diff --git a/src/petab/parameters.jl b/src/petab/parameters.jl
index 8fdf6c5..4330572 100644
--- a/src/petab/parameters.jl
+++ b/src/petab/parameters.jl
@@ -141,7 +141,7 @@ function save_parameters_table(
     net_ids = @. string(_net_ids) * "_ps"
     df_nn = DataFrame(
         parameterId = net_ids, parameterScale = :lin, lowerBound = "-inf",
-        upperBound = "inf", nominalValue = "array", estimate = Int(estimate_net_parameters)
+        upperBound = "inf", nominalValue = "array", estimate = string(estimate_net_parameters)
     )
 
     df_save = vcat(df_mech, df_nn, cols = :union)
diff --git a/src/petab/yaml.jl b/src/petab/yaml.jl
index 0956483..9afb1c3 100644
--- a/src/petab/yaml.jl
+++ b/src/petab/yaml.jl
@@ -3,7 +3,7 @@ function save_petab_yaml(
         condition_table_id::Symbol
     )
     yaml_dict = Dict(
-        :format_version => 2,
+        :format_version => "2.0.0",
         :measurement_files => ["measurements.tsv"],
         :experiment_files => ["experiments.tsv"],
         :observable_files => ["observables.tsv"],
@@ -24,7 +24,9 @@ function save_petab_yaml(
     ext = Dict(
         :hybridization_files => ["hybridization.tsv"],
         :neural_nets => Dict(),
-        :array_files => String[]
+        :array_files => String[],
+        :version => "0.1.0",
+        :required => true
     )
     for (net_id, net_info) in nets_info
         ext[:neural_nets][net_id] = Dict(
diff --git a/test_cases/initialization/001/net1_ref.hdf5 b/test_cases/initialization/001/net1_ref.hdf5
index 4e75b37..bb7c50a 100644
Binary files a/test_cases/initialization/001/net1_ref.hdf5 and b/test_cases/initialization/001/net1_ref.hdf5 differ
diff --git a/test_cases/initialization/001/petab/parameters.tsv b/test_cases/initialization/001/petab/parameters.tsv
index db703ff..98b6f55 100644
--- a/test_cases/initialization/001/petab/parameters.tsv
+++ b/test_cases/initialization/001/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_layer1	lin	-inf	inf	0.0	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_layer1	lin	-inf	inf	0.0	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/initialization/001/petab/problem.yaml b/test_cases/initialization/001/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/initialization/001/petab/problem.yaml
+++ b/test_cases/initialization/001/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/initialization/002/net1_ref.hdf5 b/test_cases/initialization/002/net1_ref.hdf5
index 0fd8fb0..8e5762d 100644
Binary files a/test_cases/initialization/002/net1_ref.hdf5 and b/test_cases/initialization/002/net1_ref.hdf5 differ
diff --git a/test_cases/initialization/002/petab/parameters.tsv b/test_cases/initialization/002/petab/parameters.tsv
index db703ff..98b6f55 100644
--- a/test_cases/initialization/002/petab/parameters.tsv
+++ b/test_cases/initialization/002/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_layer1	lin	-inf	inf	0.0	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_layer1	lin	-inf	inf	0.0	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/initialization/002/petab/problem.yaml b/test_cases/initialization/002/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/initialization/002/petab/problem.yaml
+++ b/test_cases/initialization/002/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/initialization/003/net1_ref.hdf5 b/test_cases/initialization/003/net1_ref.hdf5
index 3eda11f..98a0b25 100644
Binary files a/test_cases/initialization/003/net1_ref.hdf5 and b/test_cases/initialization/003/net1_ref.hdf5 differ
diff --git a/test_cases/initialization/003/petab/parameters.tsv b/test_cases/initialization/003/petab/parameters.tsv
index db703ff..98b6f55 100644
--- a/test_cases/initialization/003/petab/parameters.tsv
+++ b/test_cases/initialization/003/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_layer1	lin	-inf	inf	0.0	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_layer1	lin	-inf	inf	0.0	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/initialization/003/petab/problem.yaml b/test_cases/initialization/003/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/initialization/003/petab/problem.yaml
+++ b/test_cases/initialization/003/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/001/grad_mech.tsv b/test_cases/sciml_problem_import/001/grad_mech.tsv
index 8dd5bd5..e6059b2 100644
--- a/test_cases/sciml_problem_import/001/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/001/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	2538.780077320352
+alpha	2538.7800773211884
 delta	573.6670521169216
 beta	-2188.7753333246887
diff --git a/test_cases/sciml_problem_import/001/grad_net1.hdf5 b/test_cases/sciml_problem_import/001/grad_net1.hdf5
index 67701a9..31e53f2 100644
Binary files a/test_cases/sciml_problem_import/001/grad_net1.hdf5 and b/test_cases/sciml_problem_import/001/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/001/petab/parameters.tsv b/test_cases/sciml_problem_import/001/petab/parameters.tsv
index e855e0d..dcaf68d 100644
--- a/test_cases/sciml_problem_import/001/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/001/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/001/petab/problem.yaml b/test_cases/sciml_problem_import/001/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/001/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/001/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/002/grad_net1.hdf5 b/test_cases/sciml_problem_import/002/grad_net1.hdf5
index 3dd2530..8cb3a97 100644
Binary files a/test_cases/sciml_problem_import/002/grad_net1.hdf5 and b/test_cases/sciml_problem_import/002/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/002/petab/parameters.tsv b/test_cases/sciml_problem_import/002/petab/parameters.tsv
index cd46c68..92f25e5 100644
--- a/test_cases/sciml_problem_import/002/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/002/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/002/petab/problem.yaml b/test_cases/sciml_problem_import/002/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/002/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/002/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/003/grad_mech.tsv b/test_cases/sciml_problem_import/003/grad_mech.tsv
index 52287b9..9b09567 100644
--- a/test_cases/sciml_problem_import/003/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/003/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
 alpha	1484.100432040707
-delta	304.6815498857698
-beta	-984.3538661871829
+delta	304.6815497521852
+beta	-984.3538661871895
diff --git a/test_cases/sciml_problem_import/003/grad_net1.hdf5 b/test_cases/sciml_problem_import/003/grad_net1.hdf5
index f27bbc0..fa073fa 100644
Binary files a/test_cases/sciml_problem_import/003/grad_net1.hdf5 and b/test_cases/sciml_problem_import/003/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/003/petab/parameters.tsv b/test_cases/sciml_problem_import/003/petab/parameters.tsv
index cd46c68..92f25e5 100644
--- a/test_cases/sciml_problem_import/003/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/003/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/003/petab/problem.yaml b/test_cases/sciml_problem_import/003/petab/problem.yaml
index 2a3535c..3a770ad 100644
--- a/test_cases/sciml_problem_import/003/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/003/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -19,8 +19,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/004/grad_mech.tsv b/test_cases/sciml_problem_import/004/grad_mech.tsv
index 8fe693e..475d0a6 100644
--- a/test_cases/sciml_problem_import/004/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/004/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1348.3832160092732
-delta	398.79444240316656
+delta	398.79444240445616
 beta	-839.2207939522068
 gamma	431.5736554673321
diff --git a/test_cases/sciml_problem_import/004/grad_net1.hdf5 b/test_cases/sciml_problem_import/004/grad_net1.hdf5
index 566d181..7ff2006 100644
Binary files a/test_cases/sciml_problem_import/004/grad_net1.hdf5 and b/test_cases/sciml_problem_import/004/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/004/petab/parameters.tsv b/test_cases/sciml_problem_import/004/petab/parameters.tsv
index be9420a..beaaa4c 100644
--- a/test_cases/sciml_problem_import/004/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/004/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/004/petab/problem.yaml b/test_cases/sciml_problem_import/004/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/004/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/004/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/005/grad_mech.tsv b/test_cases/sciml_problem_import/005/grad_mech.tsv
