[Cse-jobs] Part-time position open to build a genome analysis interface

[Jeremy Buhler]

[Forwarded from Dr. Sarah Elgin in the Biology Department]

We are looking for a CSE student interested in part-time employment 
during the spring semester to build a web interface for genome analysis 
using modENCODE data.  Pay will be $13 -$14/hr depending on qualifications.

The modENCODE project has generated enrichment profiles (normalized 
M-values) for many chromosomal proteins and histone modifications across 
the Drosophila melanogaster (fruitfly) genome.  The desired web-based 
interface will enable users to extract a subset of the modENCODE data 
(e.g. by specifying a list of genes and/or regions and selecting a 
subset of the modENCODE datasets available). The extracted enrichment 
profiles would serve as input data for downstream analysis using the R 
statistical package. The initial web interface should enable two types 
of statistical analysis using R: a “metagene” expression analysis and a 
clustering analysis.

In the “metagene” analysis, expression profiles for all the selected 
genes are combined together into a single summary profile for each 
chromosomal protein or histone modification. In the clustering analysis, 
the software should be able to perform hierarchical or k-means 
clustering using the subset of histone modifications or chromosomal 
proteins specified by the user. Prototype scripts used to perform these 
two types of analysis are available. However, these scripts are designed 
for the interactive R environment and must be adapted for use in a 
web-based environment.

Facility with web page design (HTML, CSS, and Javascript) and R are 
required. Applicants should also be familiar with at least one 
server-side language (Java, PHP, C , etc) and at least one scripting 
language (Perl, Python, Ruby, etc). Completion of Bio 2960 would be a 
plus.  If interested, please send a resume to SCR Elgin 
(selgin at biology.wustl.edu), including a list of CSE and biology courses 
completed and the name and email addresses of two references.  Both Prof 
Elgin (Biology and Prof Jeremy Buhler (CSE; jbuhler at cse.wustl.edu) will 
be happy to answer questions and/or discuss the project further.