biocham.pl 3.69 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 Apr 01, 2016 14  Biocham is mainly composed of:  Thierry Martinez committed Oct 15, 2015 15 16 17  \\begin{itemize} \\item a rule-based language for modeling biochemical systems (compatible with SBML and SBGN),  FAGES Francois committed Apr 01, 2016 18 19 20 21 22 23  \\item static analysers for inferring various dynamical properties from the structure of the model; \\item simulators for the different semantics: continuous (differential equations), stochastic, asynchronous Boolean; \\item a temporal logic based language to formalize the temporal behaviours of biological systems, validate models with respect to such specifications by model-checking methods, infer parameter values in high dimension with temporal logic constraints, measure parameter sensitivity indices and robustness of temporal properties;  Thierry Martinez committed Oct 15, 2015 24  \\item unique features for developing/correcting/completing/reducing/coupling  FAGES Francois committed Apr 01, 2016 25  models.  Thierry Martinez committed Oct 15, 2015 26 27 28 29  \\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 30 ').  Thierry Martinez committed Oct 09, 2015 31   FAGES Francois committed Aug 05, 2016 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 % FF ca cree un bug que je ne comprends pas %:- doc(' %Biocham file names are suffixed by \\texttt{.bc}. In a Biocham file, everything following the character percent is a comment. %Some other file formats are used. %Biocham models can be imported from, and exported to, other file formats using the following suffixes: %\\begin{itemize} %\\item \\texttt{.xml} for Systems Biology Markup Language (SBML) files, more precisely SBML2 files for reaction systems and SBML3qual files for influence systems; %\\item \\texttt{.ode} for Ordinary Differential Equation files (ODEs in XXPAUT format), allowing us to import a reaction system from ODEs using a heuristic inference algorithm described in \\cite{FGS15tcs}. %\\end{itemize} %Biocham numerical data time series can be imported/exported in %\\begin{itemize} %\\item \\texttt{.csv} comma-separated values format (spreadsheet format). %\\end{itemize} %The following files can also be used to export some Biocham objects: %\\begin{itemize} %\\item \\texttt{.tex} LaTeX format for exporting ODEs and graphs; %\\item \\texttt{.dot} for exporting graphs; %\\item \\texttt{.plot} for exporting numerical data time series; %\\item \\texttt{.smv} for exporting boolean transition systems and Computation Tree Logic (CTL) queries for the NuSMV model-checker; %\\item \\texttt{.dot} for exporting graphs. %\\end{itemize} %').  Thierry Martinez committed Oct 09, 2015 56 57 58 59 60 61 start :- about, initialize, do_arguments.  Thierry Martinez committed Jul 13, 2016 62 63 64 65 66 67 68 :- dynamic(initialized/0). initialize :- initialized, !.  Thierry Martinez committed Oct 09, 2015 69 initialize :-  Thierry Martinez committed Oct 15, 2015 70  initialize_library_path,  Thierry Martinez committed Oct 16, 2015 71  set_prolog_flag(allow_variable_name_as_functor, true),  Thierry Martinez committed Oct 09, 2015 72  prolog_history(enable),  Thierry Martinez committed Oct 09, 2015 73  set_counter(item_id, 0),  Thierry Martinez committed Oct 16, 2015 74  set_plot_driver(gnu_plot),  Thierry Martinez committed Oct 23, 2015 75 76 77  set_image_viewer_driver(open_file), set_draw_graph_driver(graph_pdf), nb_setval(graph_pdf, 0),  Thierry Martinez committed Oct 25, 2015 78 79  nb_setval(current_models, []), load_biocham('library:initial'),  Thierry Martinez committed Jul 13, 2016 80 81  new_model, assertz(initialized).  Thierry Martinez committed Oct 09, 2015 82 83   Thierry Martinez committed Oct 15, 2015 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 :- 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 104 105 biocham_command :- doc('Declares a command for the top-level.').  Thierry Martinez committed Oct 15, 2015 106 107   Thierry Martinez committed Oct 16, 2015 108 109 110 111 112 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.').