diff --git a/.github/workflows/release_biosimulators.yml b/.github/workflows/release_biosimulators.yml
new file mode 100644
index 0000000000..2f0479e3cd
--- /dev/null
+++ b/.github/workflows/release_biosimulators.yml
@@ -0,0 +1,32 @@
+name: Release to BioSimulators
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  updateCliAndDockerImage:
+    name: Build and release downstream command-line interface and Docker image
+    runs-on: ubuntu-latest
+    env:
+      # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
+      DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI
+
+      # Username/token to use the GitHub API to trigger an action on the GitHub repository for the downstream
+      # command-line interface and Docker image. Tokens can be generated at https://github.com/settings/tokens.
+      # The token should have the scope `repo`
+      GH_ISSUE_USERNAME: ${{ secrets.BIOSIMULATORS_USERNAME }}
+      GH_ISSUE_TOKEN: ${{ secrets.BIOSIMULATORS_TOKEN }}
+    steps:
+      - name: Trigger GitHub action that will build and release the downstream command-line interface and Docker image
+        run: |
+          PACKAGE_VERSION="${GITHUB_REF/refs\/tags\/v/}"
+          WORKFLOW_FILE=ci.yml
+
+          curl \
+            -X POST \
+            -u ${GH_ISSUE_USERNAME}:${GH_ISSUE_TOKEN} \
+            -H "Accept: application/vnd.github.v3+json" \
+              https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
+            -d "{\"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
index 4e78e6edea..a2f463b2f4 100644
--- a/.github/workflows/test_performance.yml
+++ b/.github/workflows/test_performance.yml
@@ -4,7 +4,7 @@ on:
     branches:
       - develop
       - master
-      - speedup_reaction_ids
+      - compile_without_optimization
 
   pull_request:
     branches:
@@ -50,12 +50,7 @@ jobs:
     # import test model
     - name: Import test model
       run: |
-        cd CS_Signalling_ERBB_RAS_AKT \
-          && check_time.sh \
-          petab_import amici_import_petab -v \
-            -n 'CS_Signalling_ERBB_RAS_AKT_petab' \
-            -y 'FroehlichKes2018/PEtab/FroehlichKes2018.yaml' \
-            --no-compile
+        check_time.sh petab_import python tests/performance/test.py import
 
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
       uses: actions/upload-artifact@v1
@@ -65,29 +60,60 @@ jobs:
 
     # install model package
     - name: Install test model
-      run: |
-        check_time.sh install_model \
-          python3 CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab/setup.py install --user
+      run: >
+        check_time.sh install_model tests/performance/test.py compile;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh install_model_${opt} tests/performance/test.py compile_${opt};
+        done
 
     # run simulations
     - name: forward_simulation
-      run: |
-        check_time.sh forward_simulation tests/performance/test.py forward_simulation
+      run: >
+        check_time.sh forward_simulation tests/performance/test.py  forward_simulation;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_simulation tests/performance/test.py forward_simulation_${opt};
+        done
     - name: forward_sensitivities
-      run: |
-        check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities
+      run: >
+        check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities_${opt};
+        done
     - name: adjoint_sensitivities
-      run: |
-        check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities
+      run: >
+        check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities_${opt};
+        done
     - name: forward_simulation_non_optimal_parameters
       run: |
-        check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters
+        check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters_${opt};
+        done
     - name: adjoint_sensitivities_non_optimal_parameters
       run: |
-        check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters
+        check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters_${opt};
+        done
     - name: forward_steadystate_sensitivities_non_optimal_parameters
       run: |
-        check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters
+        check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters_${opt};
+        done
     - name: adjoint_steadystate_sensitivities_non_optimal_parameters
       run: |
-        check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters
+        check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters;
+        for opt in O0 O1 O2;
+        do
+          check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters_${opt};
+        done
diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
index d47a58631a..7dad35396d 100644
--- a/.github/workflows/test_sbml_semantic_test_suite.yml
+++ b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -4,6 +4,7 @@ on:
     branches:
       - develop
       - master
+      - release**
   pull_request:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml
diff --git a/.gitignore b/.gitignore
index 6871f44482..44053581ec 100644
--- a/.gitignore
+++ b/.gitignore
@@ -193,3 +193,4 @@ coverage_SBMLSuite.xml
 Benchmark-Models-PEtab/
 
 
+CS_Signalling_ERBB_RAS_AKT/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 875c9603a8..f3e981e425 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,19 @@
 # Changelog 
 
