Plot of integration sites on chromosomes
Location of in vivo viral integration sites of HIV-1 across all chromosomes. Data from HIRIS.

ISDB is an open-source software toolkit for building databases of viral integration sites in host genomes.

We developed ISDB to support our research into the locations of HIV-1 proviruses. 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.

You may want to use such databases yourself and therefore learn more about how ISDB works, or you may want to create your own database using ISDB tools. Read our user stories below for ways of using ISDB.

If you’re using ISDB in your own work, we’d be thrilled if you sent us an email!

User Stories

Below you’ll find example use cases ranging from the consumer of an existing database to the publisher of a new one. These are people we consider when developing ISDB.

Carla wants to analyze published in vivo integration sites from HIV-1 in light of a new gene interaction finding she’s made.

She connects to HIRIS, an public database made using ISDB, and filters the data based on the integration environment to find only the in vivo sites. Carla performs her analysis using a combination of SQL and Python.

Jesse’s publishing a paper containing data from HIV-1 integration sites and wants to add his own data to HIRIS.

He reads the documentation on how to create a new ISDB data source and gets started creating his own. Jesse gets stuck along the way but gets going again after emailing the HIRIS creators for guidance. At publication time, Jesse also publishes a Github repository containing his ISDB data souce. He emails the HIRIS creators to let them know and they load his data source into HIRIS.

Angie’s identified hundreds of HIV-1 integration sites from patient specimens. She wants to compare them to the HIV-1 IS data published in HIRIS, but doesn’t want to make her data public before publication.

Angie downloads the ISDB software and sets up her own private database by following the documentation. She loads into the database the public data sources from HIRIS. Then she creates a data source for her own pre-publication data and loads that too. Angie now has a single, standard platform for analysis which she can keep up to date as she generates more data. At publication time, Angie publishes her own data source so HIRIS and others can include it.

Nick is a bioinformatician studying HBV and wants to build a database of HBV integration sites.

Nick downloads the ISDB software and sets up a new database. He creates new data sources for each of the discrete datasets collected from his own work and previously published work. Much of the work is data curation, but once that’s done Nick loads the new sources into his database. He sets up a website and public database access and calls his database HBVIS. Nick announces HBVIS in print and invites other HBVIS researchers to use and contribute to the database.

Looking for the HIV-1 data?

You want to check out HIRIS (“high rise”), the HIV-1 Reservoirs Integration Sites database run by the Mullins Lab. HIRIS is built using ISDB.

Documentation

You can read the installation and usage documentation on this website or read the original Markdown files alongside the source code in the docs directory.

Source code

The software, documentation, and example data sources which make up the ISDB toolkit are freely available online under the Mullins Lab organization on GitHub. The primary repository is located at:

https://github.com/MullinsLab/ISDB

Citation

If you use ISDB in your work, please cite us as:

Sibley TR, Silberman EJ, and Mullins JI. 2017. ISDB. https://mullinslab.microbiol.washington.edu/isdb/.

Alternatively you may use this BibTeX notation:

@Misc{ ISDB-2017
  author = "Sibley, Thomas R. and Silberman, Evan J. and Mullins, James I.",
  title  = "ISDB",
  year   = "2017",
  url    = "https://mullinslab.microbiol.washington.edu/isdb/"
}

A manuscript is in-progress and we will update this citation once it is published.