index 6174c73..bf86182 100644
--- a/test_cases/sciml_problem_import/005/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/005/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	1352.7284608871203
-delta	390.6311104263574
+alpha	1352.7284608871169
+delta	390.6311104716752
 beta	-827.8898414562375
diff --git a/test_cases/sciml_problem_import/005/grad_net1.hdf5 b/test_cases/sciml_problem_import/005/grad_net1.hdf5
index b8097a3..36cf459 100644
Binary files a/test_cases/sciml_problem_import/005/grad_net1.hdf5 and b/test_cases/sciml_problem_import/005/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/005/petab/parameters.tsv b/test_cases/sciml_problem_import/005/petab/parameters.tsv
index c27b0ca..6e34385 100644
--- a/test_cases/sciml_problem_import/005/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/005/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/005/petab/problem.yaml b/test_cases/sciml_problem_import/005/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/005/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/005/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/006/grad_net1.hdf5 b/test_cases/sciml_problem_import/006/grad_net1.hdf5
index 2556133..e161efc 100644
Binary files a/test_cases/sciml_problem_import/006/grad_net1.hdf5 and b/test_cases/sciml_problem_import/006/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/006/petab/parameters.tsv b/test_cases/sciml_problem_import/006/petab/parameters.tsv
index 0ab6069..911672d 100644
--- a/test_cases/sciml_problem_import/006/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/006/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2_est	lin	-inf	inf	1.0	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2_est	lin	-inf	inf	1.0	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/006/petab/problem.yaml b/test_cases/sciml_problem_import/006/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/006/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/006/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/007/grad_mech.tsv b/test_cases/sciml_problem_import/007/grad_mech.tsv
index 09f4051..2ec8230 100644
--- a/test_cases/sciml_problem_import/007/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/007/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1328.8285975146716
 delta	390.63111035285544
-beta	-827.8898414812052
+beta	-827.8898414813021
 gamma	432.5840252762772
diff --git a/test_cases/sciml_problem_import/007/grad_net1.hdf5 b/test_cases/sciml_problem_import/007/grad_net1.hdf5
index 2e80dc6..7aaba47 100644
Binary files a/test_cases/sciml_problem_import/007/grad_net1.hdf5 and b/test_cases/sciml_problem_import/007/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/007/petab/parameters.tsv b/test_cases/sciml_problem_import/007/petab/parameters.tsv
index 7ee45df..eb89c2f 100644
--- a/test_cases/sciml_problem_import/007/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/007/petab/parameters.tsv
@@ -1,8 +1,8 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/007/petab/problem.yaml b/test_cases/sciml_problem_import/007/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/007/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/007/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/007/simulations.tsv b/test_cases/sciml_problem_import/007/simulations.tsv
index f1e1549..3e05df3 100644
--- a/test_cases/sciml_problem_import/007/simulations.tsv
+++ b/test_cases/sciml_problem_import/007/simulations.tsv
@@ -1,6 +1,6 @@
 observableId	experimentId	simulation	time
 prey_o	e1	0.19964323441282392	1.0
-prey_o	e1	0.48425346211988823	2.0
+prey_o	e1	0.4842534621198883	2.0
 prey_o	e1	1.606351205697663	3.0
 prey_o	e1	5.49413965595464	4.0
 prey_o	e1	3.078213487078405	5.0
@@ -10,7 +10,7 @@ prey_o	e1	0.9041408036541226	8.0
 prey_o	e1	3.1091319914981947	9.0
 prey_o	e1	8.851586911027294	10.0
 predator_o	e1	0.9224424008593018	1.0
-predator_o	e1	0.19470291525643205	2.0
+predator_o	e1	0.19470291525643207	2.0
 predator_o	e1	0.06760604257225777	3.0
 predator_o	e1	0.1418700352798915	4.0
 predator_o	e1	6.698671429685438	5.0
diff --git a/test_cases/sciml_problem_import/008/grad_net1.hdf5 b/test_cases/sciml_problem_import/008/grad_net1.hdf5
index a9cdee9..c36d4fa 100644
Binary files a/test_cases/sciml_problem_import/008/grad_net1.hdf5 and b/test_cases/sciml_problem_import/008/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/008/grad_net2.hdf5 b/test_cases/sciml_problem_import/008/grad_net2.hdf5
index fa7def8..ed83ebf 100644
Binary files a/test_cases/sciml_problem_import/008/grad_net2.hdf5 and b/test_cases/sciml_problem_import/008/grad_net2.hdf5 differ
diff --git a/test_cases/sciml_problem_import/008/petab/parameters.tsv b/test_cases/sciml_problem_import/008/petab/parameters.tsv
index 41c005b..81fcaa9 100644
--- a/test_cases/sciml_problem_import/008/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/008/petab/parameters.tsv
@@ -1,9 +1,9 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net2_input_pre1	lin	-inf	inf	2.0	0
-net2_input_pre2	lin	-inf	inf	2.0	0
-net2_ps	lin	-inf	inf	array	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net2_input_pre1	lin	-inf	inf	2.0	false
+net2_input_pre2	lin	-inf	inf	2.0	false
+net2_ps	lin	-inf	inf	array	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/008/petab/problem.yaml b/test_cases/sciml_problem_import/008/petab/problem.yaml
index a77d8b5..34274d2 100644
--- a/test_cases/sciml_problem_import/008/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/008/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net2_ps.hdf5"
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net2:
         location: "net2.yaml"
diff --git a/test_cases/sciml_problem_import/009/grad_mech.tsv b/test_cases/sciml_problem_import/009/grad_mech.tsv
index fef5615..2021bbb 100644
--- a/test_cases/sciml_problem_import/009/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/009/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1343.6843979788944
-delta	398.79451866705796
+delta	398.7945185515232
 beta	-839.2209563508285
 gamma	431.5737260861462
diff --git a/test_cases/sciml_problem_import/009/grad_net1.hdf5 b/test_cases/sciml_problem_import/009/grad_net1.hdf5
index 83cf753..04a836a 100644
Binary files a/test_cases/sciml_problem_import/009/grad_net1.hdf5 and b/test_cases/sciml_problem_import/009/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/009/grad_net2.hdf5 b/test_cases/sciml_problem_import/009/grad_net2.hdf5
index 9bee960..e54928c 100644
Binary files a/test_cases/sciml_problem_import/009/grad_net2.hdf5 and b/test_cases/sciml_problem_import/009/grad_net2.hdf5 differ
diff --git a/test_cases/sciml_problem_import/009/petab/parameters.tsv b/test_cases/sciml_problem_import/009/petab/parameters.tsv
index c1ea121..9f36006 100644
--- a/test_cases/sciml_problem_import/009/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/009/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net2_ps	lin	-inf	inf	array	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net2_ps	lin	-inf	inf	array	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/009/petab/problem.yaml b/test_cases/sciml_problem_import/009/petab/problem.yaml
index 57a520f..34a4de4 100644
--- a/test_cases/sciml_problem_import/009/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/009/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net2_ps.hdf5"
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net2:
         location: "net2.yaml"
diff --git a/test_cases/sciml_problem_import/010/grad_mech.tsv b/test_cases/sciml_problem_import/010/grad_mech.tsv
index 8caa9e8..c27e72e 100644
--- a/test_cases/sciml_problem_import/010/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/010/grad_mech.tsv
@@ -1,3 +1,3 @@
 parameterId	value
 delta	573.9959237481935
-beta	-2187.6029761424024
+beta	-2187.6029761434265
diff --git a/test_cases/sciml_problem_import/010/grad_net1.hdf5 b/test_cases/sciml_problem_import/010/grad_net1.hdf5
index 722978f..77b8036 100644
Binary files a/test_cases/sciml_problem_import/010/grad_net1.hdf5 and b/test_cases/sciml_problem_import/010/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/010/grad_net2.hdf5 b/test_cases/sciml_problem_import/010/grad_net2.hdf5
index 4a3f5e9..2d7ac72 100644
Binary files a/test_cases/sciml_problem_import/010/grad_net2.hdf5 and b/test_cases/sciml_problem_import/010/grad_net2.hdf5 differ
