Thomas R Sibley1, Evan J Silberman1, James I Mullins1,2. 1. Department of Microbiology, Global Health, and Medicine, 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 data are available at Bioinformatics online.
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 data are available at Bioinformatics online.
Authors: Yefei Han; Kara Lassen; Daphne Monie; Ahmad R Sedaghat; Shino Shimoji; Xiao Liu; Theodore C Pierson; Joseph B Margolick; Robert F Siliciano; Janet D Siliciano Journal: J Virol Date: 2004-06 Impact factor: 5.103
Authors: Sara Sunshine; Rory Kirchner; Sami S Amr; Leandra Mansur; Rimma Shakhbatyan; Michelle Kim; Alberto Bosque; Robert F Siliciano; Vicente Planelles; Oliver Hofmann; Shannan Ho Sui; Jonathan Z Li Journal: J Virol Date: 2016-04-14 Impact factor: 5.103
Authors: Liang Shan; Hung-Chih Yang; S Alireza Rabi; Hector C Bravo; Neeta S Shroff; Rafael A Irizarry; Hao Zhang; Joseph B Margolick; Janet D Siliciano; Robert F Siliciano Journal: J Virol Date: 2011-03-23 Impact factor: 5.103
Authors: F Maldarelli; X Wu; L Su; F R Simonetti; W Shao; S Hill; J Spindler; A L Ferris; J W Mellors; M F Kearney; J M Coffin; S H Hughes Journal: Science Date: 2014-06-26 Impact factor: 47.728
Authors: Thor A Wagner; Sherry McLaughlin; Kavita Garg; Charles Y K Cheung; Brendan B Larsen; Sheila Styrchak; Hannah C Huang; Paul T Edlefsen; James I Mullins; Lisa M Frenkel Journal: Science Date: 2014-07-10 Impact factor: 47.728
Authors: Scott Sherrill-Mix; Mary K Lewinski; Marylinda Famiglietti; Alberto Bosque; Nirav Malani; Karen E Ocwieja; Charles C Berry; David Looney; Liang Shan; Luis M Agosto; Matthew J Pace; Robert F Siliciano; Una O'Doherty; John Guatelli; Vicente Planelles; Frederic D Bushman Journal: Retrovirology Date: 2013-08-16 Impact factor: 4.602
Authors: Matthew J Pace; Erin H Graf; Luis M Agosto; Angela M Mexas; Frances Male; Troy Brady; Frederic D Bushman; Una O'Doherty Journal: PLoS Pathog Date: 2012-07-26 Impact factor: 6.823
Authors: Barry R Zeeberg; Joseph Riss; David W Kane; Kimberly J Bussey; Edward Uchio; W Marston Linehan; J Carl Barrett; John N Weinstein Journal: BMC Bioinformatics Date: 2004-06-23 Impact factor: 3.169
Authors: Wei Shao; Jigui Shan; Mary F Kearney; Xiaolin Wu; Frank Maldarelli; John W Mellors; Brian Luke; John M Coffin; Stephen H Hughes Journal: Retrovirology Date: 2016-07-04 Impact factor: 4.602