Proteomics allows us to see post-translational modifications and expression patterns that we cannot see with genomics and transcriptomics alone. By itself, proteomics has limited sensitivity to detect genetic variation (e.g. single-nucleotide polymorphisms and insertion/deletion mutations), but we can improve that with access to genomic data: an approach known as proteogenomics. As in many of the -omics fields, reproducibility of proteogenomic results is a problem. Since 2005, the web application âGalaxyâ has been available to improve the transparency and reproducibility of -omic analyses. However, a Galaxy server is not easy to set up, and to work around that, investigators have sometimes distributed their customizations as virtual machines (VMs). In recent years, a more efficient approach for software isolation - âcontainersâ - has become popular. A proteogenomics âflavorâ of Galaxy â Omicron â was created to simplify reproduction of proteogenomic workflows. An easy way for anyone to launch Omicron on Amazon Web Services, paired with a scalable compute cluster, was also created. Using Omicron, results from a 2014 Nature paper were partially reproduced. Due to changes in online reference data and possibly due to different tool versions, it was not possible to perfectly reproduce the previous results. However, other investigators could easily reproduce the Omicron results without digging through methods and supplemental data. Then they could easily apply the same workflow to their own data.
| Identifer | oai:union.ndltd.org:VANDERBILT/oai:VANDERBILTETD:etd-08052016-114746 |
| Date | 05 August 2016 |
| Creators | Chambers, Matthew Chase |
| Contributors | Bing Zhang, Daniel Liebler, David Tabb |
| Publisher | VANDERBILT |
| Source Sets | Vanderbilt University Theses |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.library.vanderbilt.edu/available/etd-08052016-114746/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Vanderbilt University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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