[Buffalo-pm] Job Announcement

[Shankar, Ganesh]

Hello All,
This is to announce a job opening for a Programmer in the Center of Excellence in Bioinformatics.  The Center is a multidisciplinary effort between Roswell Park and UB which utilizes the skills of scientists, statisticians and computer engineers.

Job Description

The programmer will support the research activities of statisticians, cancer researchers and bioinformaticians.  The general scientific, investigative method being used is based on microarray technology.  As such, problems arise when managing and analyzing the huge data sets generated by each experiment.

Description of data

The raw data is tabular, with approx. 20 columns and up to 20,000 rows.  These dimensions will increase but this is a good starting point.  The raw data undergoes quality control checks and initial analysis before being released to the customer.  Because of the nature of the experiment and the methods used to measure the results, the data are inherently noisy.  Therefore, they need to be statistically normalized to "reveal" the true result.  The statisticians synthesize new methods to try and do this all the time.  They'll have the ideas, and the programmer will have to code it up using statistical libraries from Bioconductor or other sources.  The result is usually a graph that is generated by the program.  We expect the new hire to pick up the nature and reasoning of the experiment in a few months.

Management of data

The raw data needs to be correctly and promptly piped from the origin (the imaging machine) to a database or Laboratory Information Management System(LIMS).  Data should be available to internal users and external customers.

Analysis of data

The raw data from the experiment needs to be analyzed.  Certain standard, quality control calculations need to performed for all data and the results stored in the database or LIMS.  Existing programs written in R will have to be modified to conform to Bioconductor standards and to integrate with the database or LIMS.  Further non-standard, exploratory analysis algorithms will be designed by the statistical or scientific leads and will have to be implemented by the programmer.

General Tasks

The programmer is initially expected to implement, modify, and integrate existing algorithms, and programs.  The programmer will also standardize the current infrastructure to increase compatibility and throughput.  Given requirements from the scientist, the programmer should be able to design and implement a program to perform the given task with minimal supervision.  The implementation should integrate or communicate with existing programs in R, Perl or Java.  


Specific Tasks

Implement computational algorithms and statistical methods for the analysis of array comparative genomic hybridization, microarray gene expression and other high throughput datasets. Summarize, document and present results generated by the analyses of datasets. Assist in the preparation of materials for publications and grant applications.

Interact with lab personnel employed by array based core resources at RPCI to facilitate a better understanding of the interplay of the underlying biological, technical, and statistical issues.

Work with IT specialists to enhance the implementation of statistical methods and computational algorithms on the available computing infrastructures. Provide documentation for custom software and algorithms. 

Examples of Projects

Develop R library of custom functions for the analysis of aCGH data. 

Develop custom interface for internal software and external software such as the Bioconductor library.

Conduct standard analyses of array data (e.g., implement data smoothers, run SAM, run GeneDirector, run GenePix, and other software platforms).


Preferred Skills

Coursework in statistics and Bachelor's degree in CS with experience programming in languages such as C, C++, R, Fortran, Perl or Java or Java. Familiarity with database management systems such as Oracle, or MySQL a plus. Should be comfortable with Unix/Linux OS.

Salary

Commensurate with education and experience.


Contact

Daniel Gaile, Ph.D.
Department of Biostatistics
School of Public Health and Health Professions
Farber Hall Rm. 249
3435 Main Street, Buffalo, NY 14214-3000
dpgaile at buffalo.edu
(716) 881-8955 office
(716) 909-1633 cell
(716) 829-2200 FAX

		OR

Jeffrey Miecznikowski, Ph.D.
Department of Biostatistics
School of Public Health and Health Professions
Farber Hall Rm. 249
3435 Main Street, Buffalo, NY 14214-3000
jcm38 at buffalo.edu
(716) 881-8957 office
(716) 829-2200 FAX


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.