GenIE-Sys

GenIE-Sys facilitates creation and dissemination of web-accessible resources for hosting, searching, visualizing, and exploring genomic and transcriptomic datasets such as RNA sequencing data.

Key Features:

• Web resource creation: Enables setup of standalone web resources for genome projects with support for searching, visualizing, and exploring genomics data.
• Data handling: Accepts and processes genomic and transcriptomic file formats including GFF3, FASTA, and FASTQ, and supports RNA sequencing datasets.
• Architecture: Uses a flat-file content management system (CMS) architecture to store and serve project data.
• Implementation: Implemented using PHP, JavaScript, and Python for data processing and web functionality.

Scientific Applications:

• Integrated genome projects: Hosting and distributing assembled genomes and associated annotation data for individual genome projects.
• Transcriptomics analysis: Visualizing and exploring RNA sequencing datasets alongside genomic features for expression studies.
• Organismal genomics: Supporting plant genomics and other organismal studies that require integrated presentation of sequence and annotation data.

Methodology:

Implemented as a flat-file CMS and developed in PHP, JavaScript, and Python, processing GFF3, FASTA, and FASTQ files including RNA-seq datasets.