Commit a5b39258 authored by FAGES Francois's avatar FAGES Francois
Browse files

doc

parent 7df163bb
......@@ -20,6 +20,7 @@ url('http://lifeware.inria.fr/biocham/').
about :-
biocham_command,
doc('lists the version, copyright, license and URL of Biocham'),
version(Version),
copyright(Copyright),
license(License),
......
......@@ -29,28 +29,6 @@
software.
').
:- 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}
').
start :-
about,
......
......@@ -8,6 +8,7 @@
]
).
:- doc('Events can be used to change some parameter values once a condition gets satisfied. This is useful to implement discrete events such as a the division of cell mass by 2 at each division in a model of the cell cycle, or hybrid automata which chain different continuous semantics (ODEs), or massively for stochastic simulators defined by events and hybrid differential-stochastic silmulators \\cite{CFJS15tomacs}. ').
:- devdoc('\\section{Commands}').
......
......@@ -12,10 +12,10 @@
]
).
:- doc('Firt-Order Linear Time Logic with linear constraints over the reals, FO-LTL(Rlin), can be used to specify semi-qualitative semi-quantitative properties of the dynamical behavior of the system, in a much more flexible manner than by curves to fit. The syntax of FO-LTL(Rlin) formulas is as follows:').
:- doc('Firt-Order Linear Time Logic with linear constraints over the reals, FO-LTL(Rlin), can be used to specify semi-qualitative semi-quantitative properties of the dynamical behavior of the system, in a much more flexible manner than by curves to fit \\cite{FT15book}. The syntax of FO-LTL(Rlin) formulas is as follows:').
:- dev('\\section{Grammar}').
:- devdoc('\\section{Grammar}').
:- devcom('FF: quantifiers exists and forall are missing.').
......
......@@ -52,6 +52,12 @@ oderef(X) :-
:- devdoc('\\section{Commands}').
:- devcom('FF: The status of ODE systems in Biocham v4 is not so clear. Are they first class or not ?').
:- devcom('FF: import_reactions_from_odes is a model inference command which should be separated from the bureaucratic commands about ode systems.').
:- devcom('FF: import_influences_from_odes should be useful also.').
new_ode_system :-
biocham_command,
......
......@@ -9,3 +9,28 @@
open_file(Filename) :-
process_create(path('open'), [Filename], [process(Pid)]),
process_wait(Pid, exit(0)).
:- 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.').
:- doc('
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}
').
......@@ -2,7 +2,7 @@
** Overview
- doc.pl
- biocham.pl
- about.pl
** Biocham files
- platform/current/platform.pl
** Installing and Running Biocham Locally
- commandline.pl
......@@ -12,6 +12,7 @@
- filename.pl
** Interpreter top-level
- toplevel.pl
- about.pl
- namespace.pl
* Biochemical and mathematical objects
** Syntax
......@@ -70,28 +71,29 @@
- invariants.pl
** Detecting model reductions and expansions
* Simulations
** ODE
** ODE simulations
- arithmetic_rules.pl
- formal_derivation.pl
- gsl.pl
- numerical_simulation.pl
** Plotting and exporting the result of simulations
- plot.pl
** Bifurcations
** Stochastic simulations
** Hybrid simulations
* Behavior specification and verification
* Qualitative behavior specification and verification
** Boolean attractors
- influence_properties.pl
** Boolean temporal logic CTL
- ctl.pl
- nusmv.pl
* Quantitative behavior specification and verification
** Numerical data time series
- tables.pl
** Numerical temporal logic FOLTL(Rlin)
** Numerical temporal logic
- foltl.pl
** Sensitivity analysis
** Robustness analysis
** Bifurcations
** Sensitivity of FO-LTL(Rlin) properties
** Robustness of FO-LTL(Rlin) properties
* Model inference
** Parameter search
** Model reduction
......
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