Add build files to project

.github/workflows/python-app.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -e . 
         pip install html2text
         cd tests
         echo "Installing CopasiSE"

examples/Array_of_oscillating_cells/ex3case1.sh

@@ -6,7 +6,7 @@
 # add 10% noise on parameter alpha
 
 
-../../sbmodelr \
+sbmodelr \
  --output ex3case1.cps \
  -t Xex \
  -k 5 \

examples/Array_of_oscillating_cells/ex3case2.sh

@@ -6,7 +6,7 @@
 # add 10% noise on parameter alpha
 
 
-../../sbmodelr \
+sbmodelr \
  --output ex3case2.cps \
  -t Xex \
  -t Yex \

examples/Cells_in_medium/case1.cps

@@ -132,7 +132,7 @@ Reaction scheme where the products are created from the reactants and the change
 <li><a href="https://doi.org/10.1016/s0303-2647(97)01688-2">Wolf J, Heinrich R (1997) Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states. BioSystems 43:1–24</a></li>
 </ul>
 </p>
-<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p><hr/><p>Processed with sbmodelr to produce a set of 2 replicas of Selkov-Wolf-Heinrich.cps</p><pre style="font-size:small">../../sbmodelr --output case1.cps --add-medium --medium-volume 10 --transport Y --transport-k 3.2 --pn X 0.1 uni --pn Y 0.1 uni Selkov-Wolf-Heinrich.cps 2</pre></body>
+<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p><hr/><p>Processed with sbmodelr to produce a set of 2 replicas of Selkov-Wolf-Heinrich.cps</p><pre style="font-size:small">sbmodelr --output case1.cps --add-medium --medium-volume 10 --transport Y --transport-k 3.2 --pn X 0.1 uni --pn Y 0.1 uni Selkov-Wolf-Heinrich.cps 2</pre></body>
     </Comment>
     <ListOfCompartments>
       <Compartment key="Compartment_1" name="Cell_1" simulationType="fixed" dimensionality="3" addNoise="false">

examples/Cells_in_medium/case2.cps

@@ -132,7 +132,7 @@ Reaction scheme where the products are created from the reactants and the change
 <li><a href="https://doi.org/10.1016/s0303-2647(97)01688-2">Wolf J, Heinrich R (1997) Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states. BioSystems 43:1–24</a></li>
 </ul>
 </p>
-<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p><hr/><p>Processed with sbmodelr to produce a set of 5 replicas of Selkov-Wolf-Heinrich_k2.5.cps</p><pre style="font-size:small">../../sbmodelr --output case2.cps --add-medium --medium-volume 25 --transport Y --transport-k 1 --pn X 0.1 uni --pn Y 0.1 uni Selkov-Wolf-Heinrich_k2.5.cps 5</pre></body>
+<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p><hr/><p>Processed with sbmodelr to produce a set of 5 replicas of Selkov-Wolf-Heinrich_k2.5.cps</p><pre style="font-size:small">sbmodelr --output case2.cps --add-medium --medium-volume 25 --transport Y --transport-k 1 --pn X 0.1 uni --pn Y 0.1 uni Selkov-Wolf-Heinrich_k2.5.cps 5</pre></body>
     </Comment>
     <ListOfCompartments>
       <Compartment key="Compartment_1" name="Cell_1" simulationType="fixed" dimensionality="3" addNoise="false">