diff --git a/test_cases/sciml_problem_import/010/petab/parameters.tsv b/test_cases/sciml_problem_import/010/petab/parameters.tsv
index 3f0c3ac..844e7b0 100644
--- a/test_cases/sciml_problem_import/010/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/010/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net2_ps	lin	-inf	inf	array	1
-net1_ps	lin	-inf	inf	array	1
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net2_ps	lin	-inf	inf	array	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/010/petab/problem.yaml b/test_cases/sciml_problem_import/010/petab/problem.yaml
index 57a520f..34a4de4 100644
--- a/test_cases/sciml_problem_import/010/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/010/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net2_ps.hdf5"
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net2:
         location: "net2.yaml"
diff --git a/test_cases/sciml_problem_import/011/grad_mech.tsv b/test_cases/sciml_problem_import/011/grad_mech.tsv
index 92c8f3d..0212be1 100644
--- a/test_cases/sciml_problem_import/011/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/011/grad_mech.tsv
@@ -1,3 +1,3 @@
 parameterId	value
-alpha	2538.780077320352
+alpha	2538.7800773211884
 delta	573.6670521169216
diff --git a/test_cases/sciml_problem_import/011/grad_net1.hdf5 b/test_cases/sciml_problem_import/011/grad_net1.hdf5
index a947c33..8fb0ca8 100644
Binary files a/test_cases/sciml_problem_import/011/grad_net1.hdf5 and b/test_cases/sciml_problem_import/011/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/011/grad_net2.hdf5 b/test_cases/sciml_problem_import/011/grad_net2.hdf5
index 3065a75..666235e 100644
Binary files a/test_cases/sciml_problem_import/011/grad_net2.hdf5 and b/test_cases/sciml_problem_import/011/grad_net2.hdf5 differ
diff --git a/test_cases/sciml_problem_import/011/petab/parameters.tsv b/test_cases/sciml_problem_import/011/petab/parameters.tsv
index 5cbaefb..d760c4e 100644
--- a/test_cases/sciml_problem_import/011/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/011/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-net2_input_pre1	lin	-inf	inf	2.0	0
-net2_input_pre2	lin	-inf	inf	2.0	0
-net2_ps	lin	-inf	inf	array	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+net2_input_pre1	lin	-inf	inf	2.0	false
+net2_input_pre2	lin	-inf	inf	2.0	false
+net2_ps	lin	-inf	inf	array	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/011/petab/problem.yaml b/test_cases/sciml_problem_import/011/petab/problem.yaml
index a74ffa8..3adb1ee 100644
--- a/test_cases/sciml_problem_import/011/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/011/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net2_ps.hdf5"
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net2:
         location: "net2.yaml"
diff --git a/test_cases/sciml_problem_import/012/grad_mech.tsv b/test_cases/sciml_problem_import/012/grad_mech.tsv
index 60cbe8a..48599c5 100644
--- a/test_cases/sciml_problem_import/012/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/012/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	2533.760727413523
+alpha	2533.7607274122674
 delta	573.6673195176297
 beta	-2188.7736160798177
diff --git a/test_cases/sciml_problem_import/012/grad_net1.hdf5 b/test_cases/sciml_problem_import/012/grad_net1.hdf5
index 3ec5c4f..a4c10bb 100644
Binary files a/test_cases/sciml_problem_import/012/grad_net1.hdf5 and b/test_cases/sciml_problem_import/012/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/012/grad_net2.hdf5 b/test_cases/sciml_problem_import/012/grad_net2.hdf5
index 4cf45d1..eac12ea 100644
Binary files a/test_cases/sciml_problem_import/012/grad_net2.hdf5 and b/test_cases/sciml_problem_import/012/grad_net2.hdf5 differ
diff --git a/test_cases/sciml_problem_import/012/petab/parameters.tsv b/test_cases/sciml_problem_import/012/petab/parameters.tsv
index ba6b383..8deb459 100644
--- a/test_cases/sciml_problem_import/012/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/012/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net2_ps	lin	-inf	inf	array	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net2_ps	lin	-inf	inf	array	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/012/petab/problem.yaml b/test_cases/sciml_problem_import/012/petab/problem.yaml
index 57a520f..34a4de4 100644
--- a/test_cases/sciml_problem_import/012/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/012/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net2_ps.hdf5"
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net2:
         location: "net2.yaml"
diff --git a/test_cases/sciml_problem_import/013/grad_net1.hdf5 b/test_cases/sciml_problem_import/013/grad_net1.hdf5
index 7a3b5d6..92dbd65 100644
Binary files a/test_cases/sciml_problem_import/013/grad_net1.hdf5 and b/test_cases/sciml_problem_import/013/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/013/grad_net2.hdf5 b/test_cases/sciml_problem_import/013/grad_net2.hdf5
index feb25ad..d86252d 100644
Binary files a/test_cases/sciml_problem_import/013/grad_net2.hdf5 and b/test_cases/sciml_problem_import/013/grad_net2.hdf5 differ
diff --git a/test_cases/sciml_problem_import/013/petab/parameters.tsv b/test_cases/sciml_problem_import/013/petab/parameters.tsv
index 755aa15..22f1ed1 100644
--- a/test_cases/sciml_problem_import/013/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/013/petab/parameters.tsv
@@ -1,8 +1,8 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net2_ps	lin	-inf	inf	array	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net2_ps	lin	-inf	inf	array	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/013/petab/problem.yaml b/test_cases/sciml_problem_import/013/petab/problem.yaml
index 07516f8..e1e03c8 100644
--- a/test_cases/sciml_problem_import/013/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/013/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net2_ps.hdf5"
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net2:
         location: "net2.yaml"
diff --git a/test_cases/sciml_problem_import/014/grad_mech.tsv b/test_cases/sciml_problem_import/014/grad_mech.tsv
index 6fc58bc..283eb49 100644
--- a/test_cases/sciml_problem_import/014/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/014/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	1328.8285973923125
-delta	390.6311105385793
-beta	-827.8898418064447
+alpha	1328.8285976140432
+delta	390.6311104716752
+beta	-827.8898414562375
diff --git a/test_cases/sciml_problem_import/014/grad_net3.hdf5 b/test_cases/sciml_problem_import/014/grad_net3.hdf5
index 7808e69..1d51689 100644
Binary files a/test_cases/sciml_problem_import/014/grad_net3.hdf5 and b/test_cases/sciml_problem_import/014/grad_net3.hdf5 differ
diff --git a/test_cases/sciml_problem_import/014/petab/parameters.tsv b/test_cases/sciml_problem_import/014/petab/parameters.tsv
index 88ead60..66c4ee4 100644
--- a/test_cases/sciml_problem_import/014/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/014/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net3_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net3_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/014/petab/problem.yaml b/test_cases/sciml_problem_import/014/petab/problem.yaml
index f73ed2f..901a34c 100644
--- a/test_cases/sciml_problem_import/014/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/014/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net3_ps.hdf5"
       - "net3_input1.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net3:
         location: "net3.yaml"
diff --git a/test_cases/sciml_problem_import/014/simulations.tsv b/test_cases/sciml_problem_import/014/simulations.tsv
index 6b2d713..a4e435f 100644
--- a/test_cases/sciml_problem_import/014/simulations.tsv
+++ b/test_cases/sciml_problem_import/014/simulations.tsv
@@ -1,21 +1,21 @@
 observableId	experimentId	simulation	time
-prey_o	e1	0.1996432344128231	1.0
-prey_o	e1	0.4842534621198982	2.0
-prey_o	e1	1.6063512056977	3.0
-prey_o	e1	5.494139655954648	4.0
-prey_o	e1	3.078213487078415	5.0
-prey_o	e1	0.19515376127176481	6.0
-prey_o	e1	0.29649755227373153	7.0
-prey_o	e1	0.9041408036540782	8.0
-prey_o	e1	3.10913199149817	9.0
-prey_o	e1	8.851586911027294	10.0
-predator_o	e1	0.9224424008593197	1.0
-predator_o	e1	0.19470291525642644	2.0
-predator_o	e1	0.06760604257225629	3.0
-predator_o	e1	0.1418700352798924	4.0
-predator_o	e1	6.698671429685438	5.0
-predator_o	e1	1.9955511106531993	6.0
-predator_o	e1	0.3922752142581838	7.0
-predator_o	e1	0.09942290206371006	8.0
-predator_o	e1	0.06834921504989715	9.0
-predator_o	e1	1.2238133862048879	10.0
