BioBike (as I'm sure you all know by now :-) is a web-based
biocomputing platform that integrates knowledge, tools, and open
programmability to enable communities of biologists to work problems in
genomics. BioBike is built on the KnowOS (Knowledge Operating System)
platform, a multi-headed multi-threaded web-based linux-driven lisp
engine. You can learn more about BioBike at http://www.biobike.org, and
about KnowOS at http://www.knowos.org. Both of these are built on
Common Lisp.
BBL is a variant of Lisp that includes special constructs and
functionality to simplify writing biocompution programs. vBBL (visual
BBL) is a method for programming in BBL through a web-based graphical
interface. vBBL represents BBL code using nested boxes instead of Lispy
parentheses. The biologist programs in vBBL through a dynamic HTML
interface (aka. Ajax) using menus to form and evaluate expressions and
even to define new functionality.
You can read how vBBL works in some detail, including taking a
walk-through demo here:
http://nostoc.stanford.edu/jeff/etc/bblvpl/bblvpl.html
We don't yet have a server open for public use (we will soon,
hopefully), but if you have a special interest in possibly using vBBL
or the technology, or possibly in applying it to your own problem areas
and/or helping to improve it, please contact the BioBike team at
··············@lists.stanford.edu.
Contributors:
* BBL Concept and Design: Jeff Elhai and others
* BBL Implementation: JP Massar, Jeff Elhai, and Mark Slupesky
* vBBL Concept: Jeff Elhai and Mike Travers
* vBBL Implementation: JP Massar, John K. Myers, Peter Seibel, Mark
Slupesky
* BioBike/KnowOS Concept: Jeff Shrager
* BioBike/KnowOS Implementation: JP Massar, Mike Travers, Jeff Shrager,
Mark Slupesky, and others
* Support: NASA, NSF, Franz, LispWorks, and a great deal of volunteer
sweat
A couple of folks have expressed concern about the speed of this
Lisp-based Ajax application because makes many round-trips between the
client and the server, and because the server sends back what appears
to be huge amounts of stuff to the client. In reality, it doesn't send
everything; many things (like typing in strings) are handled entirely
on the client. The amount of stuff sent back by the server is not that
large; the expression tree is represented by just an sexpr, and once
the menus are sent at initialization they are (mostly) fixed.
Futhermore, it doesn't always send back the entire expression tree,
only the subtree that is modified, and the client only redraws that
subtree.
Regardless, it's a valid question, but hard to answer because it's
largely a matter of how fast your connection is. I can tell you that
when I'm on campus, with the server in the next building (probably on
more-or-less the same university LAN), it's essentially instantaneous.
When I'm at home (~2 miles, and via DSL), there are microscopic lags;
I've had it lag up to a couple of seconds in a large redraw. We
regularly use it cross country (Virginia to California) with no
trouble, and we have had some experience using it internationally as
well. AFAIK these long-distance users don't seem to be yelling about
the lag.
(message (Hello ·········@gmail.com)
(you :wrote :on '(15 Dec 2006 23:04:13 -0800))
(
J> functionality to simplify writing biocompution programs. vBBL (visual
J> BBL) is a method for programming in BBL through a web-based graphical
J> interface. vBBL represents BBL code using nested boxes instead of Lispy
J> parentheses. The biologist programs in vBBL through a dynamic HTML
interface (aka.
J> Ajax) using menus to form and evaluate expressions and even to define
J> new functionality.
cool!
)
(With-best-regards '(Alex Mizrahi) :aka 'killer_storm)
"People who lust for the Feel of keys on their fingertips (c) Inity")