Konstantinos Krampis, PhD
Assistant Professor, Bioinformatics
J. Craig Venter Institute, New York, NY
Abstract: The steep drop in the cost of genomic sequencing technology during recent years has enabled broad application across different research fields. Nonetheless, analysis of sequencing datasets requires access to a range of technical capabilities including expertise in information technology, software engineering, as well as large-scale computing resources. Therefore, scientific value cannot be obtained from an investment in a sequencer, unless it is followed by an equal investment in bioinformatics infrastructure.
To help researchers in the community overcome this bottleneck, we have developed the Cloud BioLinux Virtual Machine (VM) that provides a pre-configured bioinformatics software suite, running on both desktop and cloud computing systems. Upon deployment of the VM, users have at their disposal a collection of more than 100 data analysis tools for sequence read mapping, variation discovery, visualization, genome assembly and annotation. Furthermore, the software is easily accessible through integration of Cloud BioLinux with the Galaxy web interface, while users can also instantiate on-demand cloud compute clusters for large-scale data analysis.
This seminar will give an overview of cloud systems, and their potential for providing a complete bioinformatics solution to scientists requiring high-performance computing setups for genomic data analysis. Access to Cloud BioLinux and examples on building production data pipelines using cloud computing at the J. Craig Venter Institute will be discussed. In addition, the approach for implementing an RNAseq pipeline curated from the literature will be demonstrated, along with results on differential gene expression analysis. The presentation will conclude with future development and funding plans for the project, and discussion on how the adoption of cloud computing technologies can democratize access to genomic sequencing technology regardless of institutional, economic or national boundaries.
Refreshments will be served!
Supported by the National Institute on Minority Health and Health Disparities, National Institutes of Health - 8 G12 MD007599-27
Hunter College, Biology Conference Room 926HN
charles [at] genectr.hunter.cuny.edu