File Release Notes and Changelog
Notes:
This file contains notes for the little b source code. If you are
interested in getting started right away with using little b to build
models, it may be easier to download the GUI application from the
little b website: http://littleb.org/download.html.
Little b is a Lisp-based language designed to allow the user to
build models from shared libraries. It was written and designed by
Aneil Mallavarapu at the Harvard Medical School Department of Systems
Biology in Boston.
Libraries have been developed for building ODE models of molecular networks
in multi-compartment systems such as cellular epithelia. As of version 1.5
it includes a graph-based method for representing molecular complexes.
The language contains mechanisms for rule-based reasoning, symbolic mathematics
and object-oriented definitions. The syntax is designed to be terse and
human-readable to facilitate communication. Since little b is based in Lisp,
the environment is both interactive and compilable.
The source code works on Windows XP and Linux. Mac OS support is under
development. Little b runs on these ANSI Common Lisp implementations:
* Lispworks 4.x and 5.x, commercial Lisp IDE w/ in line debugger
- little b does not run on the Free Personal Edition
because of memory restrictions
* Allegro 8.x, another high quality, fast CL implementation
* CLisp 2.39+, free, open source GPL-licensed Common Lisp
(I recommend using it with Emacs and SLIME)
Others may work too. We'd be happy to hear about it.
To run the source code, you'll need a Lisp interpreter, and an editor. Any
of the above will do. If you use CLisp, you should consider using Emacs
with SLIME, an editor mode that provides a Lisp command line and syntax
highlighting.
More information at: http://littleb.org
--------------------------------------------------------------------------------
Changes:
1.5.5 (2007-11-29)
==================
Thanks to German Enciso for his help finding these bugs.
<< User-visible changes >>
* Bug Fixes
+ every instance now being asserted into database correctly (kb-run fix)
+ reaction-generated complex-species-type are now properly canonicalized
+ examples/example5 -complexes truncation error addressed
<< Internal Changes >>
* Added Files:
+ make-release.sh (creates source file release archives)
+ compile-all.lisp (ensures little b and library fasls are produced)
Changes:
1.5.4 (2007-11-20)
=================
Many thanks to Carlos Lopez for providing the impetus for getting things working with CLisp, and his work in discovering numerous bugs and problems.
<< User-visible changes >>
* New functionality:
+ Complexes now work in multiple locations
+ Added the notion of dimensionality
* File changes:
+ b-user/non-dimensional-ode-biochemistry is deprecated (warning is issued)
include b-user/ode-biochem instead
+ b-user/3d-ode-biochemistry is deprecated
include b-user/3d-ode-biochem instead
* Portability:
+ Support for CLISP 2.42
- little b now loads, compiles and provides a working compile-library function
on CLISP (tested on Linux & Windows XP)
* Numerous bug fixes
<< Internal changes >>
* New Functionality:
+ ASDF+ includes DELETE-BINARIES, which deletes the binaries files
(not directories of an ASDF system)
USAGE: (DELETE-BINARIES system-name)
* Source tree
+ Moved platform specific code to the platform directory,
- removed editor-lispworks.lisp from utility dir
- now lispworks.lisp and clisp.lisp in platform dir
* Compliance
+ Placement of LOOP UNTIL/WHEN keywords now fixed for CLISP
(always appear after FOR now)
+ DECLARE IGNORE directives added all over
* Bug Fixes
+ fixed reader functions work with CLISP
* Misc Changes
+ introduced +top-level-pprint-dispatch+ (needed for correct printing in CLisp)
- a bug in CLisp 2.42 pprint-logical-block causes the pprint-dispatch table
to be ignored. Reported & fixed; Will be in Clisp 2.44 release.
Changes:
Changes for b1
built by cvschangelogbuilder 2.1 (build 1.47) with option listdeltabydate.