-## v0.11.14 (2021-03-16)
+## v0.X Series
+
+### v0.11.15 (2021-03-31)
+
+Fixes:
+* Fixed initial state sensitivities in adjoint preequilibration (#1468)
+* Fixed various model import / parameter mapping issues (#1469, #1473, #1475)
+
+New:
+* New AMICI releases will automatically trigger releases at
+  https://biosimulators.org/simulators/amici/latest
+* Transparent logo
+
+### v0.11.14 (2021-03-16)
 
 New features:
 * **Python import now supports SBML Events** (#1443)
@@ -33,7 +46,7 @@ Misc:
 * Micro-optimize SUNMatrixWrapper::transpose (#1439)
 * Remove constant triggers from roots in Heaviside (#1440)
 
-## v0.11.13 (2021-02-20)
+### v0.11.13 (2021-02-20)
 
 Breaking changes:
 * AMICI requires Python>=3.7
@@ -69,7 +82,7 @@ Other:
 * Various minor CI improvements
 * ...
 
-## v0.11.12 (2021-01-26)
+### v0.11.12 (2021-01-26)
 
 Features: 
 * Add expression IDs and names to generated models (#1374)
@@ -83,9 +96,9 @@ Docs:
 * Update how-to-cite (#1378)
 
 
-## v0.11.11 (2020-12-15)
+### v0.11.11 (2020-12-15)
 
-### Python
+#### Python
 * Restore support for species references (#1358)
 * Add support for noise models in pysb (#1360)
 * Proper handling of discontinuities in the ODE rhs (#1352)
@@ -93,42 +106,42 @@ Docs:
 * Extend mathml function support, particularly for numerical arguments (#1357)
 * Restore support for sympy 1.6 (#1356)
 
-### C++
+#### C++
 * Fix some compiler related warnings (#1349, #1362 )
 * Fix a rare segfault for adjoint sensitivities (#1351)
 
-### CI
+#### CI
 * Move windows tests to GHA (#1354)
 * Pin breathe to 4.24.1
 
-### Docker
+#### Docker
 * Update ubuntu to 20.04
 
-## v0.11.10 (2020-11-30)
+### v0.11.10 (2020-11-30)
 
 Bugfix release that restores compatibility with sympy 1.7
 
-## v0.11.9 (2020-11-29)
+### v0.11.9 (2020-11-29)
 
-### Python
+#### Python
 * General improvements to SBML import (#1312, #1316, #1315, #1322 , #1324 #1333, #1329)
 * Small bugfixes and improvements (#1321 )
 * Improve derivative computation for instances of `power` (#1320 )
 
-### C++
+#### C++
 * Fix FIM and residual computation for models with parameter dependent sigma. (#1338)
 * Disable chi2/residual/FIM computation for non-gaussian objective functions. (#1338)
 * Bugfix for integration failure during adjoint solve (#1327)
 
-### Doc
+#### Doc
 * Update references (#1331, #1336)
 
-### CI
+#### CI
 * Update OpenBLAS for windows (#1334)
 
-## v0.11.8 (2020-10-21)
+### v0.11.8 (2020-10-21)
 
-### Python
+#### Python
 * Fix pysb-petab support (#1288)
 * Fix ExpData constructor overloading (#1299)
 * Fix support for positivity enforcement (#1306)
@@ -136,21 +149,21 @@ Bugfix release that restores compatibility with sympy 1.7
 * Improve model generation for models with many parameters (#1300)
 * Add support for PEtab based synthetic data generation (#1283)
 
-### C++
+#### C++
 * Make HDF5 an optional dependency (#1285)
 
-### Doc
+#### Doc
 * General Improvements to Documentation (#1289, #1291, #1292, #1293, #1294, #1286, #1277, #1281)
 
-### CI
+#### CI
 * Add python 3.9 support test (#1282)
 * Allow manual triggering of GitHub actions (#1287)
 * Remove appveyor config (#1295)
 * Update GHA env and path management (#1302)
 
-## v0.11.7 (2020-09-22)
+### v0.11.7 (2020-09-22)
 
-### Python
+#### Python
 * Improve and extend available objective functions (#1235)
 * Fix processing of compartment definitions (#1223)
 * Fix replacement of reserved symbols (#1265)
@@ -158,101 +171,101 @@ Bugfix release that restores compatibility with sympy 1.7
 * Fix duplicate running of swig (#1216)
 * Overload python interface functions for amici.{Model,Solver,ExpData} and amici.{Model,Solver,ExpData}Ptr (#1271)
 