examples/Cells_in_medium/case3.cps

@@ -132,7 +132,7 @@ Reaction scheme where the products are created from the reactants and the change
 <li><a href="https://doi.org/10.1016/s0303-2647(97)01688-2">Wolf J, Heinrich R (1997) Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states. BioSystems 43:1–24</a></li>
 </ul>
 </p>
-<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p><hr/><p>Processed with sbmodelr to produce a set of 3 replicas of Selkov-Wolf-Heinrich_k1.5.cps</p><pre style="font-size:small">../../sbmodelr --output case3.cps --add-medium --medium-volume 15 --transport X --transport-k 4.16 --pn X 0.1 uni --pn Y 0.1 uni Selkov-Wolf-Heinrich_k1.5.cps 3</pre></body>
+<p style="font-size:small"><b>CC0 1.0 Universal</b>: To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Creative Commons CC0">CC0 Public Domain Dedication</a> for more information.</p><hr/><p>Processed with sbmodelr to produce a set of 3 replicas of Selkov-Wolf-Heinrich_k1.5.cps</p><pre style="font-size:small">sbmodelr --output case3.cps --add-medium --medium-volume 15 --transport X --transport-k 4.16 --pn X 0.1 uni --pn Y 0.1 uni Selkov-Wolf-Heinrich_k1.5.cps 3</pre></body>
     </Comment>
     <ListOfCompartments>
       <Compartment key="Compartment_1" name="Cell_1" simulationType="fixed" dimensionality="3" addNoise="false">

examples/Cells_in_medium/ex1case1.sh

@@ -8,7 +8,7 @@
 # that the ratio of volumes 2/10 = 0.2)
 
 
-../../sbmodelr \
+sbmodelr \
  --output case1.cps \
  --add-medium \
  --medium-volume 10 \

examples/Cells_in_medium/ex1case2.sh

@@ -9,7 +9,7 @@
 
 # total cell volume)
 
-../../sbmodelr \
+sbmodelr \
  --output case2.cps \
  --add-medium \
  --medium-volume 25 \

examples/Cells_in_medium/ex1case3.sh

@@ -9,7 +9,7 @@
 
 # total cell volume)
 
-../../sbmodelr \
+sbmodelr \
  --output case3.cps \
  --add-medium \
  --medium-volume 15 \

examples/Gene_Regulatory_Networks/ex6case1.cps

@@ -104,7 +104,7 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 3 replicas of GenExBase.cps</p><pre style="font-size:small">../../sbmodelr --output ex6case1.cps --ignore-compartments -n 3circle.gv -g G --pn G 0.8 uni --grn-V 3 --grn-a -1 --grn-h 4 GenExBase.cps 3</pre><p>notes of original file below:</p><hr/><h1>Gene expression</h1>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 3 replicas of GenExBase.cps</p><pre style="font-size:small">sbmodelr --output ex6case1.cps --ignore-compartments -n 3circle.gv -g G --pn G 0.8 uni --grn-V 3 --grn-a -1 --grn-h 4 GenExBase.cps 3</pre><p>notes of original file below:</p><hr/><h1>Gene expression</h1>
 <p>A basic model with one gene (<i>G</i>), representing a reaction for its basal rate of transcription (constant rate) and a degradation reaction (first order)</p>
 <pre>
  --> G -->

examples/Gene_Regulatory_Networks/ex6case1.sh

@@ -4,7 +4,7 @@
 
 # creates the repressilator network of 3 genes
 
-../../sbmodelr \
+sbmodelr \
  --output ex6case1.cps \
  --ignore-compartments \
  -n 3circle.gv \

examples/Neuron_networks_I/ex4case1.cps

@@ -53,7 +53,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 2 replicas of RSA_neuron.cps</p><pre style="font-size:small">../../sbmodelr --output ex4case1.cps -n ff2.dot --ode-synaptic V --synapse-g 0.08 RSA_neuron.cps 2</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 2 replicas of RSA_neuron.cps</p><pre style="font-size:small">sbmodelr --output ex4case1.cps -n ff2.dot --ode-synaptic V --synapse-g 0.08 RSA_neuron.cps 2</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
 <p>This is a 9-ODE model of a regular spiking neuron with adaptation (RSA), inspired by the Hodgin-Huxley model, first proposed by Pospischil et al. (2008) and re-used in Giannari and Astolfi (2022).</p>
 