2007-11-29
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/pattern-match.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.8 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-inference.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example5-complexes.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/core/kb.lisp 1.3 (changed):
* fixed canonicalization bugs
* fixed bug in kb-run introduced by ANSI LOOP compliance fixes
* b1@/cvsroot/littleb/b1/release/compile-all.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/release/make-release.sh 1.2 (changed):
*** empty log message ***
2007-11-28
* b1@/cvsroot/littleb/b1/b1.asd 1.9 (changed):
V1_5_5
2007-11-27
* b1@/cvsroot/littleb/b1/release/compile-all.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/release/make-release.sh 1.1 (added):
Added make-release.sh and compile-all
2007-11-26
* b1@/cvsroot/littleb/b1/libraries/examples/example5-complexes.lisp 1.3 (changed):
Fixed complexes example
2007-11-25
* b1@/cvsroot/littleb/b1/libraries/examples/example5-complexes.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/release/make-release.bat 1.2 (changed):
Fixed bug: example5 was strangely truncated... more sourceforge cvs
weirdness????
2007-11-22
* b1@/cvsroot/littleb/b1/changes.txt 1.1 (added):
Version 1.5.4
2007-11-21
* b1@/cvsroot/littleb/b1/.cvsignore 1.2 (changed):
*** empty log message ***
* b1@/cvsroot/littleb/b1/b1.asd 1.8 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.12 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/enzymatic-reaction.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/dimension.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/dimensional-methods.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/expand.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/gauss.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/math-printer.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/operators.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/sum-expression.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/util/dictionary.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/core/field-pattern.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core/lisa-extensions.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core/printer.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/src/core/rule-patterns.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/global/constants.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/global/error.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/name.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/global/object.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/global/reader-core.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/trace.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/include/include-path.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/platform/clisp.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/platform/lispworks.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/portable/clos.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/src/top-level-forms/defcon.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/top-level-forms/defrule.lisp 1.4 (changed):
Added ignore declarations which gets rid of almost all the clisp warnings
* b1@/cvsroot/littleb/b1/release/make-release.bat 1.1 (added):
Does a fresh anonymous checkout of code to build a working little b source folder
2007-11-20
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.5 (changed):
* Added DELETE-BINARIES, which does the expected.
* Fixed FILES-IN-SYSTEM so that duplicates are removed using PATHNAME-MATCH-P rather than EQUALP.
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.8 (changed):
* b1@/cvsroot/littleb/b1/src/platform/clisp.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/platform/lispworks.lisp 1.2 (changed):
*** empty log message ***
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.6 (changed):
Delete-binaries now returns a list of deleted pathnames rather than a count
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.10 (changed):
* b1@/cvsroot/littleb/b1/src/core/printer.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/src/core/query.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/include/compile-include-path.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/utility/utility.lisp 1.5 (changed):
Fixes to get compile-library working on clisp
2007-11-19
* b1@/cvsroot/littleb/b1/littleb.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/core/printer.lisp 1.5 (changed):
Fixed some clisp printing bugs
* b1@/cvsroot/littleb/b1/src/global/name.lisp 1.4 (changed):
Got rid of fields-remain argument in print-name-obj
* b1@/cvsroot/littleb/b1/src/include/compile-include-path.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/include/include-path.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/include/include.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/src/include/library.lisp 1.3 (changed):
More CLISP warning suppression (during loading)
better error reporting in INCLUDE-PATH
* b1@/cvsroot/littleb/b1/b1.asd 1.7 (changed):
Moved platform specific code to the platform directory, removed editor-lispworks.lisp from utility dir
* b1@/cvsroot/littleb/b1/src/platform/clisp.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/src/platform/lispworks.lisp 1.1 (added):
Moved platform-specific code to the platform folder
2007-11-16
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.3 (changed):
*** empty log message ***
* b1@/cvsroot/littleb/b1/src/portable/clos.lisp 1.5 (changed):
Changed ANSI-non compliant LOOP syntax: FINALLY RETURN ... to FINALLY (RETURN ...)