-### C++
+#### C++
 * Fix and extend use of sparse matrix operations (#1230, #1240, #1244, #1247, #1271) 
 * **Fix application of maximal number of steps**, MaxNumStep parameter now limit total number of steps, not number of steps between output times. (#1267)
 
-### Doc
+#### Doc
 * Move all Documentation to RTD (#1229, #1241)
 * General Improvements to Documentation (#1225, #1227, #1219, #1228, #1232, #1233, #1234, #1237,  #1238, #1239, #1243, #1253, #1255, #1262)
 
-### CI
+#### CI
 * Better check for doc building (#1226)
 * Add more gradient checks (#1213)
 * Update GHA to Ubuntu 20.04 (#1268)
 
-## v0.11.6 (2020-08-20)
+### v0.11.6 (2020-08-20)
 
-### Python
+#### Python
 * Bugfix for piecewise functions (#1199)
 * Refactor swigging - generate one single wrapper (#1213)
 
-### C++
+#### C++
 * Fix warnings: account for zero indexing in nan/inf error (#1112)
 
-### Doc
+#### Doc
 * Update Windows build instructions (#1200, #1202)
 * Update README: Projects using AMICI (#1209)
 * Add CODE_OF_CONDUCT.md (#1210)
 * Update documentation for Python interface (#1208)
 
-### CI
+#### CI
 * Create sdist on GHA using swig4.0.1 (#1204)  (Fixing broken pypi package)
 * Fix links after repository move
 * Speed-up swig build: disable all languages except python (#1211)
 * Fix doc generation on readthedocs (#1196) 
 
 
-## v0.11.5 (2020-08-07)
+### v0.11.5 (2020-08-07)
 
-### General
+#### General
 * Move repo to new organization (#1193)
 * Update Bibliography
 
-### Python
+#### Python
 * Fix bug for energyPySB models (#1191)
 
-### CI
+#### CI
 * Fix release deployment (#1189)
 
-## v0.11.4 (2020-08-06)
+### v0.11.4 (2020-08-06)
 
-### Python
+#### Python
 * Skip unnecessary expressions in pysb models (#1185)
 * MSVC compiler support (this time for real... #1152)
 
-### CI
+#### CI
 * Implement MSVC tests (#1152)
 * Rename and group GitHub actions (#1186)
 * Fix release deployment (#1186)
 
-## v0.11.3 (2020-08-06)
+### v0.11.3 (2020-08-06)
 
-### Python
+#### Python
 * Fix simplification for pysb models (#1168)
 * Pass verbosity flags to pysb network generation (#1173)
 * Enable experimental pysb-petab support (#1175)
 * Add installation instructions for Fedora (#1177)
 * Implement support for SBML rate-references (#1180)
 
-### C++
+#### C++
 * Refactoring (#1162, #1163)
 
-### CI
+#### CI
 * Move majority of tests to Github Actions (#1166, #1160)
 * Improve reporting of skipped tests in SBML testsuite (#1183)
 
-## v0.11.2 (2020-07-17)
+### v0.11.2 (2020-07-17)
 
-### Python
+#### Python
 * Speed up model import, compilation (#1123, #1112)
 * Improve/Add steady-state solver documentation (#1102)
 * Improve extension import (#1141)
 * Bugfixes SBML import (#1135, #1134, #1145, #1154)
 * Fixed issue that prevented simplification (#1158)
 
-### C++
+#### C++
 * Bugfixes (#1121, #1125, #1131, #1132, #1136)
 * Enable openMP by default (#1118)
 * Improve memoy footprint for simulations with replicates (#1153)
 * Improve steady-state solver and add option to to adjoint-steadystate hybrid (#1143, #1099, #1129, #1146)
 
-### CI
+#### CI
 * Store build artifacts from github actions (#1138)
 
-## v0.11.1 (2020-06-05)
+### v0.11.1 (2020-06-05)
 
-### Python
+#### Python
 * Upgrade to sympy 1.6.0, which is now required minimum version  (#1098, #1103)
 * Speed up model import 
   * Speed-up computation of sx0, reduce file size (#1109)
@@ -265,21 +278,21 @@ Bugfix release that restores compatibility with sympy 1.7
 * Fix MathML conversion (#1086)
 * Fix deepcopy of SymPy objects (#1091)
 
-### Matlab
+#### Matlab
 * handle empty rdata->{pre|post}eq_numlinsteps (Closes #1113), which previously made the matlab interface unusable
 * Fix generation of compileMexFile.m for matlab compilation of python code (#1115)
 
