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Informatics in the Pharmacogenetics of Asthma Treatment (PhAT) Project.

Introduction

Informatics for the PhAT is supported by a team of dedicated geneticists, statisticians, computer scientists, and software engineers from the Channing with additional support from CHIP (The Children's Hospital Informatics Program). The directive of this team is to add value to the data generated by the IIPGA through statistical data analysis and data mining with presentation of raw and analyzed data on the PhAT website for public consumption. Additionally, the team automates the SNP discovery and SNP association pipelines so as to improve the quality, speed, and efficiency of the whole process.

The Informatics Group modifies and uses public tools and resources developed elsewhere and in return offers these along with new utilities developed in house freely for use by other groups.

Major responsibilities

  1. Development, management and maintenance of the Laboratory Information Management System (OraGen) that is used for DNA purification, specimen tracking, genotyping and phenotype management.

  2. Data curation, management, and analysis.

  3. Oracle database, Web and IT systems architecture, management, disaster recovery planning and backup

  4. Internet and Web services based development, management and maintenance.

  5. Related systems and application programming.

Infrastructure Overview

The PhAT at the Channing Laboratory has implemented a robust, full-cycle software and database development environment that includes several Oracle database instances that are used for, respectively, development, testing and full production support of software applications; CVS for source code and software management; Java, Python, Visual Studio, database and Web development software for application development; and project management software for reporting and tracking enhancements and bugs.

A highly reliable, available and scalable (RAS) web services infrastructure is currently being utilized for this PhAT and all the Channing Laboratory Web sites. Genotype data and phenotype data in the Channing and their integration is accomplished through the ORACLE/LIMS system with a presentation layer consisting of Visual Basic and Java, an application layer of Java, and an Oracle back end.

Hardware

The Channing Laboratory computer facility consists of 7 Sun enterprise servers, a clustered linux compute server currently containing 10-dual processor nodes, and a highly scalable, robust terabyte Storage Area Network. This backbone is networked with thirty UNIX and Linux workstations, 150 Windows PCs, and 30 laser printers. The Sun servers are currently running solaris 8 while the compute server is running RedHat linux 7.2 in a Mosix clustered environment.

Software

SAS is the primary statistical software suite used to analyze all phenotypic and epidemiological data. Analysis of genetic and biological data involve many Unix based software programs and databases including: Splus, Sudaan, Stat Exact, STATA, Sage, FBAT, Solar, CART, Gauss, Genehunter, WU-BLAST, SRS, Merlin, WinBugs, Cyrillic, Win MLN, Genbank, SNPper, Phred, Phrap, Polyphred, Consed, Arlequin, Phase, Solar, Pedcheck and many others that have been made available to us from individual labs, such as the SNP discovery software from Deborah Nickerson.

All applications are available through the network, many are on the PhAT website for public use. Other genetic analysis tools and software are available to the Channing Laboratory or through the Channings intranet website.

Information Systems, including all database, web services and cluster services, is under the direction of the Informatics group. The system administration for the Sun Servers, SAS servers and email services is under the direction of the Channing Computer Board that meets monthly and that includes the principal research group directors and and their representatives.