Bioinformatics

The Bioinformatics Core Facility (BCF) provides consultation, training and computational resources (both hardware and software) to investigators in Nemours Biomedical Research with outreach and educational efforts aimed at Nemours’ investigators involved with the COBRE grant. It also participates in patient care by assisting researchers to find underlying mechanisms of human disease, as well as methods of treatment and diagnoses that will impact patient care. The BCF is directed by H. Timothy Bunnell, PhD and staffed by Suzanne M. McCahan, PhD, Jobayer Hossain, PhD, Chris Pennington, MS, Li Xie, MS, Dan Eckrich, MS, and Jeffrey Myers, BS.

BCF manages the primary web / email / database servers for asel.udel.edu and NemoursResearch.org with 10 computing cores, 16GB of RAM and 5TB of disk space for user accounts. Additional Linux-based research servers provide 100 CPU cores (up to 32 available for parallel computing tasks), 430 GB of RAM and 40 TB of RAID disk space for research labs. A dedicated backup system provides hourly backups of email, daily disk backups of file volumes, and weekly LTO5 tape backups which are stored off-site.

Services offered by BCF include:

  • experimental design of parallel, crossover, longitudinal, cross-section and microarray studies
  • data mining of microarray and high-throughput sequencing studies
  • standard statistical analysis
  • development of special purpose software

Software, Languages, Resources and Tools utilized by BCF:

Software

  • SPSS
  • SAS
  • R
  • Bioconductor
  • MeV
  • CMfinder
  • MOSAIK

Programming Languages

  • PERL
  • Python
  • PHP
  • C, C++, Objective C
  • Fortran
  • Unix Shell
  • Javascript

Databases & Technologies

  • MySQL
  • SQLite
  • REDCap
  • i2b2
  • Drupal
  • WordPress
  • JQuery
  • HTML, XML, JSON

 

 

 
Applications and websites developed and maintained by BCF:

  • TimeKeeper
  • Biosafety Database
  • NED (Nemours Experimental Database, an electronic lab notebook)
  • Symposia registration
  • SNAP (Scientists Networking And Profiles)
  • PAT (Psychosocial Assessment Tool)
  • MICT  (Use of Mobile Devices and the Internet to Streamline an Asthma Clnical Trial)
  • DE-CTR ACCEL website
  • Center for Pediatric Research website

BCF also manages the Nemours installation of REDCapTM (Research Electronic Data Capture from the REDCap Consortium). REDCap is a secure web application that allows users to build and manage online surveys and databases for a variety of purposes including basic, clinical, translational and behavioral research, repositories and operational support.  In addition to maintaining this application, BCF provides training and other support so that Nemours associates can utilize all the tools this resource provides.

Over the years, the BCF has expanded staffing, adding a second masters-level application developer to meet increased demand for core services. Jobayer Hossain, PhD was promoted to Manager of the Biostatistics Core, which is now a proper sub-component of Bioinformatics. Hardware resources have remained largely stable with some expansion in terms of a new high-availability server and increased storage. Management of the institution’s REDCap installation grows rapidly. We now support over 300 users on more than 250 projects that collect and organize research data and surveys. In addition, major improvements to in-house software handling effort reporting and biosafety oversight have been highly successful. The BCF has also played an integral role in cutting-edge projects investigating obesity and asthma, developing custom web-based interfaces for projects that require back-end REDCap data storage.