
      • Peptide mass fingerprinting analyses
      • Custom protein datasets
      • Visualization