[sf-perl] Job opening at Genentech.

Fred Moyer fred at redhotpenguin.com
Wed Aug 5 13:05:12 PDT 2009

On Wed, Aug 5, 2009 at 12:10 PM, Walt
Sanders<wsanders at pacificwebdesign.org> wrote:
> WOW!  If you actually find such people, and they are available, I will take
> two of them!  Walt.

There were more than two at the meeting last Tuesday.  The meetings
are a great place for job announcements, and those announcements are
heard by everyone there and tend to highlight the really serious Perl
and open source friendly employers.

> On Wednesday, at , George Hartzell wrote:
>> [I hope that posting a perl-ish job opening is ok...]

Job announcements related to Perl are welcome on the list; the only
requirement is that you include the [job] tag in the subject so that
users can filter those emails appropriately.

>> I have an opening in my group in the Bioinformatics department at
>> Genentech [South San Francisco, CA].  At the moment (for the next year
>> or so) our main focus is rebuilding and extending a system for
>> collecting, processing, and disseminating information about mutations
>> and variations (think web interfaces, relational databases,
>> alignments, workflows/pipelines).  In the future we'll pick up
>> projects related to next-gen sequencing (Me too!!!  In the future,
>> what isn't related to next-gen?), data integration, and/or
>> lab-specific projects.
>> First and foremost I'm looking for someone who's sharp and who enjoys
>> computers, biology, and technology; someone who gets excited about
>> picking up new tools but who also has a sense of responsibility and
>> restraint.
>> I'm looking for someone who's familiar with several languages and
>> tools; modern Perl complemented with C is my first choice these days,
>> supplemented with R and (when necessary) anything from the rest of the
>> programming language bestiary.  There's a fair amount of Java flying
>> around here too so familiarity with it and the JVM world will help.
>> Relational databases are part of the picture: Oracle for the big
>> stuff; SQLite, Postgresql, and MySQL play niche roles.  I generally
>> interact with them via ORM's, lately it's been Rose::DB::Object on the
>> Perl side though I've been convinced to take another look at
>> DBIx::Class.  Most of my web apps use CGI::Application, as fastcgi's,
>> mod_perl, or simple CGI scripts, but (as with ORM's) I may take
>> another look at Catalyst.
>> I'm looking for someone who's interested in building real software.
>> We'll be putting together a set of tools and data that need to hang
>> together and evolve for at least 4-5 years.  Deploy and run won't cut
>> it.  Requirements will change, so it's important to me that we build
>> things so they're as modular and flexible as possible.  Testing,
>> source control, and documentation matter.
>> A strong candidate will have an understanding of basic bioinformatics
>> concepts and the ability to pick up new biology and computer science
>> concepts as necessary.
>> At the junior end of the spectrum I'd expect a bachelor's degree + 3
>> years of experience, at the upper end would a masters + 5 years (or a
>> PhD interested in moving towards the production side of the house).
>> I can imagine running through one or more detail oriented interview
>> questions that drilled down (or took of on a tangent) from the
>> following:
>>  - What's the difference between Smith-Waterman, blast, sim4, gmap,
>>   and/or bowtie alignment algorithms or tools?  Which would you use
>>   when, and why?
>>  - Why is Moose better than Class::Accessor?  (yes, it's Perl
>>   centered, but it could spin out into any language [e.g. why is
>>   Java better than Perl?]).  What's a MOP?  Who cares?
>>  - CVS, subversion, git, mercurial.  You've already picked one?
>>   Which one?  Why?  Why not?
>>  - XML or JSON or YAML.  Pick one for moving data back and forth in
>>   an Ajax based interface.  Why?  Would it also work well in other
>>   contexts?
>>  - How would you store information about positional features on a
>>   genome so that you could get fast random access?  How would your
>>   solution tie into a larger data context?
>> Genentech's a great place to work: solid salaries, great benefits, Bay
>> Area location (who could ask for more?).  We're open source friendly
>> and with the arrival Robert Gentleman (our new Director, of
>> Bioconductor/R fame) likely to become more so.  The recent Roche
>> acquisition hasn't changed life much, it seems to mostly be a source
>> of opportunities for those of us in Research.
>> If you know anyone who fits the bill, have them drop me a note.
>> Thanks!
>> g.
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