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Project TitleBioInformatics Software Engineering with Mothur
SummaryMeasuring, re-engineering, and testing Mothur, a popular software package for 16S metagenomic analysis. A few key components of Mothur do not scale well, especially on Blue Waters, we aim to improve the performance and stability of Mothur.
Job DescriptionMothur is a popular bioinformatics package for analyzing 16S microbial rRNA gene sequences. Working with faculty in computer science and biology the intern will design, implement, and test modifications to the shared memory and distributed memory portions of Mothur's analysis tools. The intern will work with C/C++, OpenMP, MPI, and the Linux/GCC toolchain on Earlham's clusters and Blue Waters. This work will build on work done over the past year, having identified the most resource consuming components of the workflows used with Mothur (pre.cluster, cluster.split, chimera) we plan to re-engineer them for improved scalability, particularly on large data sets composed of 50+ samples.
Conditions/QualificationsKnowledge of the domain science and general knowledge of computer science. Working with Earlham student(s) would greatly improve the efficiency of the project.
Start Date06/01/2015
End Date05/31/2016
LocationCluster Computing Group
Earlham College
Richmond, Indiana
Tara Urner