roryk / isdb

A toolkit for creating databases of viral integration sites in host genomes

ISDB is an open-source software toolkit for building databases of proviral integration sites.

Using ISDB, you can curate a private database from any heterogenous 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.

As distinct from 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. The goal of ISDB is to provide a standard end-to-end platform for reliably storing, performing reproducible analyses on, and ultimately publishing integration site data.

We developed ISDB to support our research into the locations of HIV-1 proviral integrations in patients on suppressive ART. It helps us durably store and reliably manage the data we generate and provides a standard platform for our analyses across datasets.

HIRIS, our HIV-1 Reservoirs Integration Sites database, is built and published using ISDB.

Please see the ISDB website for more information, including installation instructions.