first stab at a level 3, version 1 issue of the dsmts

Author: [email protected]

dsmts-001-01.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath01 "Birth-death model (001), variant 01"
-@units
- substance=item
+@model:3.1.1=BirthDeath01 "Birth-death model (001), variant 01"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-02.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath02 "Birth-death model (001), variant 02"
-@units
- substance=item
+@model:3.1.1=BirthDeath02 "Birth-death model (001), variant 02"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-03.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath03 "Birth-death model (001), variant 03"
-@units
- substance=item
+@model:3.1.1=BirthDeath03 "Birth-death model (001), variant 03"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-04.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath04 "Birth-death model (001), variant 04"
-@units
- substance=item
+@model:3.1.1=BirthDeath04 "Birth-death model (001), variant 04"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-05.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath05 "Birth-death model (001), variant 05"
-@units
- substance=item
+@model:3.1.1=BirthDeath05 "Birth-death model (001), variant 05"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-06.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath06 "Birth-death model (001), variant 06"
-@units
- substance=item
+@model:3.1.1=BirthDeath06 "Birth-death model (001), variant 06"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-07.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath07 "Birth-death model (001), variant 07"
-@units
- substance=item
+@model:3.1.1=BirthDeath07 "Birth-death model (001), variant 07"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-08.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath08 "Birth-death model (001), variant 08"
-@units
- substance=item
+@model:3.1.1=BirthDeath08 "Birth-death model (001), variant 08"
+ s=item,t=second,v=litre
 @compartments
  Cell=1
 @species

dsmts-001-09.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath09 "Birth-death model (001), variant 09"
-@units
- substance=item
+@model:3.1.1=BirthDeath09 "Birth-death model (001), variant 09"
+ s=item,t=second,v=litre
 @compartments
  Cell=2
 @species

dsmts-001-10.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath10 "Birth-death model (001), variant 10"
-@units
- substance=item
+@model:3.1.1=BirthDeath10 "Birth-death model (001), variant 10"
+ s=item,t=second,v=litre
 @compartments
  Cell=1
 @species

dsmts-001-11.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath11 "Birth-death model (001), variant 11"
-@units
- substance=item
+@model:3.1.1=BirthDeath11 "Birth-death model (001), variant 11"
+ s=item,t=second,v=litre
 @compartments
  Cell=2
 @species

dsmts-001-12.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath12 "Birth-death model (001), variant 12"
-@units
- substance=item
+@model:3.1.1=BirthDeath12 "Birth-death model (001), variant 12"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-13.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath13 "Birth-death model (001), variant 13"
-@units
- substance=item
+@model:3.1.1=BirthDeath13 "Birth-death model (001), variant 13"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-14.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath14 "Birth-death model (001), variant 14"
-@units
- substance=item
+@model:3.1.1=BirthDeath14 "Birth-death model (001), variant 14"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-15.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath15 "Birth-death model (001), variant 15"
-@units
- substance=item
+@model:3.1.1=BirthDeath15 "Birth-death model (001), variant 15"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-16.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath16 "Birth-death model (001), variant 16"
-@units
- substance=item
+@model:3.1.1=BirthDeath16 "Birth-death model (001), variant 16"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-001-17.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath17 "Birth-death model (001), variant 17"
-@units
- substance=item
+@model:3.1.1=BirthDeath17 "Birth-death model (001), variant 17"
+ s=item,t=second,v=litre
 @compartments
  Cell=1
 @species

dsmts-001-18.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath18 "Birth-death model (001), variant 18"
-@units
- substance=item
+@model:3.1.1=BirthDeath18 "Birth-death model (001), variant 18"
+ s=item,t=second,v=litre
 @compartments
  Cell=0.5
 @species

