[Baypiggies] job posting: bioinformatics programmer

Brent Pedersen bpederse at gmail.com
Mon Oct 27 19:48:14 CET 2008

hi, i'm a bioinformatics programmer in the freeling lab at berkeley.
were looking for another programmer.  the official description is below, but
briefly, we're looking for someone with a bit of biology, and who
knows some python
and perl. much of our code-base is in perl, so the applicant should be
able to access a
database in perl and use, modify, debug existing perl code. ... as
much as that's possible.

though the rest of the lab are perl folks, i tend to do nearly all
programming in python, using
all the tools that make python great for science -- numpy, scipy,
matplotlib, cython, ipython,
sqlalchemy, etc.  pretty much anything we write can be open source.
the applicant should be
familiar with some of those tools.

the position is full-time, on-site at uc berkeley.
you can contact me directly with any questions, but i have no
authority, so cc freeling at nature.berkeley.edu

Job Description
	Posting Title: 	
Programmer/Analyst III-Ucb
Plant & Microbial Biology
Main Campus-Berkeley
Annual Salary Range: $59,676 - $85,656
	First Review Date: 	
This requisition will remain open until filled.

	Job Description:
The Department of Plant and Microbial Biology (PMB) was established in
1989 in the College of Natural Resources as a research, teaching, and
training center of the Agricultural Experiment Station. The Department
is affiliated with the USDA Plant Gene Expression Center in Albany and
has 35 regular faculty members, one cooperative extension specialist,
and nine adjunct faculty members. The faculty are involved in both
graduate and undergraduate teaching programs as well as extensive
scholarly research. In addition to faculty, there are approximately 20
administrative staff. The Department Chair, Associate Chair, and a
Chief Administrative Officer oversee the department's programs.

This position is in the Freeling laboratory, which is a part of PMB.
Our research focus is comparative plant genomes.

This job involves writing programs in a computer language, designing
related databases, web interfaces and content, of multimedia
processes. Incumbent will design, develop, modify, test, evaluate and
maintain computer programs. Work includes test-to-production
processes, quality assurance, maintenance and documentation of
applications. Includes web applications programming.  Includes some
system administration.
40%) Design, develop, modify, debug and evaluate complex programs to
enhance biological research.

(20%) Learn software languages as needed.  Determine which programming
language is needed to efficiently code for the required application.
If necessary learn new languages or develop advanced skills in a
particular language.

(20%) Work with the PI to can learn cutting-edge genetic and genomic
concepts that will inform algorithm coding. The programmer must be
able to assimilate new concepts and information and incorporate it
into programs and databases.

(5%) Analyze existing programs or work to formulate logic for new
systems, devise logic procedures, prepare flowcharting, perform
coding, data analysis, and test/debug programs through the application
of professional programming concepts.

(5%) Provide analysis for the design and use complex relational
databases. Develop and execute moderately complete test plans.
Develop conversion and system implementation plans.

(5%) Gather, analyze, prepare and summarize recommendations for
approval of system and programming documentation.

(5%) Modest system administration: backup, assure continuous server
function, work with others here.
	Requirements & Qualifications:
• B.S. or B.A. in related area and/or equivalent experience/training.
Previous expert-level experience with Linux and Perl at minimum,
either as part of an advanced degree program or in the workplace, or
both. Sound background in science
• Requiring thorough knowledge of applications programming.  Perl
essential, some experience with Python, JavaScript, actionscript
(Flash), C, bash, VBA would be helpful
• Must have knowledge relating to the design and development of
applications programs across the laboratory
• Requiring knowledge of other related areas of IT
• Requiring advanced skills associated with programming design,
modification and implementation. Requires interpersonal skills in
order to work with other members of the lab
• Must be self-motivated, work independently or sometimes as part of a
team, able to learn quickly, meet deadlines and demonstrate
problem-solving skills.  Must be available to help fix crashes. Must
have advanced skills in web applications, web programming language and
object oriented programming concepts
• Must have basic bioinformatics background and be able to use
molecular biological and genetic textbook-type material to learn
enough science to understand why one algorithm is appropriate and
another is not

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