[Pipet Devel] genentech

Harry Mangalam hjm at cx408397-a.irvn1.occa.home.com
Fri Apr 2 12:01:57 EST 1999

Hi All,

2 comments and a disclosure :)

Just a word of caution about ssh2 - it's INCOMPATIBLE with most version 1
ssh's and may cause a lot of problems (I have to use ssh1 to get to a number
of hosts and while I have both on my system, it's one more thing to handle).

Re: NCGR - I've been pretty quiet over this last few weeks writing some of
the user and SQL interface to GeneX (the Gene Expression database that NCGR
is sponsoring).  Hopefully this will be made available on a GPL basis
(almost all the componenent parts are either GPL or otherwise unencumbered
for Academic use (tho perhaps not for Genentech use - not that it should
make any difference to a Genentech)), but at any rate, it's up to NCGR and
UCI as to how it will be released.

NCGR may indeed contribute to the Loci project in either programming support
or direct $, but again, it's trying to survive as a bioinformatics
non-profit (which has some interesting problems associated with it).  They
know about Loci, but they have their fingers in a lot of pies right now and
are trying to get a solid infrastructure up and running.  Those of you
starting to look for a nice place to work could do a whole lot worse than NCGR -
terrific location (Santa Fe, NM), VERY nice, smart people, decent salaries
(especially compared to living standards/cost-of-living), decent endowment
and some good people running things.  Their biz plan is pretty good too.  If
I wasn't locked here because of spousal considerations (at least until
tenure and grant situation improves), I'd be there now.

And in the interests of full disclosure, ;) I myself have started a bioinfo
consulting .com which imposes another set of constraints on what I can
contribute (because of who pays for what development and what I want to 'get
out of my own work' (strange how rigid ideals get surprisingly flexible when
you have kids and a mortgage :)).  I'm trying to munge my biz model to
include and encourage OpenSource, but despite the success of RH, Caldera,
and others, it's not always a workable solution.

There's also the OpenSource, but non-GPL model that .coms like Sendmail and
Scriptics have used and it looks currently that I may be forced into using
their model for the time being.


On Fri, 2 Apr 1999, J.W. Bizzaro wrote:

/Justin Bradford wrote:
/> I pretty sure I'm going to be accepted for an internship at Genentech this
/> summer, working in the biocomputing division.
/Congratulations!  I know you'll be a great asset to them, as you are to us.
/> In the interview, the
/> director of this division was asking a lot of questions about Loci, and
/> seems very interested.
/That's good, I think.
/> Basically, they develop bioinformatic tools and client/middleware
/> interface software so the researchers can easily access these
/> bioinformatic tools and databases from easy-to-use interfaces over the
/> network.
/> Sound familiar?
/A little ;-)
/> So far they've basically been doing Perl/CGI access just using netscape.
/> They are wanting to start making use of Java applets to make better
/> interfaces, too.
/> I was having some trouble explaining the Loci design to him, but we're
/> basically doing the same thing. Well, except that the Loci design is
/> substantially more powerful, flexible, easier to use, and provides better
/> client views. After we're done writing it, of course ;)
/We're trying.  I'm beginning to think that our time spent thinking and
/rethinking the design of Loci has been very beneficial, even though nothing has
/been written.  Had we just jumped in and started coding, there were be less of a
/difference between Loci and other concoctions.
/But of course, vaporware is vaporware ;-)
/> I have a friend who used to work out there, and he tells me they have some
/> absolutely brilliant people in the biocomputing/bioinformatics division
/> (although they're probably doing development on the bioinformatic
/> tools rather than the interface/network stuff). Given the overlap and
/> general interest they showed towards the Loci concept, it might not be too
/> big of a stretch to get genentech interested in the project. Or, at least,
/> maybe I can attract a few developers there.
/I have no problems with the prospect that a business might get involved.  Harry
/Mangalam also mentioned that NCGR might be interested in extending Loci (see Feb
/27 e-mail from Harry).  We are licensing Loci as LGPL rather than GPL so that it
/can be extended with proprietary programs.  (This does bring up the issue of
/using _some_ GPL code in Loci...as with Dia...I'm concerned that we can't have
/any GPL code, that it has to be all LGPL.)
/Red Hat, for example, was responsible for most of the GNOME development, and it
/didn't matter that it was a business.  It is up to a company to use the GNU
/license, and by doing so they are disclaiming their "rights" to make the
/software closed and proprietary at some point in the future (the GPL and LGPL
/are indelible).
/> They have a cross-platform concern, too, with Windows and MacOS, and
/> probably some unix, desktops. Has anyone heard about a GTK port to MacOS?
/I agree with Rahul that a MacOS 10 port would be simpler than the Windows port,
/which already exists.  Of course because OS 10 is UNIX-based (it uses the Mach
/> P.S. I'll actually get around to setting up CVS, SSH, etc. on the new
/> server this weekend. I promise. Any thing else we need on it?
/I have the RPM's for SSH2 already there.  This is the directory where I like to
/archive RPM's:
/    /usr/opt/arc/RPMS/
/You'll find them there.  As for myself, I will be installing BigBrother (Web
/stats) and Mailman (list server).
/> P.S.S. Thanks J.W. for starting this project. It played a big part in this
/> getting (probably) this internship.
/You're very welcome!  This news has made my day, really.  Let me know how it
/turns out.
/J.W. Bizzaro                  mailto:bizzaro at bc.edu
/Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/
/I have always appreciated your ability to ________, whenever
/there has been a blank to fill.


Harry J Mangalam -- (949) 856 2847 -- mangalam at home.com 

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