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Bioinformatics. 2018 Aug 28. doi: 10.1093/bioinformatics/bty712. [Epub ahead of print]

ISDB: A database toolkit for storing and analyzing viral integration site data.

Author information

1
Department of Microbiology, University of Washington, Seattle, WA, USA.
2
Departments of Laboratory Medicine, Global Health, and Medicine, University of Washington, Seattle, WA, USA.

Abstract

Summary:

We introduce ISDB, a set of software tools for the creation and administration of relational databases of viral integration site (IS) data. Using ISDB, investigators can curate a private database from any heterogeneous set of data sources, including previously-published datasets and internal, work-in-progress data. To make data visible and accessible to collaborators with varying degrees of computational expertise, ISDB automatically generates web sites describing database contents and data exports in several common formats. Compared to a public depository database, the ability to build local, private databases makes ISDB suitable for use in testing hypotheses and developing analyses in the long pre-publication phase of most research.

Availability and Implementation:

Installation and usage documentation for ISDB are provided on our website https://mullinslab.microbiol.washington.edu/isdb/. Source code is available under the open source MIT license from https://github.com/MullinsLab/ISDB.

Supplementary information:

Supplementary documentation is available at Bioinformatics online.

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