dsmts-001-19.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BirthDeath01 "Birth-death model (001), variant 01"
-@units
- substance=item
+@model:3.1.1=BirthDeath01 "Birth-death model (001), variant 01"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-01.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath01 "Immigration-Death (002), variant 01"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath01 "Immigration-Death (002), variant 01"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-02.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath02 "Immigration-Death (002), variant 02"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath02 "Immigration-Death (002), variant 02"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-03.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath03 "Immigration-Death (002), variant 03"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath03 "Immigration-Death (002), variant 03"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-04.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath04 "Immigration-Death (002), variant 04"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath04 "Immigration-Death (002), variant 04"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-05.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath05 "Immigration-Death (002), variant 05"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath05 "Immigration-Death (002), variant 05"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-06.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath06 "Immigration-Death (002), variant 06"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath06 "Immigration-Death (002), variant 06"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-07.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath07 "Immigration-Death (002), variant 07"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath07 "Immigration-Death (002), variant 07"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-08.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath08 "Immigration-Death (002), variant 08"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath08 "Immigration-Death (002), variant 08"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-09.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath09 "Immigration-Death (002), variant 09"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath09 "Immigration-Death (002), variant 09"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-002-10.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=ImmigrationDeath09 "Immigration-Death (002), variant 10"
-@units
- substance=item
+@model:3.1.1=ImmigrationDeath09 "Immigration-Death (002), variant 10"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-01.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation01 "Dimerisation model (003), variant 01"
-@units
- substance=item
+@model:3.1.1=Dimerisation01 "Dimerisation model (003), variant 01"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-02.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation02 "Dimerisation model (003), variant 02"
-@units
- substance=item
+@model:3.1.1=Dimerisation02 "Dimerisation model (003), variant 02"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-03.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation03 "Dimerisation model (003), variant 03"
-@units
- substance=item
+@model:3.1.1=Dimerisation03 "Dimerisation model (003), variant 03"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-04.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation04 "Dimerisation model (003), variant 04"
-@units
- substance=item
+@model:3.1.1=Dimerisation04 "Dimerisation model (003), variant 04"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-05.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation05 "Dimerisation model (003), variant 05"
-@units
- substance=item
+@model:3.1.1=Dimerisation05 "Dimerisation model (003), variant 05"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-06.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation06 "Dimerisation model (003), variant 06"
-@units
- substance=item
+@model:3.1.1=Dimerisation06 "Dimerisation model (003), variant 06"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-003-07.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=Dimerisation06 "Dimerisation model (003), variant 06"
-@units
- substance=item
+@model:3.1.1=Dimerisation06 "Dimerisation model (003), variant 06"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-004-01.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BatchImmigrationDeath01 "Batch Immigration-Death (004), variant 01"
-@units
- substance=item
+@model:3.1.1=BatchImmigrationDeath01 "Batch Immigration-Death (004), variant 01"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-004-02.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BatchImmigrationDeath02 "Batch Immigration-Death (004), variant 02"
-@units
- substance=item
+@model:3.1.1=BatchImmigrationDeath02 "Batch Immigration-Death (004), variant 02"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-004-03.mod

@@ -1,6 +1,5 @@
-@model:2.4.1=BatchImmigrationDeath03 "Batch Immigration-Death (004), variant 03"
-@units
- substance=item
+@model:3.1.1=BatchImmigrationDeath03 "Batch Immigration-Death (004), variant 03"
+ s=item,t=second,v=litre
 @compartments
  Cell
 @species

dsmts-userguide.tex

@@ -53,7 +53,7 @@ \subsection{Contents of the Test Suite}
 
 The test directory contains the following files for each test model: 
 \begin{itemize}
-\item \verb$<model>.xml$: the SBML Level 2 test model
+\item \verb$<model>.xml$: the SBML Level 3 test model
 \item \verb$<model>-mean.csv$: means of the simulation results at $t = 0,1,\ldots,50$
 \item \verb$<model>-sd.csv$: standard deviations of the simulation results at $t = 0,1,\ldots,50$
 \item \verb$<model>.mod$: documentation on the model in the form of SBML-shorthand