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.4 (changed):
Fix for clisp unix which doesn't support posix:version-* functions
* b1@/cvsroot/littleb/b1/src/portable/misc.lisp 1.2 (changed):
Put windows-specific code in the correct conditional compilation block
to correct clisp on unix bug
2007-11-15
* b1@/cvsroot/littleb/b1/b1.asd 1.6 (changed):
* b1@/cvsroot/littleb/b1/src/core-types/concept-class.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/core-types/concept.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/core-types/property-class.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core-types/property.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core/expose.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/core/kb.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/include/compile-include-path.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/include/include-path.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/include/library.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/packages/pkgdecl.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/src/utility/utility.lisp 1.4 (changed):
* little b version is now 1.5.2
* added several ignore declarations
* delete-directory fixed for clisp
* compilation handling for clisp
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.8 (changed):
Removed a debugging output
2007-11-12
* b1@/cvsroot/littleb/b1/b1.asd 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.9 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.11 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-inference.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/timings.txt 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/matlab/ode-translation.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/util/dictionary.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/littleb.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/core/printer.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/global/error.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/src/global/field.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/src/global/fieldinfo.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/include/clear.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/include/include.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/portable/clos.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/reader/field-reader.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/reader/token-reader.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/top-level-forms/initialize.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/utility/utility.lisp 1.3 (changed):
Several changes to bring code into line with ANSI standard & CLisp (still not yet working fully on CLisp, though):
* LOOP compliance:
not using THE HASH-KEYS/-VALUES OF instead THE HASH-KEYS/-VALUES IN
using FINALLY (RETURN ..) instead of FINALLY RETURN
* moved error into global dir, since it is needed for some conditions defined in global
* fixed reader functions
* reintroduced +top-level-pprint-dispatch+ (needed for CLisp)
2007-11-09
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/b1.asd 1.4 (changed):
* b1@/cvsroot/littleb/b1/littleb.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/portable/clos.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/utility/utility.lisp 1.2 (changed):
Initial set of bug fixes for clisp
2007-11-07
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.9 (changed):
*** empty log message ***
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.10 (changed):
Fixed bug in define-custom-rate
2007-11-05
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.8 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/std-rate-functions.lisp 1.6 (changed):
*** empty log message ***
2007-11-03
* b1@/cvsroot/littleb/b1/b1.asd 1.3 (changed):
Version 1.5
2007-11-01
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.10 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.8 (changed):
Complex reactions in multiple locations are working!
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.9 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example5-complexes.lisp 1.1 (added):
Updated spherical cell to use preferred :outer and :inner fields of membrane
added compelxes example
2007-10-29
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.8 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/membrane-apposition.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/std-rate-functions.lisp 1.5 (changed):
Complex reactions in multiple locations are working!
2007-10-25
* b1@/cvsroot/littleb/b1/src/core/printer.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b-user/3d-ode-biochem.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b-user/3d-ode-biochemistry.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b-user/non-dimensional-ode-biochemistry.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b-user/ode-biochem.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/basic-ode-modelling.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/pattern-match.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization/2d.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization/3d.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization/null.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/enzymatic-reaction.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/membrane-apposition.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-type.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/std-rate-functions.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/util/dictionary.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/egfr-mapk.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example1-alternate.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example1-reversible.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example1.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example2-reversible.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example3-manual es complex.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/example4-enzymatic-reaction.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/g6pi-d.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/g6pi-er.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/g6pi.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/g6pi2.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/locations/cell.lisp 1.2 (changed):
* complex-reaction tenatively working with both localizations and rate functions
* switched from b-user/3d-ode-biochemistry and b-user/non-dimensional-ode-biochemistry
to b-user/3d-ode-biochem and b-user/ode-biochem
* added notion of a location class's dimensionality, (normally 3 for compartments, 2 for membranes, 1 for membrane interfaces);
- accessible via generic function location-class-dimensionality
- location-class-dimension is now implemented as a ordinary fn which calls location-class-dimensionality
* b1@/cvsroot/littleb/b1/libraries/b/_config.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/test.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/dimension.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/math-concept.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/operators.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/quantity.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/unit.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core/printer.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/constants.lisp 1.4 (changed):
* this checkin has a bug which prevents .moles models from being produced
* b/biochem/complex/ files are now compiled
* moved test code to separate file b/biochem/complex/test
* fixed complex-reaction-type.set-rate-function bug
* location.size var default values are handled in base class now
* fixed field printing when *print-level* is bound (no longer prints #.field); removed b-debugger hook
* quote printer now always prints 'A even when *print-pretty* is nil
* using simplify-number in b/math to reduce values to floats (rather than rationals)
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/test.lisp 1.2 (changed):
*** empty log message ***
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/std-rate-functions.lisp 1.4 (changed):
Changed argument order in underlying custom rate-functions - user-supplied constants are now the first arg (better for constructing arglist dynamically)
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.5 (changed):
Complex-reaction-exists rule now generates dynamic rule naming it after complex reaction
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.9 (changed):
Defmonomer documentation string now comes before site definitions
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.7 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.8 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/util/dictionary.lisp 1.3 (changed):
Looks like complex reactions and rate functions are working!!
