CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

Background: Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software.

Results: We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources.

Ergatis: a web interface and scalable software system for bioinformatics workflows.

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users.

GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database.

The Gemina system (http://gemina.igs.umaryland.

Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.

The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions.