Sys Admin Job

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Applications for this position are closed as of 6/25/2007... thanks for your interest!


Wanted: System Administrator / Programmer

Location: University of California, Berkeley, CA, USA

Title code: Programmer Analyst, Level 3


The Holmes lab ([[1]]) works in evolutionary bioinformatics and computational bioengineering. We are building probabilistic tools for reconstructing the ghosts of Genomes Past, along with Web 2.0 applications for browsing their Present and designing their Future.

We are a small group of computationally savvy programmers, looking for a full-time experienced Linux systems administrator who is also interested in developing & applying bioinformatics algorithms. We're all varying shades of Unix geek, so we don't need our hands held, but are looking for someone to manage our 40U rack and help us build machines that dream of DNA.

("UCB invaded by penguins", June 2007)


The Holmes lab seeks an experienced system administrator to help us build & maintain infrastructure for computational biology research (specifically high-throughput genome analysis including detection & phylogeny of noncoding RNAs, transposons & other genetic elements).

As well as "typical" sysadmin tasks involving maintenance of intranet & internet services (basic flavors of email, HTTP, DNS, source code control, etc.) the job will call for the development & application of custom software for the comparative analysis of whole genomes. This will include e.g. adaptation of automated build tools for the construction of bioinformatics pipelines; use of probabilistic modeling software for profiling genomic features; and assisting the development of "Web 2.0" tools for genomic databases (wikis, blogs, forums, Ajax, etc.)


The successful applicant should have the following skills, or be poised to acquire them:

  • significant experience administering Linux systems (Mac OS X, BSD, and other Unix flavors a plus)
  • scripting/programming experience
  • excellent knowledge and understanding of computer networking (especially TCP/IP) and network security
  • specific skills/experience including several among the following:
    • Unix system administration:
      • Linux administration: CentOS, Fedora, and/or RedHat; building RPMs
      • Apache HTTP Server administration
      • CVS, Subversion, and/or other version control systems (e.g. darcs)
      • DNS servers (djbdns preferred)
      • Mail services: SMTP, IMAP, webmail
      • NFS and/or other networked Unix file systems
    • Unix programming & applications:
      • Perl programming
      • GNU Make
      • shell scripting
      • autoconf
      • SQL database administration (MySQL preferred)
      • PHP programming a plus; MediaWiki hacking a double-plus
    • maintenance of a parallel compute cluster (Sun Grid Engine, LSF, OpenPBS or other queueing system preferred)
    • scientific computing background desirable (bioinformatics/computational biology background most wanted)


The position is open until filled. Please contact with enquiries.

You can also find this job with ID # 006514 on However, that site serves the whole UC Berkeley campus and tends to be a bit garbled or out of date. This page offers a more current description of the job search.

A considerably more detailed (and subject-to-change) task list is available for this position.