[Pipet Devel] collaboratories - was Check out this URL

J.W. Bizzaro bizzaro at bc.edu
Fri Feb 26 19:16:26 EST 1999

Hello Harry.

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 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.

***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

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/

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