 <p>Since this model is based on voltages and intensities, all variables and differential equations are defined under Global Quantities (there are no reactions and no species here). The model includes a sequence of current pulses (10 &micro;A/cm<sup>2</sup> for 1ms), spaced according to a Poisson distribution with an average of 1 pulse per 25 ms, which eventually cause action potentials.</p>

examples/Neuron_networks_I/ex4case1.sh

@@ -5,7 +5,7 @@
 # create a simple 2 neuron network where 1 feeds into 2
 
 
-../../sbmodelr \
+sbmodelr \
  --output ex4case1.cps \
  -n ff2.dot \
  --ode-synaptic V \

examples/Neuron_networks_I/ex4case2.cps

@@ -53,7 +53,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 2 replicas of RSA_neuron.cps</p><pre style="font-size:small">../../sbmodelr --output ex4case2.cps -n fb2.dot --ode-synaptic V --synapse-g 0.08 RSA_neuron.cps 2</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 2 replicas of RSA_neuron.cps</p><pre style="font-size:small">sbmodelr --output ex4case2.cps -n fb2.dot --ode-synaptic V --synapse-g 0.08 RSA_neuron.cps 2</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
 <p>This is a 9-ODE model of a regular spiking neuron with adaptation (RSA), inspired by the Hodgin-Huxley model, first proposed by Pospischil et al. (2008) and re-used in Giannari and Astolfi (2022).</p>
 
 <p>Since this model is based on voltages and intensities, all variables and differential equations are defined under Global Quantities (there are no reactions and no species here). The model includes a sequence of current pulses (10 &micro;A/cm<sup>2</sup> for 1ms), spaced according to a Poisson distribution with an average of 1 pulse per 25 ms, which eventually cause action potentials.</p>

examples/Neuron_networks_I/ex4case2.sh

@@ -5,7 +5,7 @@
 # create a simple 2 neuron network where 1 feeds into 2 and 2 feedsback to 1
 
 
-../../sbmodelr \
+sbmodelr \
  --output ex4case2.cps \
  -n fb2.dot \
  --ode-synaptic V \

examples/Neuron_networks_I/ex4case3.cps

@@ -53,7 +53,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 3 replicas of RSA_neuron.cps</p><pre style="font-size:small">../../sbmodelr --output ex4case3.cps -n ff3.dot --ode-synaptic V --synapse-g 0.08 --cn 0 uni RSA_neuron.cps 3</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 3 replicas of RSA_neuron.cps</p><pre style="font-size:small">sbmodelr --output ex4case3.cps -n ff3.dot --ode-synaptic V --synapse-g 0.08 --cn 0 uni RSA_neuron.cps 3</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
 <p>This is a 9-ODE model of a regular spiking neuron with adaptation (RSA), inspired by the Hodgin-Huxley model, first proposed by Pospischil et al. (2008) and re-used in Giannari and Astolfi (2022).</p>
 
 <p>Since this model is based on voltages and intensities, all variables and differential equations are defined under Global Quantities (there are no reactions and no species here). The model includes a sequence of current pulses (10 &micro;A/cm<sup>2</sup> for 1ms), spaced according to a Poisson distribution with an average of 1 pulse per 25 ms, which eventually cause action potentials.</p>

examples/Neuron_networks_I/ex4case3.sh

@@ -5,7 +5,7 @@
 # create a 3-neuron network where 1 feeds into 2, 2 into 3, and 1 also into 3
 
 
-../../sbmodelr \
+sbmodelr \
  --output ex4case3.cps \
  -n ff3.dot \
  --ode-synaptic V \

examples/Neuron_networks_I/ex4case4.cps

@@ -53,7 +53,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 6 replicas of RSA_neuron.cps</p><pre style="font-size:small">../../sbmodelr --output scpg.cps -n scpg.dot --ode-synaptic V --synapse-g 0.08 --cn 0 uni RSA_neuron.cps 6</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 6 replicas of RSA_neuron.cps</p><pre style="font-size:small">sbmodelr --output scpg.cps -n scpg.dot --ode-synaptic V --synapse-g 0.08 --cn 0 uni RSA_neuron.cps 6</pre><p>notes of original file below:</p><hr /><h1>RSA Neuron</h1>
 <p>This is a 9-ODE model of a regular spiking neuron with adaptation (RSA), inspired by the Hodgin-Huxley model, first proposed by Pospischil et al. (2008) and re-used in Giannari and Astolfi (2022).</p>
 
