INBRE Bioinformatics Core

Summary:

The goals of the Bioinformatics Core are:

* To increase the research capacity in bioinformatics in the State of Hawaii
* Provide hardware, access, and support to researchers who utilize genomic and proteomic data
* Provide a web-based gateway with access to a variety of bioinformatics applications, including available proprietary software such as Celera, and support for this software
* Undertake collaborative project with INBRE researchers to develop novel tools or applications that address specific needs
* Develop an academic program in bioinformatics with the John A. Burns School of Medicine (JABSOM)
* Recruit a full-time junior faculty member to lead the academic program
* Conduct training workshops and courses, and run a user support helpdesk

Affiliations:

• Department of Computer & Information Sciences, College of Natural Sciences

People:

• PI: Holmes, Eric, Ph.D.
  

Member: Belcaid, Mahdi, Ph.D.
Role: Director, Bioinformatics Core


Member: Poisson, Guylaine, Ph.D.
Role: Advisor, Bioinformatics Core, Assistant Professor

Resources:

Instruments

• Apple Mac Pro server ( Computer server )
  

• Dell Precision T7400 server ( Computer server )
  

• INBRE UH Dell cluster ( Computer cluster )
  

  The INBRE UH Dell cluster is composed of 54 computer nodes and 3 service nodes; each node has the following specifications: dual 3.2GHz Intel Xeon Processors, 4GB of RAM, dual GB ethernet ports, 36 GB hard drives for local scratch space; space: the cluster has 15TBytes of redundant shared storage accessible to all nodes.

• PowerEdge 1700 Dell server ( Computer server )
  

• PowerEdge 1800 Dell server ( Computer server )
  

• PowerEdge 830 Dell server ( Computer server )
  

• PowerEdge730 Dell server ( Computer server )
  

Services

• "Divide and conquer" approach service ( Analysis service )
  

• Bioinformatics analysis and consulting service ( Data analysis service )
  

  Standard bioinformatic and programming tools are also used for consulting services purposes.

• Bioinformatics support service ( Support service )
  

• Bioinformatics training service ( Training service )
  

  Includes training on PERL programing and Genespring. Standard bioinformatic and programming tools are used for bioinformatics training purposes.

• Introduction to bioformatics workshop ( Training service )
  

Software

• Anacle ( Software )
  

• FragAnchor ( Software )
  

  "GPI-anchored protein prediction tandem system."

• GeneSpring GX ( Software )
  

  "GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data. Designed specifically for the needs of biologists, GeneSpring GX offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context."

• GPI-DB ( Software )
  

  "A GPI-anchor prediction database for fragAnchor."

• JMP ( Software )
  

  "Data visualization and deep analytics for the desktop – software that now reaches out to users of Microsoft Excel, R and advanced data mining and modeling techniques."

• Sequencher ( Software )
  

  "DNA sequence assembly software."

Web Links:

• http://inbre.jabsom.hawaii.edu/guest/Guest.vm;jsessionid=3F
  716CF5D5D6CC445A28D61046BBB253?method=displayCorePage&id=1