-### C++
+#### C++
 * Reduce memory requirements and speedup compilation of large models (#1105)
 * Place generated code into own namespace (#937) (#1112)
 * Fix several msvc compiler warnings (#1116) (Note that MSVC support is still experimental) **breaking change for users of C++ interface**
 * Fix swig warning: ensure base class ContextManager is known before use (Fixes #1092) (#1101)
 
-### CI
+#### CI
 * Don't install/run valgrind on travis CI (done with github actions… (#1111)
 
 
-## v0.11.0 (2020-05-10)
+### v0.11.0 (2020-05-10)
 
 Python:
 
@@ -304,7 +317,7 @@ CI:
 - Move from Codacy to Sonarcloud (#1065)
 - Run SBML Testsuite when appropriate (#1058)
 
-## v0.10.21 (2020-04-04)
+### v0.10.21 (2020-04-04)
 
 Library:
 * Fix: Handle paths with blanks in build scripts
@@ -317,7 +330,7 @@ CI:
 * Fix: benchmark problem test should fail on missing files (Closes #1015)
 
 
-## v0.10.20 (2020-03-18)
+### v0.10.20 (2020-03-18)
 
 * Fixed (re)initialization of sensitivities if ExpData::fixedParametersPreequilibration is set (#994)
 * Fixed sensitivities for parameters in sigma expressions for Python/SBML in case provided expression was not just a single parameter ID
@@ -342,7 +355,7 @@ CI:
 * Removed mention of 'mex' in warning/error ids (#968)
 * More informative errors on SWIG interface import failures (#959)
 
-## v0.10.19 (2020-02-13)
+### v0.10.19 (2020-02-13)
 
 Python:
 * Fix logo display on pypi
@@ -351,7 +364,7 @@ Python:
 Matlab:
 * Fix compilation errors due to switch to C++14
 
-## v0.10.18 (2020-02-11)
+### v0.10.18 (2020-02-11)
 
 General:
 * AMICI now comes with a logo
@@ -378,7 +391,7 @@ CI:
 
 ... and various minor fixes/updates
 
-## v0.10.17 (2020-01-15)
+### v0.10.17 (2020-01-15)
 
 - **added python 3.8 support, dropped python 3.6 support** (#898) 
 - Added logging functionality (#900)
@@ -388,7 +401,7 @@ CI:
 - Improved petab support (#886, #888, #891)
 - CI related fixes (#865, #896)
 
-## v0.10.16 (2019-12-11)
+### v0.10.16 (2019-12-11)
 
 * **Sparsify dwdp to reduce computation time for adjoints (#858)**
 * Fix(matlab) update example name example_dae_events->example_calvetti (Closes #866)
@@ -397,13 +410,13 @@ CI:
 * Fix pysb_import (fixes #878)
 
 
-## v0.10.15 (2019-12-03)
+### v0.10.15 (2019-12-03)
 
 Bugfix release due to incorrect sensitivities w.r.t. sigmas introduced in 0.10.14.
 
 No other changes.
 
-## v0.10.14 (2019-12-02)
+### v0.10.14 (2019-12-02)
 
 **NOTE: For Python-imported SBML-models this release may compute incorrect sensitivities w.r.t. sigma. Bug introduced in 0.10.14, fixed in 0.10.15.**
 
@@ -436,7 +449,7 @@ Misc:
 * Update documentation and FAQ for CBLAS requirement and others
 * Update reference list
 
-## v0.10.13 (2019-10-09)
+### v0.10.13 (2019-10-09)
 
 * BREAKING CHANGE: Renaming {get|set}tNewtonPreequilibration to {get|set}Preequilibration (Closes #720)
 * Make wurlitzer non-optional requirement for AMICI python package (Fixes missing AMICI errors when running from jupyter notebooks)
@@ -450,7 +463,7 @@ Misc:
 * Update workflow figure to include PySB (Closes #799)
 * Fix compiler warnings
 
-## v0.10.12 (2019-09-28)
+### v0.10.12 (2019-09-28)
 
 * Fix handling of species specified in PEtab condition table (#813)
 * Fix some Visual C++ issues, update cppcheck handling, cleanup (VisualC++ still not fully supported)
@@ -458,7 +471,7 @@ Misc:
 * Create SBML test suite result files for upload to http://sbml.org/Facilities/Database/ (#798)
 