+prey_o	e1	0.19964323441282023	1.0
+prey_o	e1	0.4842534621198607	2.0
+prey_o	e1	1.6063512056973333	3.0
+prey_o	e1	5.494139655954669	4.0
+prey_o	e1	3.0782134870784272	5.0
+prey_o	e1	0.19515376127175768	6.0
+prey_o	e1	0.2964975522737117	7.0
+prey_o	e1	0.9041408036540876	8.0
+prey_o	e1	3.1091319914980744	9.0
+prey_o	e1	8.851586911027413	10.0
+predator_o	e1	0.9224424008593343	1.0
+predator_o	e1	0.19470291525644529	2.0
+predator_o	e1	0.06760604257226344	3.0
+predator_o	e1	0.14187003527988604	4.0
+predator_o	e1	6.698671429685512	5.0
+predator_o	e1	1.9955511106531847	6.0
+predator_o	e1	0.3922752142581998	7.0
+predator_o	e1	0.0994229020637052	8.0
+predator_o	e1	0.06834921504989125	9.0
+predator_o	e1	1.2238133862046814	10.0
diff --git a/test_cases/sciml_problem_import/014/solutions.yaml b/test_cases/sciml_problem_import/014/solutions.yaml
index 11467b4..0f809d2 100644
--- a/test_cases/sciml_problem_import/014/solutions.yaml
+++ b/test_cases/sciml_problem_import/014/solutions.yaml
@@ -4,6 +4,6 @@ tol_grad: 0.1
 grad_files:
   mech: "grad_mech.tsv"
   net3: "grad_net3.hdf5"
-llh: 33.306381502951396
+llh: 33.3063815029473
 tol_simulations: 0.001
 tol_llh: 0.001
diff --git a/test_cases/sciml_problem_import/015/grad_mech.tsv b/test_cases/sciml_problem_import/015/grad_mech.tsv
index f20cea9..f37760d 100644
--- a/test_cases/sciml_problem_import/015/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/015/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	1484.35600690352
-delta	304.7728387882481
-beta	-984.4987605162647
+alpha	1484.356007051502
+delta	304.7728389355431
+beta	-984.4987606926684
diff --git a/test_cases/sciml_problem_import/015/grad_net3.hdf5 b/test_cases/sciml_problem_import/015/grad_net3.hdf5
index 66391c4..98ec69d 100644
Binary files a/test_cases/sciml_problem_import/015/grad_net3.hdf5 and b/test_cases/sciml_problem_import/015/grad_net3.hdf5 differ
diff --git a/test_cases/sciml_problem_import/015/petab/parameters.tsv b/test_cases/sciml_problem_import/015/petab/parameters.tsv
index 88ead60..66c4ee4 100644
--- a/test_cases/sciml_problem_import/015/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/015/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net3_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net3_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/015/petab/problem.yaml b/test_cases/sciml_problem_import/015/petab/problem.yaml
index 7f5cf4b..74b20ca 100644
--- a/test_cases/sciml_problem_import/015/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/015/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net3_ps.hdf5"
       - "net3_input2.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net3:
         location: "net3.yaml"
diff --git a/test_cases/sciml_problem_import/015/simulations.tsv b/test_cases/sciml_problem_import/015/simulations.tsv
index 9941bc2..869536a 100644
--- a/test_cases/sciml_problem_import/015/simulations.tsv
+++ b/test_cases/sciml_problem_import/015/simulations.tsv
@@ -1,41 +1,41 @@
 observableId	experimentId	simulation	time
-prey_o	e1	0.1996432213599251	1.0
-prey_o	e1	0.4842534122931591	2.0
-prey_o	e1	1.606351007036983	3.0
-prey_o	e1	5.494138728583467	4.0
-prey_o	e1	3.0782089229068963	5.0
-prey_o	e1	0.1951537276033331	6.0
-prey_o	e1	0.29649760449871376	7.0
-prey_o	e1	0.9041410068561255	8.0
-prey_o	e1	3.109132642131885	9.0
-prey_o	e1	8.851583477989651	10.0
-predator_o	e1	0.9224424633341638	1.0
-predator_o	e1	0.19470294266203902	2.0
-predator_o	e1	0.06760606576802042	3.0
-predator_o	e1	0.14187017213641684	4.0
-predator_o	e1	6.698671661725177	5.0
-predator_o	e1	1.9955502786844945	6.0
-predator_o	e1	0.39227508144331347	7.0
-predator_o	e1	0.0994228939653806	8.0
-predator_o	e1	0.06834926869480501	9.0
-predator_o	e1	1.223816858674027	10.0
+prey_o	e1	0.1996432213599237	1.0
+prey_o	e1	0.48425341229315494	2.0
+prey_o	e1	1.6063510070368017	3.0
+prey_o	e1	5.494138728583478	4.0
+prey_o	e1	3.078208922906972	5.0
+prey_o	e1	0.19515372760332517	6.0
+prey_o	e1	0.29649760449869456	7.0
+prey_o	e1	0.9041410068561169	8.0
+prey_o	e1	3.109132642131626	9.0
+prey_o	e1	8.851583477989726	10.0
+predator_o	e1	0.9224424633341811	1.0
+predator_o	e1	0.19470294266203983	2.0
+predator_o	e1	0.06760606576802435	3.0
+predator_o	e1	0.14187017213641487	4.0
+predator_o	e1	6.698671661725244	5.0
+predator_o	e1	1.9955502786844843	6.0
+predator_o	e1	0.392275081443328	7.0
+predator_o	e1	0.09942289396537778	8.0
+predator_o	e1	0.06834926869479717	9.0
+predator_o	e1	1.2238168586737321	10.0
 prey_o	e2	0.19136749240335596	1.0
-prey_o	e2	0.45308487158172284	2.0
-prey_o	e2	1.4827794389191593	3.0
-prey_o	e2	4.908416225540576	4.0
-prey_o	e2	1.4092350639279347	5.0
-prey_o	e2	0.18130167962774593	6.0
-prey_o	e2	0.3253179190549205	7.0
-prey_o	e2	1.0131210339737602	8.0
-prey_o	e2	3.4292206201803155	9.0
-prey_o	e2	4.863230857407191	10.0
-predator_o	e2	0.9628324437183196	1.0
-predator_o	e2	0.2123555154084897	2.0
-predator_o	e2	0.08303065274093115	3.0
-predator_o	e2	0.24730200729200888	4.0
-predator_o	e2	6.320932815298152	5.0
-predator_o	e2	1.5953488983625213	6.0
-predator_o	e2	0.3304382377783172	7.0
-predator_o	e2	0.09913253198176014	8.0
-predator_o	e2	0.11917759593869119	9.0
-predator_o	e2	4.455220054220248	10.0
+prey_o	e2	0.45308487158172256	2.0
+prey_o	e2	1.482779438919158	3.0
+prey_o	e2	4.908416225540572	4.0
+prey_o	e2	1.4092350639280227	5.0
+prey_o	e2	0.18130167962774174	6.0
+prey_o	e2	0.32531791905494656	7.0
+prey_o	e2	1.0131210339736951	8.0
+prey_o	e2	3.4292206201802005	9.0
+prey_o	e2	4.8632308574076095	10.0
+predator_o	e2	0.9628324437183179	1.0
+predator_o	e2	0.21235551540848976	2.0
+predator_o	e2	0.0830306527409313	3.0
+predator_o	e2	0.2473020072920063	4.0
+predator_o	e2	6.320932815298211	5.0
+predator_o	e2	1.5953488983625406	6.0
+predator_o	e2	0.33043823777827247	7.0
+predator_o	e2	0.09913253198176049	8.0
+predator_o	e2	0.11917759593869	9.0
+predator_o	e2	4.455220054219919	10.0
diff --git a/test_cases/sciml_problem_import/015/solutions.yaml b/test_cases/sciml_problem_import/015/solutions.yaml
index f911ded..9b8d0ff 100644
--- a/test_cases/sciml_problem_import/015/solutions.yaml
+++ b/test_cases/sciml_problem_import/015/solutions.yaml
@@ -4,6 +4,6 @@ tol_grad: 0.1
 grad_files:
   mech: "grad_mech.tsv"
   net3: "grad_net3.hdf5"
-llh: 68.96501052725615
+llh: 68.96501052725134
 tol_simulations: 0.001
 tol_llh: 0.001
diff --git a/test_cases/sciml_problem_import/016/grad_mech.tsv b/test_cases/sciml_problem_import/016/grad_mech.tsv
index 8dd5bd5..e6059b2 100644
--- a/test_cases/sciml_problem_import/016/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/016/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	2538.780077320352
+alpha	2538.7800773211884
 delta	573.6670521169216
 beta	-2188.7753333246887
diff --git a/test_cases/sciml_problem_import/016/petab/parameters.tsv b/test_cases/sciml_problem_import/016/petab/parameters.tsv
index 35e6b6d..4551ac7 100644
--- a/test_cases/sciml_problem_import/016/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/016/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_ps	lin	-inf	inf	array	0
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_ps	lin	-inf	inf	array	false
diff --git a/test_cases/sciml_problem_import/016/petab/problem.yaml b/test_cases/sciml_problem_import/016/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/016/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/016/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/017/petab/parameters.tsv b/test_cases/sciml_problem_import/017/petab/parameters.tsv
index 4e1c9b7..d934a33 100644
--- a/test_cases/sciml_problem_import/017/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/017/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net1_ps	lin	-inf	inf	array	0
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net1_ps	lin	-inf	inf	array	false
diff --git a/test_cases/sciml_problem_import/017/petab/problem.yaml b/test_cases/sciml_problem_import/017/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/017/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/017/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/018/grad_mech.tsv b/test_cases/sciml_problem_import/018/grad_mech.tsv
index 8fe693e..475d0a6 100644
--- a/test_cases/sciml_problem_import/018/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/018/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1348.3832160092732
-delta	398.79444240316656
+delta	398.79444240445616
 beta	-839.2207939522068
 gamma	431.5736554673321
diff --git a/test_cases/sciml_problem_import/018/petab/parameters.tsv b/test_cases/sciml_problem_import/018/petab/parameters.tsv
