notebooks

library/examples/tutorial/oscillator.bc

+% Minimal mitotic oscillator after Albert Goldbeter 1991 PNAS
+% in Biocham v4 by F. Fages
+
+parameter(VM1=3, VM3=1, Kc=0.5, vi=0.025,
+kd=0.01, vd=0.25, Kd=0.02, K1=0.005,
+V2=1.5, K2=0.005, K3=0.0051, K4=0.005, V4=0.5). 
+
+vi for _=>Cyclin. 
+
+kd*Cyclin for Cyclin=>_. 
+
+Kinase*V2/(K2+Kinase) for Kinase=>KinaseP. 
+
+VM1*(KinaseP/(K1+KinaseP))*Cyclin/(Kc+Cyclin) for KinaseP=[Cyclin]=>Kinase. 
+
+Kinase*Protease*VM3/(K3+Protease) for Protease=[Kinase]=>ProteaseP. 
+
+ProteaseP*V4/(K4+ProteaseP) for ProteaseP=>Protease. 
+
+vd*Cyclin/(Kd+Cyclin)*ProteaseP for Cyclin=[ProteaseP]=>_. 
+
+
+present(Cyclin,0.01). present(Kinase,0.01). present(ProteaseP,0.01). present(KinaseP,0.99). present(Protease,0.99). 
+
+option(time:100).
+

library/examples/tutorial/tutorialLongHistory.ipynb

+tutorial17cmsb.ipynb
\ No newline at end of file

web/index.html

@@ -108,7 +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/MPCE/ASSB.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>) on our server.</p>
+<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>
 
 <p>
 Try the other examples, or upload your own ones, on our <a href="http://lifeware.inria.fr:8888/">online notebook</a>.