 
-## v0.10.11 (2019-08-31)
+### v0.10.11 (2019-08-31)
 
 * Fixed setting initial conditions for preequilibration (#784) 
 * Fixed species->parameter conversion during PEtab import (#782) 
@@ -467,7 +480,7 @@ Misc:
 * Fix various SBML import issues
 * Run SBML test suite using github actions instead of travisCI (#789)
 
-## v0.10.10 (2019-08-07)
+### v0.10.10 (2019-08-07)
 
 * Simplify/fix AMICI installation
    * If available use environment modules to detect dependencies
@@ -504,11 +517,11 @@ Detaills:
     * Allow overriding cmake executable with environment variables in build scripts (Closes #738)
  
 
-## v0.10.9 (2019-07-24)
+### v0.10.9 (2019-07-24)
 
 Fixup for missing version bump in v0.10.8 release. No code changes compared to v0.10.8.
 
-## v0.10.8 (2019-07-24)
+### v0.10.8 (2019-07-24)
 
 Changes in this release:
 
@@ -526,12 +539,12 @@ Python:
 
 ... and various other minor fixes/improvements
 
-## v0.10.7 (2019-05-01)
+### v0.10.7 (2019-05-01)
 
 Python
 * fix unset noise distribution when automatically generating observables in case None are passed (#691)
 
-## v0.10.6 (2019-04-19)
+### v0.10.6 (2019-04-19)
 
 C++
 - Add SuperLUMT support (#681)
@@ -544,7 +557,7 @@ Python
 - Fix dynamic override in PETab
 
 
-## v0.10.5 (2019-04-08)
+### v0.10.5 (2019-04-08)
 
 Bugfix release
 
@@ -563,7 +576,7 @@ Python
 - Updated PEtab import to allow for different noise models
 
 
-## v0.10.4 (2019-03-21)
+### v0.10.4 (2019-03-21)
 
 Features / improvements:
 
@@ -575,7 +588,7 @@ Bugfixes:
 
 + Speedup and fix travis build
 
-## v0.10.3 (2019-03-13)
+### v0.10.3 (2019-03-13)
 
 Features / improvements:
 
@@ -588,7 +601,7 @@ Bugfixes:
 
 - fixed symbolic processing for unreleased pysb features
 
-## v0.10.2 (2019-03-07)
+### v0.10.2 (2019-03-07)
 
 Features / improvements:
 
@@ -598,13 +611,13 @@ Bugfixes:
 
 - fixed output values of `ReturnData::x_ss` and `ReturnData::sx_ss`
 
-## v0.10.1 (2019-03-04)
+### v0.10.1 (2019-03-04)
 
 * travis-ci.com migration
 * fix problem with has{variable} functions
 * allow to import sbml model from string, not only file
 
-## v0.10.0 (2019-03-01)
+### v0.10.0 (2019-03-01)
 
 Features / improvements:
 
@@ -616,7 +629,7 @@ Bugfixes:
 
 - fixed return value of `rz` when no data is provided.
 
-## v0.9.5 (2019-02-26)
+### v0.9.5 (2019-02-26)
 
 Features / improvements:
 
@@ -634,13 +647,13 @@ Maintenance:
 
 - use newer CI images 
 
-## v0.9.4 (2019-02-11)
+### v0.9.4 (2019-02-11)
 
 Minor fixes only:
 - fix(core) Get solver diagnostics for first(last) timepoint (#588) (Closes #586)
 - fix(ci) Fix autodeploy (Closes #589)
 
-## v0.9.3 (2019-02-07)
+### v0.9.3 (2019-02-07)
 
 **CRITICAL FIXES**
 - **fix(python) fix symbolic computations for adjoint (#583)**
@@ -657,7 +670,7 @@ Minor fixes only:
 
 
 
-## v0.9.2 (2019-01-30)
+### v0.9.2 (2019-01-30)
 
 Bugfixes:
 
@@ -669,7 +682,7 @@ Bugfixes:
 - #559 
 
 
-## v0.9.1 (2019-01-21)
+### v0.9.1 (2019-01-21)
 
 Features / improvements:
 
@@ -686,7 +699,7 @@ Maintenance:
 
 - attempt to fix automatic deploy to pypi via travis
 
-## v0.9.0 (2019-01-18)
+### v0.9.0 (2019-01-18)
 
 Features / improvements:
 
@@ -703,7 +716,7 @@ Maintenance:
 - Reenable run of SBML testsuite
 
 
-## v0.8.2 (2019-01-07)
+### v0.8.2 (2019-01-07)
 