index 6c6db2b..8304e59 100644
--- a/test_cases/sciml_problem_import/018/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/018/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net1_ps	lin	-inf	inf	array	0
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net1_ps	lin	-inf	inf	array	false
diff --git a/test_cases/sciml_problem_import/018/petab/problem.yaml b/test_cases/sciml_problem_import/018/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/018/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/018/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/019/grad_mech.tsv b/test_cases/sciml_problem_import/019/grad_mech.tsv
index f86a7e8..813ea11 100644
--- a/test_cases/sciml_problem_import/019/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/019/grad_mech.tsv
@@ -1,3 +1,3 @@
 parameterId	value
 delta	432.80892943594046
-beta	-1062.1699857385913
+beta	-1062.1699857385877
diff --git a/test_cases/sciml_problem_import/019/grad_net4.hdf5 b/test_cases/sciml_problem_import/019/grad_net4.hdf5
index 48e0c22..18a6f61 100644
Binary files a/test_cases/sciml_problem_import/019/grad_net4.hdf5 and b/test_cases/sciml_problem_import/019/grad_net4.hdf5 differ
diff --git a/test_cases/sciml_problem_import/019/petab/parameters.tsv b/test_cases/sciml_problem_import/019/petab/parameters.tsv
index ef42a14..edb38ae 100644
--- a/test_cases/sciml_problem_import/019/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/019/petab/parameters.tsv
@@ -1,4 +1,4 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net4_ps	lin	-inf	inf	array	1
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net4_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/019/petab/problem.yaml b/test_cases/sciml_problem_import/019/petab/problem.yaml
index c7941fb..700cfe7 100644
--- a/test_cases/sciml_problem_import/019/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/019/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net4_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net4:
         location: "net4.yaml"
diff --git a/test_cases/sciml_problem_import/019/simulations.tsv b/test_cases/sciml_problem_import/019/simulations.tsv
index 62f0f07..717273c 100644
--- a/test_cases/sciml_problem_import/019/simulations.tsv
+++ b/test_cases/sciml_problem_import/019/simulations.tsv
@@ -16,6 +16,6 @@ predator_o	e1	0.11848161421915242	4.0
 predator_o	e1	6.6592286673751655	5.0
 predator_o	e1	1.9979001134744026	6.0
 predator_o	e1	0.390972827191549	7.0
-predator_o	e1	0.09182437675988887	8.0
+predator_o	e1	0.09182437675988889	8.0
 predator_o	e1	0.07516129994864439	9.0
 predator_o	e1	1.221754332337903	10.0
diff --git a/test_cases/sciml_problem_import/020/grad_mech.tsv b/test_cases/sciml_problem_import/020/grad_mech.tsv
index a861d42..4cd9e5b 100644
--- a/test_cases/sciml_problem_import/020/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/020/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1330.0184817447196
-delta	382.7943289062745
+delta	382.7943287566048
 beta	-830.0079162287896
 gamma	428.2868258207031
diff --git a/test_cases/sciml_problem_import/020/grad_net4.hdf5 b/test_cases/sciml_problem_import/020/grad_net4.hdf5
index 9415bd0..f003c95 100644
Binary files a/test_cases/sciml_problem_import/020/grad_net4.hdf5 and b/test_cases/sciml_problem_import/020/grad_net4.hdf5 differ
diff --git a/test_cases/sciml_problem_import/020/petab/parameters.tsv b/test_cases/sciml_problem_import/020/petab/parameters.tsv
index f68daa3..adbcd53 100644
--- a/test_cases/sciml_problem_import/020/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/020/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net4_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net4_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/020/petab/problem.yaml b/test_cases/sciml_problem_import/020/petab/problem.yaml
index c7941fb..700cfe7 100644
--- a/test_cases/sciml_problem_import/020/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/020/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net4_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net4:
         location: "net4.yaml"
diff --git a/test_cases/sciml_problem_import/021/grad_mech.tsv b/test_cases/sciml_problem_import/021/grad_mech.tsv
index 7836ec7..a4fce37 100644
--- a/test_cases/sciml_problem_import/021/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/021/grad_mech.tsv
@@ -1,3 +1,3 @@
 parameterId	value
-delta	390.6311105282792
-beta	-827.8898417215598
+delta	390.6311105282943
+beta	-827.8898417215922
diff --git a/test_cases/sciml_problem_import/021/grad_net4.hdf5 b/test_cases/sciml_problem_import/021/grad_net4.hdf5
index 7744f0a..18a98e8 100644
Binary files a/test_cases/sciml_problem_import/021/grad_net4.hdf5 and b/test_cases/sciml_problem_import/021/grad_net4.hdf5 differ
diff --git a/test_cases/sciml_problem_import/021/petab/parameters.tsv b/test_cases/sciml_problem_import/021/petab/parameters.tsv
index 9812b5a..8eab181 100644
--- a/test_cases/sciml_problem_import/021/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/021/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net4_ps	lin	-inf	inf	array	1
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net4_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/021/petab/problem.yaml b/test_cases/sciml_problem_import/021/petab/problem.yaml
index 5254f49..fb5d46c 100644
--- a/test_cases/sciml_problem_import/021/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/021/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net4_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net4:
         location: "net4.yaml"
diff --git a/test_cases/sciml_problem_import/021/simulations.tsv b/test_cases/sciml_problem_import/021/simulations.tsv
index 7af45f0..fca4463 100644
--- a/test_cases/sciml_problem_import/021/simulations.tsv
+++ b/test_cases/sciml_problem_import/021/simulations.tsv
@@ -14,7 +14,7 @@ predator_o	e1	0.19470291525643446	2.0
 predator_o	e1	0.06760604257225866	3.0
 predator_o	e1	0.14187003527989137	4.0
 predator_o	e1	6.698671429685424	5.0
-predator_o	e1	1.9955511106532229	6.0
+predator_o	e1	1.995551110653223	6.0
 predator_o	e1	0.3922752142581829	7.0
 predator_o	e1	0.09942290206371376	8.0
 predator_o	e1	0.06834921504989673	9.0
diff --git a/test_cases/sciml_problem_import/022/grad_mech.tsv b/test_cases/sciml_problem_import/022/grad_mech.tsv
index bcf9695..072bc24 100644
--- a/test_cases/sciml_problem_import/022/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/022/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
 alpha	1188.5489404986652
 delta	457.0027110699171
-beta	-410.066612249925
+beta	-410.06661224986
diff --git a/test_cases/sciml_problem_import/022/grad_net4.hdf5 b/test_cases/sciml_problem_import/022/grad_net4.hdf5
index 0e605e1..a22396e 100644
Binary files a/test_cases/sciml_problem_import/022/grad_net4.hdf5 and b/test_cases/sciml_problem_import/022/grad_net4.hdf5 differ
diff --git a/test_cases/sciml_problem_import/022/petab/parameters.tsv b/test_cases/sciml_problem_import/022/petab/parameters.tsv
index 129c8d5..d75e440 100644
--- a/test_cases/sciml_problem_import/022/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/022/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net4_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net4_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/022/petab/problem.yaml b/test_cases/sciml_problem_import/022/petab/problem.yaml
index c7941fb..700cfe7 100644
--- a/test_cases/sciml_problem_import/022/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/022/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net4_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net4:
         location: "net4.yaml"
diff --git a/test_cases/sciml_problem_import/023/grad_mech.tsv b/test_cases/sciml_problem_import/023/grad_mech.tsv
index 8dd5bd5..e6059b2 100644
--- a/test_cases/sciml_problem_import/023/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/023/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	2538.780077320352
+alpha	2538.7800773211884
 delta	573.6670521169216
 beta	-2188.7753333246887
diff --git a/test_cases/sciml_problem_import/023/grad_net1.hdf5 b/test_cases/sciml_problem_import/023/grad_net1.hdf5
index 5e32aba..567ff37 100644
Binary files a/test_cases/sciml_problem_import/023/grad_net1.hdf5 and b/test_cases/sciml_problem_import/023/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/023/petab/parameters.tsv b/test_cases/sciml_problem_import/023/petab/parameters.tsv
index ebb1471..a537ee2 100644