(still need to fix the matlab code generation bug, though)
* b1@/cvsroot/littleb/b1/src/core/expose.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core/rule-patterns.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/global/constants.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/include/include.lisp 1.4 (changed):
Misc changes - got rid of bug where circular package dependencies causes stack overflow
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.6 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.3 (changed):
Now exporting location-class-dimensionality from b/biochem
2007-10-23
* b1@/cvsroot/littleb/b1/libraries/b/biochem/aggregate.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/enzymatic-reaction.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/localization.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/membrane-apposition.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-inference.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-type.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/species-type.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/species.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/std-rate-functions.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core-types/concept.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/constants.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/field.lisp 1.5 (changed):
Major update:
* reaction inference now implemented by dynamic rules (via ADD-RULE)
* def-custom-rate-function introduced; mass-action, hill function and custom-rate are now defined with this macro
- required changes to .SET-RATE-FUNCTION field
- necessary first step to accomodate complex-species-type rate calculators
* changed LOCATION-REQUIREMENT to LOCALIZATION object, now generated using @ infix operator
* tested examples/example4-enzymatic-reaction and segment-polarity/2cell and /dros-stripes-yippie
* running a bit slower; may need to tune math system
2007-10-22
* b1@/cvsroot/littleb/b1/src/global/field.lisp 1.4 (changed):
Changed anonymous-fld-function print-object to pretty printer function
* b1@/cvsroot/littleb/b1/src/packages/pkgdecl.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/top-level-forms/defrule.lisp 1.3 (changed):
Fixed ADD-RULE bug - using INTERN in macro leads; add-rule is now exported from B package
* b1@/cvsroot/littleb/b1/src/include/include.lisp 1.3 (changed):
Fixed circular include dependency message
* b1@/cvsroot/littleb/b1/src/global/field.lisp 1.3 (changed):
Fixed printing of anonymous fld functions
2007-10-20
* b1@/cvsroot/littleb/b1/src/global/field.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/packages/portable-pkg.lisp 1.2 (changed):
Added anonymous-fld-function funcallable object which has find-or-create semantics and prints as ?.(F ARGS) or ?.F
* b1@/cvsroot/littleb/b1/src/portable/clos.lisp 1.2 (changed):
Removed redundant functions class-slots1 class-slot-list
2007-10-18
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.5 (changed):
* b1@/cvsroot/littleb/b1/src/include/compile-include-path.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/reader/token-reader.lisp 1.3 (changed):
*** empty log message ***
* b1@/cvsroot/littleb/b1/src/core/query.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/global/object.lisp 1.4 (changed):
* b1@/cvsroot/littleb/b1/src/packages/pkgdecl.lisp 1.4 (changed):
Added lookup (fast-query) capability
2007-10-17
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.4 (changed):
Graphs of complex-patterns are now canonicalized properly
2007-10-15
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/include/include.lisp 1.2 (changed):
Fixed include warn bug - when included file modifies an unrelated package
* b1@/cvsroot/littleb/b1/libraries/b/biochem.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/ode.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/pattern-match.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core-types/concept-class.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/core/rule-patterns.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/object.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/packages/pkgdecl.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/top-level-forms/defrule.lisp 1.2 (changed):
Separated out reaction inference functionality
2007-10-10
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-inference.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/reaction-type.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex/species-type.lisp 1.1 (added):
*** empty log message ***
* b1@/cvsroot/littleb/b1/get-cvs-modules.bat 1.2 (changed):
Now correctly checksout lisa from sourceforge
2007-10-09
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/membrane-apposition.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-type.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/species-type.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/math-printer.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/b/math/reader.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/examples/g6pi.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/core/query.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/name.lisp 1.3 (changed):