 Features / improvements:
 * Speedup symbolic processing for ODE generation in python
@@ -724,7 +737,7 @@ Maintenance:
 * Update documentation and tests
 * Add python version check and raise required version to 3.6 to prevent cryptic error messages when encountering f-strings
 
-## v0.8.1 (2018-11-25)
+### v0.8.1 (2018-11-25)
 
 - [all] **critical** Fix long standing bugs in solving steadystate problems (including preequilibration) (#471)
 - [all] Fix AmiVector constructor from std::vector (#471)
@@ -732,24 +745,24 @@ Maintenance:
 - Update documentation
 
 
-## v0.8.0 (2018-11-25)
+### v0.8.0 (2018-11-25)
 
 - replaced symengine by sympy for symbolic processing in python *which fixes several critical bugs* that were due to bugs in symengine (#467)
 
 
-## v0.7.13 (2018-11-18)
+### v0.7.13 (2018-11-18)
 
 - fixes a critical bug in objective function computation for models compiled using `sbml2amici` and `pysb2amici` that was introduced in v0.7.12
 - fixes a critical bug in sensitivity computation when`model.reinitializeFixedParameterInitialStates` was set to true
 - readds the python interface to the ExpData copy constructor that was inadvertently removed in 0.7.12 and streamlines the respective convenience wrapper to provide access to the full range of constructors.
 
-## v0.7.12 (2018-11-17)
+### v0.7.12 (2018-11-17)
 
 - fixed a critical bug in `amici.constructEdataFromDataFrame`
 - enabled multithreaded simulation of multiple experiments (requires compilation with openMP)
 - modularized sbml import and added pysb import
 
-## v0.7.11 (2018-10-15)
+### v0.7.11 (2018-10-15)
 
 - [python] Added numpy and python wrappers that provide a more user friendly python API
 - [python] Enable import of SBML models with non-float assignment rules 
@@ -758,27 +771,27 @@ Maintenance:
 - [core] Provide an API for more fine-grained control over sensitivity tolerances and steady-state tolerances
 - [core] Provide an API to specify non-negative state variables (this feature is still preliminary)
 
-## v0.7.10 (2018-08-29)
+### v0.7.10 (2018-08-29)
 
 - Fixed python SBML import `log()` issues (#412)
 
-## v0.7.9 (2018-08-24)
+### v0.7.9 (2018-08-24)
 
 - fixes MATLAB compilation of models
 - adds option to perform steady state sensitivity analysis via FSA
 - condition dependent intitial conditions are now newly set after preequilibration is done
 
-## v0.7.8 (2018-08-19)
+### v0.7.8 (2018-08-19)
 
 - bugfixes for the ExpData interface
 - created build configuration that enables debugging of c++ extensions on os x
 - fixed python sbml import when stoichiometry is empty
 
-## v0.7.7 (2018-08-17)
+### v0.7.7 (2018-08-17)
 
 Fixes a couple of bugs just introduced in v0.7.6
 
-## v0.7.6 (2018-08-13)
+### v0.7.6 (2018-08-13)
 
 Important: **Use AMICI v0.7.7 due to https://github.com/ICB-DCM/AMICI/pull/403/commits/3a495d3db2fdbba70c2b0d52a3d4655c33c817a2**
 
@@ -791,7 +804,7 @@ Bug fixes:
 Breaking C++ API changes:
 - Revised ExpData interface (#388)
 
-## v0.7.5 (2018-07-30)
+### v0.7.5 (2018-07-30)
 
 Features/enhancements:
 - Add computation of residuals, residuals sensitivity, Fisher information matrix (#223)
@@ -802,7 +815,7 @@ Minor fixes:
 - Condition parameters in ExpData now only temporarily override Model parameters (#371)
 - Ensure non-negative states for Newton solver (#378)
 
-## v0.7.4 (2018-07-27)
+### v0.7.4 (2018-07-27)
 
 Features/enhancements:
 - Check SBML model validity (#343)
@@ -816,7 +829,7 @@ Minor fixes:
 - Fix compiler warnings (#353)
 - Plotting, SBML example mode, ...
 