--- a/test_cases/sciml_problem_import/023/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/023/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_layer1	lin	-inf	inf	array	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_layer1	lin	-inf	inf	array	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/023/petab/problem.yaml b/test_cases/sciml_problem_import/023/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/023/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/023/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/024/grad_net1.hdf5 b/test_cases/sciml_problem_import/024/grad_net1.hdf5
index 16ce551..73a9874 100644
Binary files a/test_cases/sciml_problem_import/024/grad_net1.hdf5 and b/test_cases/sciml_problem_import/024/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/024/petab/parameters.tsv b/test_cases/sciml_problem_import/024/petab/parameters.tsv
index 16c8f41..e82339e 100644
--- a/test_cases/sciml_problem_import/024/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/024/petab/parameters.tsv
@@ -1,8 +1,8 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net1_layer1	lin	-inf	inf	array	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net1_layer1	lin	-inf	inf	array	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/024/petab/problem.yaml b/test_cases/sciml_problem_import/024/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/024/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/024/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/025/grad_mech.tsv b/test_cases/sciml_problem_import/025/grad_mech.tsv
index 8fe693e..475d0a6 100644
--- a/test_cases/sciml_problem_import/025/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/025/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1348.3832160092732
-delta	398.79444240316656
+delta	398.79444240445616
 beta	-839.2207939522068
 gamma	431.5736554673321
diff --git a/test_cases/sciml_problem_import/025/grad_net1.hdf5 b/test_cases/sciml_problem_import/025/grad_net1.hdf5
index 81328a3..1988252 100644
Binary files a/test_cases/sciml_problem_import/025/grad_net1.hdf5 and b/test_cases/sciml_problem_import/025/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/025/petab/parameters.tsv b/test_cases/sciml_problem_import/025/petab/parameters.tsv
index 4f93bd7..320fdfd 100644
--- a/test_cases/sciml_problem_import/025/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/025/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net1_layer1	lin	-inf	inf	array	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net1_layer1	lin	-inf	inf	array	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/025/petab/problem.yaml b/test_cases/sciml_problem_import/025/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/025/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/025/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/026/grad_mech.tsv b/test_cases/sciml_problem_import/026/grad_mech.tsv
index 8dd5bd5..e6059b2 100644
--- a/test_cases/sciml_problem_import/026/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/026/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	2538.780077320352
+alpha	2538.7800773211884
 delta	573.6670521169216
 beta	-2188.7753333246887
diff --git a/test_cases/sciml_problem_import/026/grad_net1.hdf5 b/test_cases/sciml_problem_import/026/grad_net1.hdf5
index 51b67d9..e0da0fe 100644
Binary files a/test_cases/sciml_problem_import/026/grad_net1.hdf5 and b/test_cases/sciml_problem_import/026/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/026/petab/parameters.tsv b/test_cases/sciml_problem_import/026/petab/parameters.tsv
index ee6a085..3384f47 100644
--- a/test_cases/sciml_problem_import/026/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/026/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_layer1_weight	lin	-inf	inf	array	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_layer1_weight	lin	-inf	inf	array	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/026/petab/problem.yaml b/test_cases/sciml_problem_import/026/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/026/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/026/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/027/grad_net1.hdf5 b/test_cases/sciml_problem_import/027/grad_net1.hdf5
index e908487..5b66f6c 100644
Binary files a/test_cases/sciml_problem_import/027/grad_net1.hdf5 and b/test_cases/sciml_problem_import/027/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/027/petab/parameters.tsv b/test_cases/sciml_problem_import/027/petab/parameters.tsv
index 626e11b..f0ccc15 100644
--- a/test_cases/sciml_problem_import/027/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/027/petab/parameters.tsv
@@ -1,8 +1,8 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net1_layer1_weight	lin	-inf	inf	array	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net1_layer1_weight	lin	-inf	inf	array	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/027/petab/problem.yaml b/test_cases/sciml_problem_import/027/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/027/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/027/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/028/grad_mech.tsv b/test_cases/sciml_problem_import/028/grad_mech.tsv
index 8fe693e..475d0a6 100644
--- a/test_cases/sciml_problem_import/028/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/028/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1348.3832160092732
-delta	398.79444240316656
+delta	398.79444240445616
 beta	-839.2207939522068
 gamma	431.5736554673321
diff --git a/test_cases/sciml_problem_import/028/grad_net1.hdf5 b/test_cases/sciml_problem_import/028/grad_net1.hdf5
index 42f5a8d..ca06cab 100644
Binary files a/test_cases/sciml_problem_import/028/grad_net1.hdf5 and b/test_cases/sciml_problem_import/028/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/028/petab/parameters.tsv b/test_cases/sciml_problem_import/028/petab/parameters.tsv
index 5460bd9..5efe002 100644
--- a/test_cases/sciml_problem_import/028/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/028/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net1_layer1_weight	lin	-inf	inf	array	0
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net1_layer1_weight	lin	-inf	inf	array	false
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/028/petab/problem.yaml b/test_cases/sciml_problem_import/028/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/028/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/028/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/029/grad_mech.tsv b/test_cases/sciml_problem_import/029/grad_mech.tsv
index 8dd5bd5..e6059b2 100644
--- a/test_cases/sciml_problem_import/029/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/029/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	2538.780077320352
+alpha	2538.7800773211884
 delta	573.6670521169216
 beta	-2188.7753333246887
diff --git a/test_cases/sciml_problem_import/029/grad_net5.hdf5 b/test_cases/sciml_problem_import/029/grad_net5.hdf5
index 3fb3e07..89b9e34 100644
Binary files a/test_cases/sciml_problem_import/029/grad_net5.hdf5 and b/test_cases/sciml_problem_import/029/grad_net5.hdf5 differ
diff --git a/test_cases/sciml_problem_import/029/petab/parameters.tsv b/test_cases/sciml_problem_import/029/petab/parameters.tsv
index 2f79395..07703d4 100644
--- a/test_cases/sciml_problem_import/029/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/029/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net5_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net5_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/029/petab/problem.yaml b/test_cases/sciml_problem_import/029/petab/problem.yaml
index cd08d41..dfec799 100644
--- a/test_cases/sciml_problem_import/029/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/029/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net5_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net5:
         location: "net5.yaml"
diff --git a/test_cases/sciml_problem_import/030/grad_net5.hdf5 b/test_cases/sciml_problem_import/030/grad_net5.hdf5
index 1eee7d0..a41f2bf 100644
Binary files a/test_cases/sciml_problem_import/030/grad_net5.hdf5 and b/test_cases/sciml_problem_import/030/grad_net5.hdf5 differ
diff --git a/test_cases/sciml_problem_import/030/petab/parameters.tsv b/test_cases/sciml_problem_import/030/petab/parameters.tsv
index dbd5c86..6565312 100644
--- a/test_cases/sciml_problem_import/030/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/030/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_input_pre1	lin	-inf	inf	1.0	0