 <p>Since this model is based on voltages and intensities, all variables and differential equations are defined under Global Quantities (there are no reactions and no species here). The model includes a sequence of current pulses (10 &micro;A/cm<sup>2</sup> for 1ms), spaced according to a Poisson distribution with an average of 1 pulse per 25 ms, which eventually cause action potentials.</p>

examples/Neuron_networks_I/ex4case4.sh

@@ -3,7 +3,7 @@
 # example 4, case 4
 # spinal central pattern generator
 
-../../sbmodelr \
+sbmodelr \
  --output ex4case4.cps \
  -n scpg.dot \
  --ode-synaptic V \

examples/Neuron_networks_II/ex5case1.cps

@@ -72,7 +72,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">../../sbmodelr --output ex5case1.cps -n network100-200.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr/>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">sbmodelr --output ex5case1.cps -n network100-200.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr/>
 <h1>Izhikevich neuron model</h1>
     <p>This neuron model, formulated by Izhikevich, is a minimal model that still has easy biological interpretation, yet is as computationally efficient as the integrate-and-fire model. Known types of neurons can be simulated with this model by using different values for the parameters <i>a</i>, <i>b</i>, <i>c</i>, and <i>d</i> in the model.</p>
 <ul>

examples/Neuron_networks_II/ex5case1.sh

@@ -5,7 +5,7 @@
 # create network of 100 Izhikevic neurons connected in an Erdos topology with chemical synapses
 
 
-../../sbmodelr \
+sbmodelr \
  --output ex5case1.cps \
  -n network100-200.dot \
  --ode-synaptic v \

examples/Neuron_networks_II/ex5case1ready.cps

@@ -72,7 +72,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">../../sbmodelr --output ex5case1.cps -n network100-200.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr />
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">sbmodelr --output ex5case1.cps -n network100-200.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr />
 <h1>Izhikevich neuron model</h1>
     <p>This neuron model, formulated by Izhikevich, is a minimal model that still has easy biological interpretation, yet is as computationally efficient as the integrate-and-fire model. Known types of neurons can be simulated with this model by using different values for the parameters <i>a</i>, <i>b</i>, <i>c</i>, and <i>d</i> in the model.</p>
 <ul>

examples/Neuron_networks_II/ex5case2.cps

@@ -72,7 +72,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">../../sbmodelr --output ex5case2.cps -n network100-200_sf.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr/>
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">sbmodelr --output ex5case2.cps -n network100-200_sf.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr/>
 <h1>Izhikevich neuron model</h1>
     <p>This neuron model, formulated by Izhikevich, is a minimal model that still has easy biological interpretation, yet is as computationally efficient as the integrate-and-fire model. Known types of neurons can be simulated with this model by using different values for the parameters <i>a</i>, <i>b</i>, <i>c</i>, and <i>d</i> in the model.</p>
 <ul>

examples/Neuron_networks_II/ex5case2.sh

@@ -5,7 +5,7 @@
 # create network of 100 Izhikevic neurons connected in a scale free topology with chemical synapses
 # the network topology is supplied in the file network100-200_sf.dot
 
-../../sbmodelr \
+sbmodelr \
  --output ex5case2.cps \
  -n network100-200_sf.dot \
  --ode-synaptic v \

examples/Neuron_networks_II/ex5case2ready.cps

@@ -72,7 +72,7 @@
 
     </MiriamAnnotation>
     <Comment>
-      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">../../sbmodelr --output ex5case2.cps -n network100-200_sf.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr />
+      <body xmlns="http://www.w3.org/1999/xhtml"><p>Processed with sbmodelr to produce a set of 100 replicas of Izhikevich.cps</p><pre style="font-size:small">sbmodelr --output ex5case2.cps -n network100-200_sf.dot --ode-synaptic v --synapse-g 0.2 --synapse-link-g Izhikevich.cps 100</pre><p>notes of original file below:</p><hr />
 <h1>Izhikevich neuron model</h1>
     <p>This neuron model, formulated by Izhikevich, is a minimal model that still has easy biological interpretation, yet is as computationally efficient as the integrate-and-fire model. Known types of neurons can be simulated with this model by using different values for the parameters <i>a</i>, <i>b</i>, <i>c</i>, and <i>d</i> in the model.</p>
 <ul>