-## v0.7.3 (2018-07-13)
+### v0.7.3 (2018-07-13)
 
 Features:
 - Added symbol names to python-wrapped models and make available via Model.getParameterNames(), model.getStateNames(), ...
@@ -824,7 +837,7 @@ Features:
 
 Python package available via pypi: https://pypi.org/project/amici/0.7.3/
 
-## v0.7.2 (2018-07-03)
+### v0.7.2 (2018-07-03)
 
 Features:
 - Python package: more flexible HDF5 library localization
@@ -838,7 +851,7 @@ Minor fixes:
 - Various fixes for mingw compilation of python source distribution
 - Cmake compatibility with < 3.8 restored
 
-## v0.7.1 (2018-06-12)
+### v0.7.1 (2018-06-12)
 
 Features:
 - Allow specifying sigma-parameters from Python interface
@@ -846,7 +859,7 @@ Features:
 Major bugfixes:
 - Fix dsigma_y/dp and downstream sensitivity errors
 
-## v0.7.0 (2018-06-09)
+### v0.7.0 (2018-06-09)
 
 - Major revision of documentation
 - Improved Python interface
@@ -857,7 +870,7 @@ Major bugfixes:
 WARNING:
 - For models with sigma-parameters and dsigma_y/dp != 0, dsigma_y/dp was computed incorrectly. This propagates to all dependent sensitivities. This applies also to some older releases and has been fixed in v0.7.1.
 
-## v0.6.0 (2018-05-22)
+### v0.6.0 (2018-05-22)
 
 Implement experimental support for python via swig.
 Python interface is now usable, but API will still receive some updates in the future.
@@ -867,7 +880,7 @@ WARNING:
 - Matlab C++ compilation will fail due to undefined M_PI
 -> Please use v0.7.0
 
-## v0.5.0 (2018-03-15)
+### v0.5.0 (2018-03-15)
 
 Main new features are:
 
@@ -882,14 +895,14 @@ Main new features are:
 - Rewrote large parts of the code as proper c++11 code to allow easier code maintanance
 - Substantially extended testing in continuous integration to assure code quality
 
-## v0.4.0 (2017-05-15)
+### v0.4.0 (2017-05-15)
 
 * First citable version of AMICI (via zenodo integration).
 * Better support for standalone compilation
 * Improved SBML import scripts
 * General Code Cleanup
 
-## v0.3.0 (2016-09-05)
+### v0.3.0 (2016-09-05)
 
 This update comes with many improvements, bug fixes and several new features. Most notably:
 
@@ -899,12 +912,12 @@ This update comes with many improvements, bug fixes and several new features. Mo
 4) AMICI now supports more SBML, SBML v2 and rate rules
 
 
-## 0.2.1 (2016-05-09)
+### 0.2.1 (2016-05-09)
 
 Bugfix release. This release also includes some changes that should improve the performance on the new R2016a release of MATLAB.
 
 
-## v0.2 (2016-03-17)
+### v0.2 (2016-03-17)
 
 This update comes with many improvements to the computation time for both compilation and simulation. Moreover several new features were included:
 
@@ -912,6 +925,6 @@ This update comes with many improvements to the computation time for both compil
 2) Correct treatment of parameter/state dependent discontinuities for both forward and adjoint sensitivities
 
 
-## v0.1 (2015-11-05)
+### v0.1 (2015-11-05)
 
 This is the initial release of the toolbox
diff --git a/docker/README.md b/docker/README.md
index ec7ecc6771..97c0722545 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -12,4 +12,4 @@ cd docker && docker build -t $USER/amici:latest .
 ## Published images
 
 AMICI docker images are regularly published to
-https://hub.docker.com/layers/dweindl/amici/.
+https://hub.docker.com/r/dweindl/amici.
diff --git a/documentation/gfx/banner.png b/documentation/gfx/banner.png
index a88c2da489..40016b4da0 100644
Binary files a/documentation/gfx/banner.png and b/documentation/gfx/banner.png differ
diff --git a/documentation/gfx/logo.png b/documentation/gfx/logo.png
index 3f22c92a86..7810c1e7ce 100644
Binary files a/documentation/gfx/logo.png and b/documentation/gfx/logo.png differ
diff --git a/documentation/gfx/logo_text.png b/documentation/gfx/logo_text.png
index 22354e62b1..c72388e941 100644
Binary files a/documentation/gfx/logo_text.png and b/documentation/gfx/logo_text.png differ
diff --git a/documentation/rtd_requirements.txt b/documentation/rtd_requirements.txt
index 58ccbff6d3..154f12a9dc 100644
--- a/documentation/rtd_requirements.txt
+++ b/documentation/rtd_requirements.txt
@@ -21,4 +21,4 @@ git+https://github.com/dweindl/exhale@ea77a313777c1382a7830ce9ee6c405ce47f5f3b#e
 -e git+https://github.com/mithro/sphinx-contrib-mithro#egg=sphinx-contrib-exhale-multiproject&subdirectory=sphinx-contrib-exhale-multiproject
 sphinxcontrib-matlabdomain
 sphinxcontrib-napoleon
-pygments==2.4.1
+pygments==2.7.4
diff --git a/include/amici/rdata.h b/include/amici/rdata.h
index 1637f67ede..c0c42b78a5 100644
--- a/include/amici/rdata.h
+++ b/include/amici/rdata.h
@@ -618,10 +618,12 @@ class ReturnData: public ModelDimensions {
      * if preequilibration was run in adjoint mode
      * @param model model that was used for forward/backward simulation
      * @param preeq SteadystateProblem for preequilibration
+     * @param llhS0 contribution to likelihood for initial state sensitivities
+     * of preequilibration
      * @param xQB vector with quadratures from adjoint computation
      */
     void handleSx0Backward(const Model &model, SteadystateProblem const &preeq,
-                           AmiVector &xQB) const;
+                           std::vector<realtype> &llhS0, AmiVector &xQB) const;
 
