little b discuss Google Group

Re: Wrestling with little b syntax...

2008-09-29T20:09:31Z

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

Re: Wrestling with little b syntax...

2008-09-29T19:59:09Z

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

-- Dominick

Re: Wrestling with little b syntax...

2008-09-29T17:50:26Z

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...

2008-09-29T15:59:49Z

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...

2008-09-28T12:56:41Z

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...

2008-09-27T19:56:25Z

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...

2008-09-27T13:04:18Z

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...

2008-09-24T05:59:36Z

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...

2008-09-24T03:40:33Z

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...

2008-09-24T01:30:42Z

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

2008-08-28T21:42:03Z

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

2007-11-01T12:39:49Z

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

2007-11-01T10:53:29Z

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

2007-10-30T11:21:40Z

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

2007-01-13T02:39:11Z

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