[sf-perl] Job opening at Genentech.

Walt Sanders wsanders at pacificwebdesign.org
Wed Aug 5 12:10:23 PDT 2009

WOW!  If you actually find such people, and they are available, I will  
take two of them!  Walt.

On Wednesday, at , George Hartzell wrote:

> [I hope that posting a perl-ish job opening is ok...]
> 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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