usenix conference policies
You are here
BioLite, a Lightweight Bioinformatics Framework with Automated Tracking of Diagnostics and Provenance
| 12 Tuesday | 13 Wednesday | 14 Thursday | 15 Friday |
|---|---|---|---|
| HotCloud '12 | TaPP '12 | ||
| WiAC '12 | USENIX ATC '12 | ||
| UCMS '12 | HotStorage '12 | NSDR '12 | |
| USENIX Cyberlaw '12 | WebApps '12 |
||
Mark Howison, Nicholas A. Sinnott-Armstrong, and Casey W. Dunn, Brown University
We present a new Python/C++ framework, BioLite, for implementing bioinformatics pipelines for Next-Generation Sequencing (NGS) data. BioLite tracks provenance of analyses, automates the collection and reporting of diagnostics (such as summary statistics and plots at intermediate stages), and profiles computational requirements. These diagnostics can be accessed across multiple stages of a pipeline, from other pipelines, and in HTML reports. Finally, we describe several use cases for diagnostics in our own analyses.
Open Access Media
USENIX is committed to Open Access to the research presented at our events. Papers and proceedings are freely available to everyone once the event begins. Any video, audio, and/or slides that are posted after the event are also free and open to everyone. Support USENIX and our commitment to Open Access.
title = {{BioLite}, a Lightweight Bioinformatics Framework with Automated Tracking of Diagnostics and Provenance},
booktitle = {4th USENIX Workshop on the Theory and Practice of Provenance (TaPP 12)},
year = {2012},
address = {Boston, MA},
url = {https://www.usenix.org/conference/tapp12/workshop-program/presentation/Howison},
publisher = {USENIX Association},
month = jun
}
connect with us