-net1_input_pre2	lin	-inf	inf	1.0	0
-net5_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_input_pre1	lin	-inf	inf	1.0	false
+net1_input_pre2	lin	-inf	inf	1.0	false
+net5_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/030/petab/problem.yaml b/test_cases/sciml_problem_import/030/petab/problem.yaml
index 61231bb..d9c2fe1 100644
--- a/test_cases/sciml_problem_import/030/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/030/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net5_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net5:
         location: "net5.yaml"
diff --git a/test_cases/sciml_problem_import/031/grad_mech.tsv b/test_cases/sciml_problem_import/031/grad_mech.tsv
index 8fe693e..475d0a6 100644
--- a/test_cases/sciml_problem_import/031/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/031/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1348.3832160092732
-delta	398.79444240316656
+delta	398.79444240445616
 beta	-839.2207939522068
 gamma	431.5736554673321
diff --git a/test_cases/sciml_problem_import/031/grad_net5.hdf5 b/test_cases/sciml_problem_import/031/grad_net5.hdf5
index 135e08e..47c4f44 100644
Binary files a/test_cases/sciml_problem_import/031/grad_net5.hdf5 and b/test_cases/sciml_problem_import/031/grad_net5.hdf5 differ
diff --git a/test_cases/sciml_problem_import/031/petab/parameters.tsv b/test_cases/sciml_problem_import/031/petab/parameters.tsv
index 7b7b85b..56850d5 100644
--- a/test_cases/sciml_problem_import/031/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/031/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net5_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net5_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/031/petab/problem.yaml b/test_cases/sciml_problem_import/031/petab/problem.yaml
index cd08d41..dfec799 100644
--- a/test_cases/sciml_problem_import/031/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/031/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net5_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net5:
         location: "net5.yaml"
diff --git a/test_cases/sciml_problem_import/032/grad_mech.tsv b/test_cases/sciml_problem_import/032/grad_mech.tsv
index e33c83f..7afefb9 100644
--- a/test_cases/sciml_problem_import/032/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/032/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	1328.8285975198448
-delta	390.6311104472732
-beta	-827.8898417171047
+alpha	1328.8285975198899
+delta	390.63111044731846
+beta	-827.8898417171947
diff --git a/test_cases/sciml_problem_import/032/grad_net1.hdf5 b/test_cases/sciml_problem_import/032/grad_net1.hdf5
index fce3144..189d15b 100644
Binary files a/test_cases/sciml_problem_import/032/grad_net1.hdf5 and b/test_cases/sciml_problem_import/032/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/032/petab/parameters.tsv b/test_cases/sciml_problem_import/032/petab/parameters.tsv
index 0923f3b..0d1852d 100644
--- a/test_cases/sciml_problem_import/032/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/032/petab/parameters.tsv
@@ -1,7 +1,7 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
-alpha	lin	0.0	15.0	1.3	1	uniform	0.0;15.0
-delta	lin	0.0	15.0	1.8	1	uniform	0.0;15.0
-beta	lin	0.0	15.0	0.9	1	uniform	0.0;15.0
-net1_input_pre1	lin	-Inf	Inf	1.0	0		
-net1_input_pre2	lin	-Inf	Inf	1.0	0		
-net1_ps	lin	-Inf	Inf	array	1	normal	0.0;1.0
+alpha	lin	0.0	15.0	1.3	true	uniform	0.0;15.0
+delta	lin	0.0	15.0	1.8	true	uniform	0.0;15.0
+beta	lin	0.0	15.0	0.9	true	uniform	0.0;15.0
+net1_input_pre1	lin	-Inf	Inf	1.0	false		
+net1_input_pre2	lin	-Inf	Inf	1.0	false		
+net1_ps	lin	-Inf	Inf	array	true	normal	0.0;1.0
diff --git a/test_cases/sciml_problem_import/032/petab/problem.yaml b/test_cases/sciml_problem_import/032/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/032/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/032/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/032/solutions.yaml b/test_cases/sciml_problem_import/032/solutions.yaml
index 6231d07..18ea186 100644
--- a/test_cases/sciml_problem_import/032/solutions.yaml
+++ b/test_cases/sciml_problem_import/032/solutions.yaml
@@ -5,5 +5,5 @@ grad_files:
   mech: "grad_mech.tsv"
   net1: "grad_net1.hdf5"
 tol_simulations: 0.001
-log_posterior: -22.83360800261655
+log_posterior: -22.833608002616536
 tol_log_posterior: 0.001
diff --git a/test_cases/sciml_problem_import/033/grad_mech.tsv b/test_cases/sciml_problem_import/033/grad_mech.tsv
index 7beb0fa..3476268 100644
--- a/test_cases/sciml_problem_import/033/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/033/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	1328.8285975198223
-delta	390.6311104472362
-beta	-827.8898417172687
+alpha	1328.8285975197307
+delta	390.6311104474263
+beta	-827.889841717137
diff --git a/test_cases/sciml_problem_import/033/grad_net1.hdf5 b/test_cases/sciml_problem_import/033/grad_net1.hdf5
index 5ff738d..5b4debb 100644
Binary files a/test_cases/sciml_problem_import/033/grad_net1.hdf5 and b/test_cases/sciml_problem_import/033/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/033/petab/parameters.tsv b/test_cases/sciml_problem_import/033/petab/parameters.tsv
index 67a23b5..8ca1b99 100644
--- a/test_cases/sciml_problem_import/033/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/033/petab/parameters.tsv
@@ -1,8 +1,8 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
-alpha	lin	0.0	15.0	1.3	1	uniform	0.0;15.0
-delta	lin	0.0	15.0	1.8	1	uniform	0.0;15.0
-beta	lin	0.0	15.0	0.9	1	uniform	0.0;15.0
-net1_input_pre1	lin	-Inf	Inf	1.0	0		
-net1_input_pre2	lin	-Inf	Inf	1.0	0		
-net1_layer1_prior	lin	-Inf	Inf	array	1	normal	0.0;2.0
-net1_ps	lin	-Inf	Inf	array	1	normal	0.0;1.0
+alpha	lin	0.0	15.0	1.3	true	uniform	0.0;15.0
+delta	lin	0.0	15.0	1.8	true	uniform	0.0;15.0
+beta	lin	0.0	15.0	0.9	true	uniform	0.0;15.0
+net1_input_pre1	lin	-Inf	Inf	1.0	false		
+net1_input_pre2	lin	-Inf	Inf	1.0	false		
+net1_layer1_prior	lin	-Inf	Inf	array	true	normal	0.0;2.0
+net1_ps	lin	-Inf	Inf	array	true	normal	0.0;1.0
diff --git a/test_cases/sciml_problem_import/033/petab/problem.yaml b/test_cases/sciml_problem_import/033/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/033/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/033/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/033/solutions.yaml b/test_cases/sciml_problem_import/033/solutions.yaml
index 7ba9e2e..24e3ba9 100644
--- a/test_cases/sciml_problem_import/033/solutions.yaml
+++ b/test_cases/sciml_problem_import/033/solutions.yaml
@@ -5,5 +5,5 @@ grad_files:
   mech: "grad_mech.tsv"
   net1: "grad_net1.hdf5"
 tol_simulations: 0.001
-log_posterior: -32.93800974538561
+log_posterior: -32.93800974538559
 tol_log_posterior: 0.001
diff --git a/test_cases/sciml_problem_import/034/grad_mech.tsv b/test_cases/sciml_problem_import/034/grad_mech.tsv
index b570a5f..7638029 100644
--- a/test_cases/sciml_problem_import/034/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/034/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
-alpha	1328.8285975198362
-delta	390.6311104473259
-beta	-827.889841717214
+alpha	1328.8285975197587
+delta	390.63111044746506
+beta	-827.8898417170853
diff --git a/test_cases/sciml_problem_import/034/grad_net1.hdf5 b/test_cases/sciml_problem_import/034/grad_net1.hdf5
index bd3f32e..247df65 100644
Binary files a/test_cases/sciml_problem_import/034/grad_net1.hdf5 and b/test_cases/sciml_problem_import/034/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/034/petab/parameters.tsv b/test_cases/sciml_problem_import/034/petab/parameters.tsv
index a51e72e..4e1c24a 100644
--- a/test_cases/sciml_problem_import/034/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/034/petab/parameters.tsv
@@ -1,8 +1,8 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
-alpha	lin	0.0	15.0	1.3	1	uniform	0.0;15.0
-delta	lin	0.0	15.0	1.8	1	uniform	0.0;15.0
-beta	lin	0.0	15.0	0.9	1	uniform	0.0;15.0
-net1_input_pre1	lin	-Inf	Inf	1.0	0		
-net1_input_pre2	lin	-Inf	Inf	1.0	0		
-net1_layer1_weight_prior	lin	-Inf	Inf	array	1	normal	0.0;2.0
-net1_ps	lin	-Inf	Inf	array	1	normal	0.0;1.0
+alpha	lin	0.0	15.0	1.3	true	uniform	0.0;15.0
+delta	lin	0.0	15.0	1.8	true	uniform	0.0;15.0
+beta	lin	0.0	15.0	0.9	true	uniform	0.0;15.0
+net1_input_pre1	lin	-Inf	Inf	1.0	false		
+net1_input_pre2	lin	-Inf	Inf	1.0	false		
+net1_layer1_weight_prior	lin	-Inf	Inf	array	true	normal	0.0;2.0
+net1_ps	lin	-Inf	Inf	array	true	normal	0.0;1.0
diff --git a/test_cases/sciml_problem_import/034/petab/problem.yaml b/test_cases/sciml_problem_import/034/petab/problem.yaml
