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<div class="authors">
<p>
EPI Lifeware, Inria Saclay - Ile de France <br>
<a href="http://lifeware.inria.fr/">EP Lifeware</a>, Inria Saclay - Ile de France <br>
<a href="http://lifeware.inria.fr/biocham4/">http://lifeware.inria.fr/biocham4/</a><br>
<br>
developpers mailing list: <a href="mailto:biocham@inria.fr">biocham@inria.fr</a><br>
......@@ -54,21 +54,51 @@ Biocham 4 was released in September
<h2>Overview</h2>
<p>The Biochemical Abstract Machine (Biocham) is a modelling
environment for systems biology, with some unique features for
static and dynamic analyses using temporal logic constraints.<br>
environment for systems biology and synthetic biology.<br>
</p>
<p>Biocham is mainly composed of :<br>
</p>
<ul>
<li>a rule-based language for modeling biochemical systems
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 simulate) 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>
<li>unique features for developing/analyzing/correcting/completing/calibrating/coupling/synthesizing
reaction and influence systems with respect to formal specifications of their behaviour.<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>
</ul>
<p>
Biocham implements some unique features for:
<ul>
<li>
combining reaction and influence systems <a href="https://lifeware.inria.fr/wiki/Main/Publications#FMRS18tcbb">[FMRS18tcbb]</a> and interpreting them in a hierarchy of continuous, stochastic, discrete and Boolean semantics related by abstraction <a href="https://lifeware.inria.fr/wiki/Main/Publications#FS08tcs">[FS088tcs]</a> or approximation relationships,
</li>
<li>
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>,
</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>,
</li>
<li>
reducing reaction systems with a CTL specification of their behavior <a href="https://lifeware.inria.fr/wiki/Main/Publications#CCFS06tcsb">[CCFS06tcsb]</a>,
</li>
<li>
analyzing numerical traces in First-Order Linear Time Logic with constraints over the reals, FO-LTL(Rlin) <a href="https://lifeware.inria.fr/wiki/Main/Publications#FT14book">[FT14book]</a>,
</li>
<li>
measuring the satisfaction, sensitivity and robustness of FO-LTL(Rlin) properties w.r.t. parameter distributions in differential or stochastic models <a href="https://lifeware.inria.fr/wiki/Main/Publications#RBFS11tcs">[RBFS11tcs]</a> <a href="https://lifeware.inria.fr/wiki/Main/Publications#RBFS09bi">[RBFS09bi]</a>,
</li>
<li>
optimizing model parameters for satisfying FO-LTL(Rlin) constraints including robustness constraints,
</li>
<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
GPL version 2</a>. This is an Open Source license that allows free
......@@ -78,7 +108,7 @@ 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/tutorial17cmsb.ipynb">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/tutorial17cmsb.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></p>
<p> Try the <a href="http://lifeware.inria.fr:8888/notebooks/examples/tutorial/tutorial17cmsb.ipynb">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/tutorial17cmsb.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>)</p>
<p>
Try the other examples, or upload your own ones, on our <a href="http://lifeware.inria.fr:8888/">online notebook</a>.
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