Bioinformatics

Providing bioinformatics and data integration expertise to facilitate cutting-edge biomedical research and assist Cancer Center investigators to become more computationally competitive.

Description

This shared facility provides bioinformatics and computational support for biomedical research. The facility is equipped with high-performance computer hardware, specialized software, and advanced database systems. The hardware includes a PowerWulf Compute Engine, which contains 208 total processor cores, 800GB system RAM, 84TB Raw RAID6 storage with 10GigE access to switch, and an Overland Tape Backup System, a Windows server for software, which is only compatible with that environment, a database server, and a web server.

The services of this facility are integrated with those of the Department of Clinical Sciences to assure access to specialized statistics and data management expertise. Our goal is to foster collaborations and provide assistance with grant writing for proposals seeking to integrate modern computational techniques in research activities.

Services

  • Sequencing data processing and analysis: The resource has developed processing and analysis pipelines for high-throughput next-generation sequence (NGS) data such as RNA-seq, ChIP-seq, miRNA-seq, and CLIP-seq. The input to the NGS pipeline is either raw reads from the sequencing machines or mapped reads from alignment software.
  • Microarray data processing and analysis: Bioinformatics personnel will help investigators on microarray data processing and analysis, including background correction, normalization, summarization, quality control, detecting differentially expressed genes, and correlation of gene expression with phenotypes or clinical variables.
  • Bioinformatics: The resource is available to help investigators with bioinformatics analysis such as pathway and gene function enrichment analysis and gene network analysis.
  • Database, software, and web interface development: Services include design and implementation of interactive web applications as well as the underlying database back-ends. Support is available for investigators with problems concerning data acquisition, management, and analysis.
  • High-performance computing systems access: Bioinformatics personnel can configure, maintain, and administer high-performance computing resources for Cancer Center investigators. The resource has a suite of servers and computer clusters available for researchers to analyze and store data.
  • Grant-writing assistance: Support is available for proposals seeking to integrate modern computational techniques in research activities; practical training; and data analysis.
  • ‘Walk-in’ clinics and other training: Free consultations for Cancer Center members are available weekly on data analysis and accessing computation servers. Also, the resource provides hands-on practical workshops on how to access the high-performance computational cluster, Unix/Linux environment, and basic programming skills.

Fees

Consultations related to new grant submissions in cancer research: no charge for Cancer Center Members; $120/hour for non-members.

Bioinformatics Analysis: $90/hour for Cancer Center members; $120/hour for non-members.

Database development and data integration: Depending on different projects.