biocham.pl 1.79 KB
 Thierry Martinez committed Oct 08, 2015 1 2 3 :- module( biocham, [  Thierry Martinez committed Oct 09, 2015 4 5  start/0, initialize/0,  Thierry Martinez committed Oct 15, 2015 6  biocham_command/0,  Thierry Martinez committed Oct 15, 2015 7 8  biocham_command/1, library_path/1  Thierry Martinez committed Oct 08, 2015 9 10  ]).  Thierry Martinez committed Oct 15, 2015 11 12 13 :- doc(' The Biochemical Abstract Machine (Biocham) is a software environment for modeling and analyzing biochemical systems.  Thierry Martinez committed Oct 16, 2015 14  Biocham is mainly composed of~:  Thierry Martinez committed Oct 15, 2015 15 16 17 18 19 20 21 22 23 24 25 26 27  \\begin{itemize} \\item a rule-based language for modeling biochemical systems (compatible with SBML and SBGN), \\item different simulators (Boolean, differential, stochastic), \\item a temporal logic based language to formalize the temporal properties of a biological system and validate models with respect to such specifications, \\item unique features for developing/correcting/completing/reducing/coupling models, including the inference of kinetic parameters in high dimension from temporal logic constraints. \\end{itemize} Biocham is a free software protected by the GNU General Public License GPL version 2. This is an Open Source license that allows free usage of this software.  Thierry Martinez committed Oct 15, 2015 28 ').  Thierry Martinez committed Oct 09, 2015 29 30 31 32 33 34 35 36  start :- about, initialize, do_arguments. initialize :-  Thierry Martinez committed Oct 15, 2015 37  initialize_library_path,  Thierry Martinez committed Oct 09, 2015 38  prolog_history(enable),  Thierry Martinez committed Oct 09, 2015 39 40  set_counter(item_id, 0), new_model.  Thierry Martinez committed Oct 09, 2015 41 42   Thierry Martinez committed Oct 15, 2015 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 :- dynamic(library_path/1). initialize_library_path :- ( getenv('BIOCHAMLIB', LibraryPath) -> true ; executable_filename(ExecutableFilename), absolute_file_name( 'library/gsl_solver.c', LibraryFile, [relative_to(ExecutableFilename)] ), file_directory_name(LibraryFile, LibraryPath) ), assertz(library_path(LibraryPath)).  Thierry Martinez committed Oct 16, 2015 63 64 biocham_command :- doc('Declares a command for the top-level.').  Thierry Martinez committed Oct 15, 2015 65 66   Thierry Martinez committed Oct 16, 2015 67 68 69 70 71 biocham_command(_) :- doc(' With a * : declares a command for the top-level that can take an unlimited number of arguments. The additional arguments are given as a list in the last parameter.').