little b discuss Google Group

Re: Wrestling with little b syntax...

aneilba...@gmail.com (Aneil Mallavarapu) — Mon, 29 Sep 2008 20:09:31 UT

The last line should have been:
{a @ :outer + b -> a @ :inner + b}.(set-rate-function 'custom-rate {a *

Re: Wrestling with little b syntax...

dom.layfi...@gmail.com (Dom Layfield) — Mon, 29 Sep 2008 19:59:09 UT

I see. Great, I'll try that workaround.
Thanks for your assistance.

-- Dominick

Re: Wrestling with little b syntax...

aneilba...@gmail.com (Aneil Mallavarapu) — Mon, 29 Sep 2008 17:50:26 UT

In the future, it's possible that little b will support up a
non-generalizable (location-dependent) reaction syntax. I can see why this
would be convenient. We just don't have time to work on this right now.
The easiest way to do this is to define the reaction-type in terms of a
second species-type which sits in the membrane:

Re: Wrestling with little b syntax...

dom.layfi...@gmail.com (Dom Layfield) — Mon, 29 Sep 2008 15:59:49 UT

Right: reactions are location-independent. That makes a lot of sense,
and I appreciate the philosophy of making rules as general as
possible.

I guess I wanted to hijack the reaction syntax and to use this to
describe transport phenomena. This was tempting, as it seemed that
the reaction-rate and location-specifying infrastructure could easily

Re: Wrestling with little b syntax...

aneilba...@gmail.com (Aneil Mallavarapu) — Sun, 28 Sep 2008 12:56:41 UT

In little b, reactions are based on reaction-types. The
expression{species-type @ location -> ...}uses the reaction-type
constructor operator
*->*. You are actually constructing a reaction-type object here.
Reaction-types are *location-independent - *they don't contain location
information. Conceptually, reaction-types represent properties of

Re: Wrestling with little b syntax...

dom.layfi...@gmail.com (Dom Layfield) — Sat, 27 Sep 2008 19:56:25 UT

Hi Aneil,

Thanks for the reply, and the clarification on the newer syntax.

I think perhaps you may have overlooked the second (and more
important) half of my post. I'm still perplexed as to why little b
prevents me from saying {species @ location -> etc.}, and only allows
{species @ location-class.subcompartment -> etc.}. As I tried to

Re: Wrestling with little b syntax...

aneilba...@gmail.com (Aneil Mallavarapu) — Sat, 27 Sep 2008 13:04:18 UT

Little b's curly braces provide infix syntax. The expression in the
tutorial is
from an older version of little b:
{[ion] @ :inner @ membrane ->> [ion] @ :outer}
But, let me explain this anyway:
The expression contains 2 infix operators:
@ and ->>
ION and MEMBRANE are Lisp symbols which are bound to predefined values.

Re: Wrestling with little b syntax...

dom.layfi...@gmail.com (Dom Layfield) — Wed, 24 Sep 2008 05:59:36 UT

I just read that document ([link]
quickstart.html). One aspect that I found confusing is that it is not
obvious which identifiers are keywords, and which are variable names.
(I know this is not quite the right terminology for LISP, but I hope

{[ion] @ :inner @ membrane ->> [ion] @ :outer}

Re: Wrestling with little b syntax...

aneilba...@gmail.com (Aneil Mallavarapu) — Wed, 24 Sep 2008 03:40:33 UT

Hi Dominic -
The best place to look is under Locations in
[link]. Reactions
need to be specified with respect to location-classes, not locations,
so they can be generalized for other situations. c1 and c2 are
locations based on the location-class COMPARTMENT.

Wrestling with little b syntax...

dom.layfi...@gmail.com (Dom Layfield) — Wed, 24 Sep 2008 01:30:42 UT

I'm trying to figure out how to use little b to describe multi-
compartment models.

I started by trying to write the simplest possible model that I could
think of: a single species that repartitions between two
compartments. Unfortunately, I can't even get this working.

Here's the code:

Little b short course

aneilba...@gmail.com (Aneil Mallavarapu) — Thu, 28 Aug 2008 21:42:03 UT

Hi All -
The little b short course is over. I've posted materials at the
website - [link]. This thread is open for
feedback on the course.
Thanks,
Aneil

Re: Documentation pointers are broken

dhcr...@gmail.com (David Croll) — Thu, 01 Nov 2007 12:39:49 UT

Aneil,
Thanks for your quick response, I've been waiting. I assume this is the one
with the graphs implemented? I've been swamped with administrivia, but
eager to work with it and now have some free time following midterms etc.
I'll give it a go now.
dhc

Re: Documentation pointers are broken

aneilba...@gmail.com (Aneil Mallavarapu) — Thu, 01 Nov 2007 10:53:29 UT

Hi Peter,
Thanks for the heads-up. The links should be working now.
Also, little b version 1.5 is now available for download.
Cheers,
Aneil

Documentation pointers are broken

peter.c.ma...@gmail.com (Peter) — Tue, 30 Oct 2007 11:21:40 UT

Hello,
I'm new to the group.
The documentation pointers on the download page [link]
seem to be broken. Are those documents still available?
Thanks,
Peter

Re: Problems version 1.0

aneilba...@gmail.com — Sat, 13 Jan 2007 02:39:11 UT

Little b requires the latest Microsoft C Runtime Library (msvcr80.dll).
It is now accessible from the download page.
aneil