[Pipet Devel] collaboratories - was Check out this URL

Harry Mangalam hjm at cx408397-a.irvn1.occa.home.com
Sat Feb 27 10:40:39 EST 1999

On Sat, 27 Feb 1999, J.W. Bizzaro wrote:

/It does sound as if the project you described is a great example of how Loci
/could be used as a collaboratory.  Even if the base installation of Loci does
/not include every tool needed to do this, the license would allow NCGR to extend
/it and repackage it...providing the original Loci code remains LGPL.

I have to make a distinction here - NCGR is paying me to develop code
that does a particular job in support of a project they're very interested
in.  While I have my own agenda in terms of freedom and redistribution of
code (to which they're surprisingly open), they have their own agenda.  They
are a non-profit org, but they were set up as a hot-house agency to spin off
for-profits if possible.  SO while they plan to make all the services they
develop freely available to the public, they want to reserve the right to
spin off a com to exploit that code for companies that want to replicate the
system behind their firewall.  Therefore, there are some additional problems
in basing their code on LOCI.

I know that they're aware of LOCI because I told them about it (one of my
functions is to find out about ideas out there that seem to be worth paying
attention to, like gnome and other CORBA services, like BSML, like Bioperl,
etc that look like they are worthwhile), but it's up to their executive to
decide which to support.

So while I support the idea of LOCI, it and will spend time trying to
integrate aspects of the genex db with LOCI, it doesn;t mean that NCGR will
officially support it.  The problem with who owns intellectual property is
HUGE in SW (I just resigned from UCI because of it to work on NCGR's
project), so don't go looking for large developers to leap onto the freee
software bandwagon - there is huge resistancce, especially from their legal
depts.  Yhe success of Redhat and Gnu/Linux is changing that, but slowly. 
I'm counting on it b/c I'm starting a company to try to do (sort of) the
same thing, with my software - the core software is free, but I'll sell
support, customization, and interface components to those who want/need

That said, for what NCGR wants to do, it seems to me that the software is
almost incidental; what they're really selling is the integration technology
and support (not unlike Redhat itself).  They COULD give the software,
charge only for support and that would in fact make more $ for
them, as they would then benefit from other free software developers to
contribute to the code base.

/I don't know if they'd like to sell it (you said they'd like to rewrite it at
/commercial quality), but contrary to popular belief, GNU programs can be sold,
/just like Linux.  The key is that you don't make it proprietary; you're just
/selling packaged media and support.

EXACTLY.  You put the words right in my mouth ;).

/***We're hitting on an important strategy here for Loci.  What is most important
/is that Loci becomes ubiquitous and highly accepted.  By not restricting
/commercial use or redistribution, we're going a long way toward that goal.
/Personally, I don't care about getting rich off of anything.  But anyone can
/make money from Loci, by distributing CD-ROM's, manuals, etc.  I think even
/selling server time for those server-side analyses is an option.
/Yeah, any kind of collaboratory may be implemented once we set Loci up to do
/that sort of thing.  I don't see it being a big step beyond the whole concept of
/a distributed workflow system.  Public or private, open or closed, we can do
/it.  Harry, were you referring to an open collaboratory or a closed one?

/Can you guys imagine the impact this could have on the field if Loci were to be

Yup - it would have a big impact, but there are lots of similar projects
going on in 'coopetition', so it's important to actually produce something.
Bio-perl has already started regular dists of their package, and EMPRESS
will start soon.

It's demo or die.  (I'm one to speak - I really haven't done anthing yet
except flap my lips (they move when I type), but as soon as I finish the
commandline version of tacg V3 (in final packaging for beta release and
documentation now), I'll put some time on trying to LOCI-lize it.)

