Merge branch 'main' of https://github.com/sys-bio/temp-biomodels

sys-bio · Jun 3, 2024 · 412eb6a · 412eb6a
2 parents c4279f6 + 1ce6fb4
commit 412eb6a
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diff --git a/final/BIOMD0000000250/BIOMD0000000250_url.sedml b/final/BIOMD0000000250/BIOMD0000000250_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000251/BIOMD0000000251_url.sedml b/final/BIOMD0000000251/BIOMD0000000251_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000252/BIOMD0000000252_url.sedml b/final/BIOMD0000000252/BIOMD0000000252_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000253/BIOMD0000000253_url.sedml b/final/BIOMD0000000253/BIOMD0000000253_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000254/BIOMD0000000254_url.sedml b/final/BIOMD0000000254/BIOMD0000000254_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000255/BIOMD0000000255_url.sedml b/final/BIOMD0000000255/BIOMD0000000255_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000256/BIOMD0000000256_url.sedml b/final/BIOMD0000000256/BIOMD0000000256_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000257/BIOMD0000000257_url.sedml b/final/BIOMD0000000257/BIOMD0000000257_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000258/BIOMD0000000258_url.sedml b/final/BIOMD0000000258/BIOMD0000000258_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000259/BIOMD0000000259_url.sedml b/final/BIOMD0000000259/BIOMD0000000259_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000260/BIOMD0000000260_url.sedml b/final/BIOMD0000000260/BIOMD0000000260_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000261/BIOMD0000000261_url.sedml b/final/BIOMD0000000261/BIOMD0000000261_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000262/BIOMD0000000262_url.sedml b/final/BIOMD0000000262/BIOMD0000000262_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000263/BIOMD0000000263_url.sedml b/final/BIOMD0000000263/BIOMD0000000263_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000264/BIOMD0000000264_url.sedml b/final/BIOMD0000000264/BIOMD0000000264_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000265/BIOMD0000000265_url.sedml b/final/BIOMD0000000265/BIOMD0000000265_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000266/BIOMD0000000266_url.sedml b/final/BIOMD0000000266/BIOMD0000000266_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000267/BIOMD0000000267_url.sedml b/final/BIOMD0000000267/BIOMD0000000267_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000268/BIOMD0000000268_url.sedml b/final/BIOMD0000000268/BIOMD0000000268_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000269/BIOMD0000000269_url.sedml b/final/BIOMD0000000269/BIOMD0000000269_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000270/BIOMD0000000270_url.sedml b/final/BIOMD0000000270/BIOMD0000000270_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000271/BIOMD0000000271_url.sedml b/final/BIOMD0000000271/BIOMD0000000271_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000272/BIOMD0000000272_url.sedml b/final/BIOMD0000000272/BIOMD0000000272_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000273/BIOMD0000000273_url.sedml b/final/BIOMD0000000273/BIOMD0000000273_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000274/BIOMD0000000274_url.sedml b/final/BIOMD0000000274/BIOMD0000000274_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000275/BIOMD0000000275_url.sedml b/final/BIOMD0000000275/BIOMD0000000275_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000276/BIOMD0000000276_url.sedml b/final/BIOMD0000000276/BIOMD0000000276_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000277/BIOMD0000000277_url.sedml b/final/BIOMD0000000277/BIOMD0000000277_url.sedml
@@ -5,7 +5,7 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
-      <algorithm name="CVODE" kisaoID="KISAO:0000019"/>
+      <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
   <listOfTasks>

diff --git a/final/BIOMD0000000278/lemaire04_addB.sedml b/final/BIOMD0000000278/lemaire04_addB.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_addC.sedml b/final/BIOMD0000000278/lemaire04_addC.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_addOPG.sedml b/final/BIOMD0000000278/lemaire04_addOPG.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_addOPG_addRANKL.sedml b/final/BIOMD0000000278/lemaire04_addOPG_addRANKL.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="100">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_addPTH.sedml b/final/BIOMD0000000278/lemaire04_addPTH.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_addR.sedml b/final/BIOMD0000000278/lemaire04_addR.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_removeB.sedml b/final/BIOMD0000000278/lemaire04_removeB.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_removeC.sedml b/final/BIOMD0000000278/lemaire04_removeC.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000278/lemaire04_removeR.sedml b/final/BIOMD0000000278/lemaire04_removeR.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="140" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000279/figA_blue.sedml b/final/BIOMD0000000279/figA_blue.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="150" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>

diff --git a/final/BIOMD0000000279/figA_green.sedml b/final/BIOMD0000000279/figA_green.sedml
@@ -5,10 +5,10 @@
   </listOfModels>
   <listOfSimulations>
     <uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="150" numberOfSteps="1000">
-      <algorithm name="Deterministic (LSODA)" kisaoID="KISAO_0000560">
+      <algorithm name="ODE solver" kisaoID="KISAO_0000694">
         <listOfAlgorithmParameters>
           <algorithmParameter name="Relative Tolerance" kisaoID="KISAO:0000209" value="1e-06"/>
-          <algorithmParameter name="Absolute Tolerance" kisaoID="KISAO:0000211" value="1e-12"/>
+          <algorithmParameter name="Absolute tolerance adjustment factor" kisaoID="KISAO:0000571" value="1e-12"/>
           <algorithmParameter name="Integrate Reduced Model" kisaoID="KISAO:0000216" value="0"/>
           <algorithmParameter name="Max Internal Steps" kisaoID="KISAO:0000415" value="10000"/>
         </listOfAlgorithmParameters>