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Commit 2e667515 authored by FAGES Francois's avatar FAGES Francois
Browse files

video on the web

parent b88ee038
......@@ -37,7 +37,7 @@ infer_reactions_from_pivp(PIVP) :-
parameters:set_parameter(fast, Fast).
:- doc('
\\begin{example} In the this example dual species are introduced for x because of its initial negative value but not for y: \n
\\begin{example} In this example dual species are introduced for x because of its initial negative value but not for y: \n
').
:- biocham_silent(clear_model).
:- biocham(infer_reactions_from_pivp((-1,(d(x)/dt= y-x)); (0,(d(y)/dt=2-y)))).
......
......@@ -32,7 +32,7 @@
</head>
<body>
<h1>The Biochemical Abstract Machine BIOCHAM 4</h1>
<h1>version 4.1.25 January 2019</h1>
<h1>version 4.1.26 March 2019</h1>
<div class="authors">
<p>
......@@ -52,7 +52,7 @@ Biocham 4 was released in September
It also lacks some features of Biocham 3 concerning model comparisons (by subgraph epimorphisms), sensitivity analyses and the graphical user interface.
For these reasons Biocham 3 is still active on <a href="http://lifeware.inria.fr/biocham3">http://lifeware.inria.fr/biocham3</a> but no longer maintained.
<h2>Overview</h2>
<h2>Overview (see <a href="biocham4.mov" biocham4.mov>video</a>)</h2>
<p>The Biochemical Abstract Machine (Biocham) is a modelling
environment for systems biology and synthetic biology.<br>
</p>
......@@ -62,7 +62,9 @@ environment for systems biology and synthetic biology.<br>
<li>a rule-based language for modeling biochemical processes
with reactions (compatible with SBML) and/or influences (compatible with QualSBML),</li>
<li>a hierarchy of semantics (differential, stochastic, Petri Net, Boolean) to interpret and analyze such models,</li>
<li>a temporal logic based language to formalize the temporal behaviors of biochemical systems and validate models with respect to such specifications.<br>
<li>a temporal logic based language to formalize imprecise behaviors of biochemical systems and validate or synthesize models with respect to such specifications.<br>
</li>
<li>a command line language interfaced with jupyter for the notebook (i.e. time line view of the commands) and the grapical user interface (i.e. static view of the commands).
</li>
</ul>
<p>
......@@ -75,7 +77,10 @@ combining reaction and influence systems <a href="https://lifeware.inria.fr/wiki
infering reaction systems from ODEs <a href="https://lifeware.inria.fr/wiki/Main/Publications#FGS15tcs">[FGS15tcs]</a> (used for importing Matlab models in SBML within <a href="https://github.com/sbmlteam/moccasin">Mocassin</a>),
</li>
<li>
synthesizing reaction systems for computing real functions presented as solutions of polynomial initial value problems (PIVPs) <a href="https://lifeware.inria.fr/wiki/Main/Publications#FLBP17cmsb">[FLBP17cmsb]</a>,
detecting model reductions between reaction models and in model repositories such as biomodels <a href="https://lifeware.inria.fr/wiki/Main/Publications#GFS10bi">[FS10bi]</a> , based on reaction graph structures (concept of subgraph epimorphisms <a href="https://lifeware.inria.fr/wiki/Main/Publications#GFMSS14dam">[GFMSS14dam]</a>).
