GEMAT: GENOMIC EXPERIMENT MANAGEMENT AND ANALYSIS TOOL
Version 2.0, Released 2009
|
GEMAT: GENOMIC EXPERIMENT MANAGEMENT AND ANALYSIS TOOL Version 2.0, Released 2009
|
|
GEMAT is designed as a software platform to systematically facilitate data management in oligonucleotide microarray experiments (eg. GeneChip, Affymetrix). It is implemented in the LAMPP (Linux-Apache-MySQL-Perl/PHP) environment as a three-tier architecture. The client-tier is a web-browser that uses a thin-client HTTP to request resources and display responses to the user. The middle tier consists of an Apache web server, PHP scripting language, the Zend (PHP script) engine. The database tier uses MySQL RDBMS. Data Models and Entity-Relationships have been defined for handling data at various levels.
Some of the features of GEMAT are:
User Management: Multiple user settings, password authentication and access restriction depending on user role Project Management: Project tracking, online availability of experiment status, experiment results, coordinators information, timeline and date records of the project. Scheduling & Workflow Control: Tracks the workflow using unique codes for gels and target plates, controls workflow step-skipping and erroneous data entry, systematically schedules next step in the process, lists pending jobs Data Capture: Form-based data entry, automatic mapping and transfer of large project files using FTP protocols, data can also be entered in a simple EXCEL sheet and uploaded Data Integration & Analysis: Web based result publication and access, RTPCR data integration, Affymetrix/dChip/RMA data format Data Mining & Presentation: Cluster analysis, data filter, t-test, enrichment analysis, Biological pathway visualization, Ingenuity pathways |