[Pipet Devel] where is piper going?

J.W. Bizzaro jeff at bioinformatics.org
Sat Sep 9 13:58:48 EDT 2000

Where is Piper going next?  Who knows?  Actually, we do have a pretty clear
idea, but we want to keep our options open.

Historically, Piper's design has always been in a state of flux, and I think
that is a Good Thing.

Piper started out (from the "Loci" end) as "The Lowell Package".  It was
supposed to be "the GNU equivalent of The Wisconsin Package (or GCG)", a
commercial, mostly console-based, suite of sequence analysis tools.  I don't
even know if there is anyone on this list who was with me back then.

And then about one and a half years ago, I discovered that Piper (under the
new acronym "TULIP") had the same design goal as a project called "EMBOSS":


I spent a bit of time afterward concerned that we would be duplicating the
efforts of another GPL'd project.  Anyone who knows me knows that that is what
drives my decision making with respect to my own projects.  So, I decided that
we should not concentrate on tools, as EMBOSS did, but on an infrastructure
for distributing tools.

Shortly thereafter, I decided to not make Piper (which became "Loci" after
TULIP) specifically for bioinformatics, for reasons some here have heard over
and over: A general-purpose system would attract more users, and thus
developers, which would be better for bioinformatics users in the long run. 
We would not have Jarl (GMS) and Jean-Marc (Overflow) collaborating with us
had I not made that decision.

And, just prior to GMS and Overflow merging with Loci, Piper was only going to
provide interfaces between existing programs.  Overflow introduced the whole
concept of "small nodes" to us (and Loci would provide "nodes over the
Internet" for Overflow).

So, Piper (from any end) has been through a lot of changes.  Had a design be
written immutably in stone, none of us would be reading this e-mail right
now.  FLEXIBILITY, rather than a pre-defined path, has been, and always will
be, most important.

But, our objectives are becoming clearer.  We know at this point that Piper is
not a Post-It Notes program :-)  We have written a number of documents on the
overall objective.  Check out the poster written by Brad:

  (warning: very large)

Along with the e-mail I sent to Cameron Laird about Piper vs. .NET, we have 2
very recent and clearly thought out design documents.  But things can still

What should we be coding next?  Actually, I should be used to these questions
from Brad.  He told me very early on that he's a code monkey and not a
coordinator.  What we should code on next is whatever anyone thinks will help
us reach the most recently drafted design goals.  I can't dictate the coding
any closer than that, and I probably shouldn't.  We've had some heated
arguments at the times I told Brad what should be done with his code.  Plus, I
don't have the depth of knowledge that Jean-Marc and Jarl have regarding how
their particular code bases can be developed.

I hope everyone understands my position on the direction of Piper.  I don't
want anyone to get the impression at any time that I have abandoned the
project or that it is in complete chaos.  We're all too dedicated and smart
for that.

J.W. Bizzaro                                           jeff at bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"Injustice anywhere is a threat to justice everywhere."
               -- Martin Luther King, Jr.

More information about the Pipet-Devel mailing list