</li>
<li>
synthesizing reaction systems for executing imperative programs or computing real functions presented as solutions of polynomial initial value problems (PIVPs) <a href="https://lifeware.inria.fr/wiki/Main/Publications#FLBP17cmsb">[FLBP17cmsb]</a>,
</li>
<li>
checking or enumerating temporal properties of the (asynchronous non-deterministic) Boolean dynamics in Computation Tree Logic (CTL) using a symbolic model-checker <a href="https://lifeware.inria.fr/wiki/Main/Publications#CF03cmsb">[CF03cmsb]</a>,
......@@ -95,9 +100,6 @@ optimizing model parameters for satisfying FO-LTL(Rlin) constraints including ro
<li>
solving tropical equilibration problems for reasoning about orders of magnitudes in quantitative models <a href="https://lifeware.inria.fr/wiki/Main/Publications#SFR14amb">[SFR14amb]</a>,
</li>
<li>
(in Biocham 3, available in Biocham 4 in Fall 2018) the detection of model reductions within model repositories such as biomodels <a href="https://lifeware.inria.fr/wiki/Main/Publications#GFS10bi">[FS10bi]</a> , based on the structure of the reaction graphs (subgraph epimorphisms <a href="https://lifeware.inria.fr/wiki/Main/Publications#GFMSS14dam">[GFMSS14dam]</a>).
</li>
</ul>
<p>Biocham is a free software protected by the <a
href="http://www.gnu.org/copyleft/gpl.html">GNU General Public License
......@@ -108,24 +110,31 @@ of this software.<br>
<p>Feedback on the use of Biocham in applications, research or teaching
are particularly welcomed. </p>
<h2>Biocham notebook online</h2>
<p> Try the <a href="http://lifeware.inria.fr:8888/notebooks/examples/tutorial/tutorialShort.ipynb">short tutorial</a> notebook (presented at <a href="https://assb.lri.fr/fr/programme.php"> aSSB 2018</a>) or the <a href="http://lifeware.inria.fr:8888/notebooks/examples/tutorial/tutorialLongHistory.ipynb">historical tutorial</a> notebook (presented at <a href="https://www.etit.tu-darmstadt.de/cmsb2017/cmsb_2/home/index.en.jsp"> CMSB 2017</a>) on our server.</p>
<ul>
<li>Demonstration <a href="biocham4.mov" biocham4.mov>video</a> (with comments in French)</li>
<li> Try the <a href="http://lifeware.inria.fr:8888/notebooks/examples/tutorial/tutorialShort.ipynb">short tutorial</a> notebook (on our server presented at <a href="https://assb.lri.fr/fr/programme.php"> aSSB 2018</a>)</li>
<li> or the <a href="http://lifeware.inria.fr:8888/notebooks/examples/tutorial/tutorialLongHistory.ipynb">historical tutorial</a> notebook (presented at <a href="https://www.etit.tu-darmstadt.de/cmsb2017/cmsb_2/home/index.en.jsp"> CMSB 2017</a>).</li>
<p>
<li>
Try the other examples, or upload your own ones, on our <a href="http://lifeware.inria.fr:8888/">online notebook</a>.
</p>
</li>
</ul>
<h2>Documentation</h2>
<p>Reference manual in <a href="doc/index.html">html</a></p>
<ul>
<li>Reference manual in <a href="doc/index.html">html</a></li>
</ul>
<h2>Download and Installation</h2>
<p><span style="text-decoration: underline;">Source version:</span>&nbsp;
<a href="biocham.zip">biocham.zip</a>. </p>
<p>The installation then basically proceeds by using the Unix shell script<br>
<ul>
<li><span style="text-decoration: underline;">Source version:</span>&nbsp;
<a href="biocham.zip">biocham.zip</a>. </li>
<li>The installation then basically proceeds by using the Unix shell script<br>
<code>./install.sh</code>
</p>
<p><span style="text-decoration: underline;">Previous versions:</span>&nbsp;
<a href="biocham4.0.zip">biocham4.0.zip</a>, <a href="http://lifeware.inria.fr/biocham3/">biocham3</a>. </p>
</li>
<li><span style="text-decoration: underline;">Previous versions:</span>&nbsp;
<a href="biocham4.0.zip">biocham4.0.zip</a>, <a href="http://lifeware.inria.fr/biocham3/">biocham3</a>. </li>
</ul>
<h2>Feedback and bug reports:</h2>
<p>Mail to <a href="mailto:biocham@inria.fr">biocham@inria.fr</a>
</p>
......
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