/bizzaro at bc.edu
/Harry Mangalam wrote:
/> Hi Again,
/>    Well, this wasn;t part of my original interest in this group and may be
/> well-suited for it, but let me describe one of the things I'm
/> working on (partially supported by National Center for Genomic Resources
/> (NCGR, out of Santa Fe, NM) in support of a yeast genomics project at UC
/> Irvine.
/> The UCI group has gotten an Affymetrix Genechip machine and is busy
/> subjecting yeast to various stresses, generating whole-genome datasets for
/> time points along this stress.  I'm building a relational database with a
/> web interface that will suck up those datasets (and be amenable to accepting
/> data from other such gene expression studies) and allow it to be queried on
/> various params, as well as subjecting the returned values to various
/> statistical analyses with the stats language 'R' (a clone of S/SPlus), using
/> gnuplots for the simple outputs, VRML for complex viz's.
/> Because the size of the datasets are so large (6k orfs x 4 timepoints, plus
/> associated pointers, descriptors, images, etc) and the number of them is
/> going to be pretty big, I'm using mysql as a prototyping system, with perl
/> glue, talking thru Apache/FASTCGI, replacing the perl with C as I
/> identify bottlenecks. There will be a generic interface to commandline apps
/> (other clustering routines, tacg, clustalw, blast, etc, so that it can
/> become pretty extensible.  NCGR may rewrite it at commercial
/> quality to support their plant genomics project, but I get to do the fun
/> part...
/> I hadn't considered it, but you bring up the possibility of using such a
/> system as a collaboratory by making the analyses persistent in some way,
/> either as paths thru an analysis or the analysis itself (altho that would
/> get very large very fast) so that they might be re-used or extended by
/> others interested in the topic.  Or maybe just the paths thru an analysis
/> would be an important resource - if I could somehow record the 'analysis
/> track' that users took, I could identify, then automate them so that the
/> whole pathway could be boiled down to a button.
/> This is WELL off the LOCI topic, but perhaps the 2 could be designed to
/> communicate at some level.
/> As I said, it was never the intent for the above-described project to use
/> LOCI, but if they can be made to better co-exist so much the better.
/> Cheers
/> Harry
/> On Fri, 26 Feb 1999 david.lapointe at umassmed.edu wrote:
/> /Yeah, I realized that just after I sent that message.
/> /
/> /$2M ? Seems like a lot but if you've invested $20 million( or more)
/> /in sequencing hardware what's $2M to make it work?
/> /
/> /Are you talking about Collaboratories? That is an interesting concept.
/> /
/> /
/> /David
/> /
/> /David Lapointe
/> /Manager - Research Computing Services
/> /UMass Medical School
/> /Worcester, MA 01655
/> /508/856-5141
/> /
/> /
/> /> -----Original Message-----
/> /> From: J.W. Bizzaro [mailto:bizzaro at bc.edu]
/> /> Sent: Friday, February 26, 1999 5:06 PM
/> /> To: tulip-list at busboy.sped.ukans.edu
/> /> Subject: Re: [Pipet Devel] Check out this URL
/> />
/> />
/> /> Jeeeez!  Does the concept seem a little familiar?  BTW, this
/> /> is the same company
/> /> from which I got the first pics.
/> />
/> /> You know, I have been thinking seriously about taking Loci
/> /> one step further and  making it a system for Internet-wide research
/> /collaboratives,
/> /> between loosely affiliated people.  It's something I still have to clear
/> /with
/> /> Ken Marx, but I was thinking that we, The BIC Group, could use Loci to
/> /> collaborate on some "open" research projects, making an "open laboratory"
/> /that
/> /> treats scientific research like a GNU software project.  Any thoughts?
/> />
/> />
/> /> Jeff
/> /> bizzaro at bc.edu
/> />
/> /
/> Cheers,
/> Harry
/> Harry J Mangalam -- (949) 856 2899 -- mangalam at home.com
/J.W. Bizzaro                  Phone: 617-552-3905
/Boston College                mailto:bizzaro at bc.edu
/Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/


Harry J Mangalam -- (949) 856 2899 -- mangalam at home.com 

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