index 8fd38b4..fc2aac9 100644
--- a/test_cases/sciml_problem_import/034/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/034/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/034/solutions.yaml b/test_cases/sciml_problem_import/034/solutions.yaml
index 0fa9901..6004a0c 100644
--- a/test_cases/sciml_problem_import/034/solutions.yaml
+++ b/test_cases/sciml_problem_import/034/solutions.yaml
@@ -5,5 +5,5 @@ grad_files:
   mech: "grad_mech.tsv"
   net1: "grad_net1.hdf5"
 tol_simulations: 0.001
-log_posterior: -29.54253953842064
+log_posterior: -29.542539538420627
 tol_log_posterior: 0.001
diff --git a/test_cases/sciml_problem_import/035/grad_net1.hdf5 b/test_cases/sciml_problem_import/035/grad_net1.hdf5
index d93b93d..e5c07fd 100644
Binary files a/test_cases/sciml_problem_import/035/grad_net1.hdf5 and b/test_cases/sciml_problem_import/035/grad_net1.hdf5 differ
diff --git a/test_cases/sciml_problem_import/035/petab/parameters.tsv b/test_cases/sciml_problem_import/035/petab/parameters.tsv
index e855e0d..dcaf68d 100644
--- a/test_cases/sciml_problem_import/035/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/035/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net1_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net1_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/035/petab/problem.yaml b/test_cases/sciml_problem_import/035/petab/problem.yaml
index 4377bf4..4e2b5ab 100644
--- a/test_cases/sciml_problem_import/035/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/035/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -17,8 +17,10 @@ extensions:
   sciml:
     array_files:
       - "net1_ps.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net1:
         location: "net1.yaml"
diff --git a/test_cases/sciml_problem_import/036/grad_mech.tsv b/test_cases/sciml_problem_import/036/grad_mech.tsv
index 1cb05fb..0d2ab34 100644
--- a/test_cases/sciml_problem_import/036/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/036/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
 alpha	1476.38108308259
-delta	436.42503474376264
-beta	-917.1696536617616
+delta	436.4250347436417
+beta	-917.1696536617436
diff --git a/test_cases/sciml_problem_import/036/grad_net6.hdf5 b/test_cases/sciml_problem_import/036/grad_net6.hdf5
index db472b9..28baf69 100644
Binary files a/test_cases/sciml_problem_import/036/grad_net6.hdf5 and b/test_cases/sciml_problem_import/036/grad_net6.hdf5 differ
diff --git a/test_cases/sciml_problem_import/036/petab/parameters.tsv b/test_cases/sciml_problem_import/036/petab/parameters.tsv
index 21be1f6..9e9d3d9 100644
--- a/test_cases/sciml_problem_import/036/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/036/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net6_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net6_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/036/petab/problem.yaml b/test_cases/sciml_problem_import/036/petab/problem.yaml
index 42b4ccd..9948723 100644
--- a/test_cases/sciml_problem_import/036/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/036/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net6_ps.hdf5"
       - "net6_input1.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net6:
         location: "net6.yaml"
diff --git a/test_cases/sciml_problem_import/037/grad_mech.tsv b/test_cases/sciml_problem_import/037/grad_mech.tsv
index 38356cc..5242101 100644
--- a/test_cases/sciml_problem_import/037/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/037/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
 alpha	1328.1824099458936
-delta	390.09408136779973
-beta	-826.4877862059785
-gamma	432.77547288165096
+delta	390.0940813679303
+beta	-826.4877862052066
+gamma	432.7754728816143
diff --git a/test_cases/sciml_problem_import/037/grad_net6.hdf5 b/test_cases/sciml_problem_import/037/grad_net6.hdf5
index 5a81dae..23d793f 100644
Binary files a/test_cases/sciml_problem_import/037/grad_net6.hdf5 and b/test_cases/sciml_problem_import/037/grad_net6.hdf5 differ
diff --git a/test_cases/sciml_problem_import/037/petab/parameters.tsv b/test_cases/sciml_problem_import/037/petab/parameters.tsv
index 23e9c13..3fcacaf 100644
--- a/test_cases/sciml_problem_import/037/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/037/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net6_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net6_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/037/petab/problem.yaml b/test_cases/sciml_problem_import/037/petab/problem.yaml
index 42b4ccd..9948723 100644
--- a/test_cases/sciml_problem_import/037/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/037/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net6_ps.hdf5"
       - "net6_input1.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net6:
         location: "net6.yaml"
diff --git a/test_cases/sciml_problem_import/038/grad_mech.tsv b/test_cases/sciml_problem_import/038/grad_mech.tsv
index c677b56..5661d76 100644
--- a/test_cases/sciml_problem_import/038/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/038/grad_mech.tsv
@@ -1,4 +1,4 @@
 parameterId	value
 alpha	1828.9047969080623
-delta	413.75275506748926
+delta	413.7528846294025
 beta	-1190.4202737098512
diff --git a/test_cases/sciml_problem_import/038/grad_net6.hdf5 b/test_cases/sciml_problem_import/038/grad_net6.hdf5
index c98c6c2..9cfe47b 100644
Binary files a/test_cases/sciml_problem_import/038/grad_net6.hdf5 and b/test_cases/sciml_problem_import/038/grad_net6.hdf5 differ
diff --git a/test_cases/sciml_problem_import/038/petab/parameters.tsv b/test_cases/sciml_problem_import/038/petab/parameters.tsv
index 21be1f6..9e9d3d9 100644
--- a/test_cases/sciml_problem_import/038/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/038/petab/parameters.tsv
@@ -1,5 +1,5 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-net6_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+net6_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/038/petab/problem.yaml b/test_cases/sciml_problem_import/038/petab/problem.yaml
index 3dc6f65..9498a53 100644
--- a/test_cases/sciml_problem_import/038/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/038/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net6_ps.hdf5"
       - "net6_input2.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net6:
         location: "net6.yaml"
diff --git a/test_cases/sciml_problem_import/039/grad_mech.tsv b/test_cases/sciml_problem_import/039/grad_mech.tsv
index d49a697..b3e0ada 100644
--- a/test_cases/sciml_problem_import/039/grad_mech.tsv
+++ b/test_cases/sciml_problem_import/039/grad_mech.tsv
@@ -1,5 +1,5 @@
 parameterId	value
-alpha	384.67420907758566
-delta	-77.22463242359656
+alpha	384.67420907589553
+delta	-77.22463242359517
 beta	-398.4233563340724
-gamma	546.9861905045999
+gamma	546.9861905024623
diff --git a/test_cases/sciml_problem_import/039/grad_net6.hdf5 b/test_cases/sciml_problem_import/039/grad_net6.hdf5
index 368d2fc..923c167 100644
Binary files a/test_cases/sciml_problem_import/039/grad_net6.hdf5 and b/test_cases/sciml_problem_import/039/grad_net6.hdf5 differ
diff --git a/test_cases/sciml_problem_import/039/petab/parameters.tsv b/test_cases/sciml_problem_import/039/petab/parameters.tsv
index 23e9c13..3fcacaf 100644
--- a/test_cases/sciml_problem_import/039/petab/parameters.tsv
+++ b/test_cases/sciml_problem_import/039/petab/parameters.tsv
@@ -1,6 +1,6 @@
 parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-alpha	lin	0.0	15.0	1.3	1
-delta	lin	0.0	15.0	1.8	1
-beta	lin	0.0	15.0	0.9	1
-gamma	lin	0.0	15.0	0.8	1
-net6_ps	lin	-inf	inf	array	1
+alpha	lin	0.0	15.0	1.3	true
+delta	lin	0.0	15.0	1.8	true
+beta	lin	0.0	15.0	0.9	true
+gamma	lin	0.0	15.0	0.8	true
+net6_ps	lin	-inf	inf	array	true
diff --git a/test_cases/sciml_problem_import/039/petab/problem.yaml b/test_cases/sciml_problem_import/039/petab/problem.yaml
index 3dc6f65..9498a53 100644
--- a/test_cases/sciml_problem_import/039/petab/problem.yaml
+++ b/test_cases/sciml_problem_import/039/petab/problem.yaml
@@ -6,7 +6,7 @@ measurement_files:
   - "measurements.tsv"
 observable_files:
   - "observables.tsv"
-format_version: 2
+format_version: "2.0.0"
 experiment_files:
   - "experiments.tsv"
 parameter_files:
@@ -18,8 +18,10 @@ extensions:
     array_files:
       - "net6_ps.hdf5"
       - "net6_input2.hdf5"
+    version: "0.1.0"
     hybridization_files:
       - "hybridization.tsv"
+    required: true
     neural_nets:
       net6:
         location: "net6.yaml"