* b1@/cvsroot/littleb/b1/src/reader/token-reader.lisp 1.2 (changed):
* fixed assert-instances bug inside QUERY
2007-10-07
* b1@/cvsroot/littleb/b1/src/global/name.lisp 1.2 (changed):
*** empty log message ***
2007-09-28
* b1@/cvsroot/littleb/b1/src/core-types/concept-class.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/global/object.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/packages/pkgdecl.lisp 1.2 (changed):
* b1@/cvsroot/littleb/b1/src/top-level-forms/initialize.lisp 1.2 (changed):
Fixed object-expander bug (old object-expanders were not deleted on INIT)
2007-09-25
* b1@/cvsroot/littleb/b1/.cvsignore 1.1 (added):
* b1@/cvsroot/littleb/b1/asdf/LICENSE 1.1 (added):
* b1@/cvsroot/littleb/b1/asdf/README 1.1 (added):
* b1@/cvsroot/littleb/b1/asdf/asdf+.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/b1.asd 1.1 (added):
* b1@/cvsroot/littleb/b1/b1.asd 1.2 (changed):
* b1@/cvsroot/littleb/b1/libraries/.cvsignore 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b-user/3d-ode-biochemistry.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b-user/non-dimensional-ode-biochemistry.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/.cvsignore 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/_config.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/2-dimensional.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/3-dimensional.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/aggregate.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/basic-ode-modelling.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/complex.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization/2d.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization/3d.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/dimensionalization/null.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/enzymatic-reaction.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/location.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/membrane-apposition.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell/flat-lattice.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multisided-cell/hex-lattice.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/multistate-reactant.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/non-dimensional.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/ode.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-inference.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction-type.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/reaction.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/species-type.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/species.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/std-rate-functions.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/biochem/timings.txt 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/graph.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/gui.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/b/math/defer-expression.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/dimension.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/dimensional-methods.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/b/math/math-concept.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/math-expression.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/math-printer.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/non-dimensionalize.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/ode-var.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/operators.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/product-expression-printer.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/product-expression.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/b/math/sum-expression-printer.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/b/math/sum-expression.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/b/matlab/ode-translation.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/b/units/standard.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/examples/example2-reversible.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/examples/example3-manual es complex.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/examples/example4-enzymatic-reaction.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/examples/g6pi-er.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/libraries/examples/g6pi.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/libraries/examples/species/mkp.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/readme.txt 1.1 (added):
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* b1@/cvsroot/littleb/b1/src/reader/bq-reader.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/src/reader/char-reader.lisp 1.1 (added):
* b1@/cvsroot/littleb/b1/src/reader/field-reader.lisp 1.1 (added):
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* b1@/cvsroot/littleb/b1/src/reader/more-editor-funcs.lisp 1.1 (added):
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*** empty log message ***
* b1@/cvsroot/littleb/b1/get-cvs-modules.bat 1.1 (added):
* b1@/cvsroot/littleb/b1/get-cvs-modules.sh 1.1 (added):
Initial commit