     /**
      * @brief Updates contribution to likelihood for initial state sensitivities
diff --git a/include/amici/serialization.h b/include/amici/serialization.h
index f816d56633..7906a2cc48 100644
--- a/include/amici/serialization.h
+++ b/include/amici/serialization.h
@@ -290,16 +290,19 @@ char *serializeToChar(T const& data, int *size) {
 
 template <typename T>
 T deserializeFromChar(const char *buffer, int size) {
+    namespace ba = ::boost::archive;
+    namespace bio = ::boost::iostreams;
+
+    bio::basic_array_source<char> device(buffer, size);
+    bio::stream<bio::basic_array_source<char>> s(device);
+
+    T data;
+
     try {
-        ::boost::iostreams::basic_array_source<char> device(buffer, size);
-        ::boost::iostreams::stream<::boost::iostreams::basic_array_source<char>> s(
-            device);
-        ::boost::archive::binary_iarchive iar(s);
-        T data;
+        ba::binary_iarchive iar(s);
         iar >> data;
-
         return data;
-    } catch(::boost::archive::archive_exception const& e) {
+    } catch(ba::archive_exception const& e) {
         throw AmiException("Deserialization from char failed: %s", e.what());
     }
 }
@@ -314,19 +317,20 @@ T deserializeFromChar(const char *buffer, int size) {
 
 template <typename T>
 std::string serializeToString(T const& data) {
+    namespace ba = ::boost::archive;
+    namespace bio = ::boost::iostreams;
+
+    std::string serialized;
+    bio::back_insert_device<std::string> inserter(serialized);
+    bio::stream<bio::back_insert_device<std::string>> os(inserter);
+
     try {
-        std::string serialized;
-        ::boost::iostreams::back_insert_device<std::string> inserter(serialized);
-        ::boost::iostreams::stream<
-            ::boost::iostreams::back_insert_device<std::string>>
-            s(inserter);
-        ::boost::archive::binary_oarchive oar(s);
+        ba::binary_oarchive oar(os);
 
         oar << data;
-        s.flush();
 
         return serialized;
-    } catch(::boost::archive::archive_exception const& e) {
+    } catch(ba::archive_exception const& e) {
         throw AmiException("Serialization to string failed: %s", e.what());
     }
 }
@@ -341,21 +345,22 @@ std::string serializeToString(T const& data) {
 
 template <typename T>
 std::vector<char> serializeToStdVec(T const& data) {
+    namespace ba = ::boost::archive;
+    namespace bio = ::boost::iostreams;
+
+    std::vector<char> buffer;
+    bio::stream<
+        bio::back_insert_device<
+            std::vector<char>>> os(buffer);
+
     try{
-        std::string serialized;
-        ::boost::iostreams::back_insert_device<std::string> inserter(serialized);
-        ::boost::iostreams::stream<::boost::iostreams::back_insert_device<std::string>>
-            s(inserter);
-        ::boost::archive::binary_oarchive oar(s);
+        ba::binary_oarchive oar(os);
 
         oar << data;
-        s.flush();
-
-        std::vector<char> buf(serialized.begin(), serialized.end());
 
-        return buf;
-    } catch(::boost::archive::archive_exception const& e) {
-        throw AmiException("Serialization to StdVec failed: %s", e.what());
+        return buffer;
+    } catch(ba::archive_exception const& e) {
+        throw AmiException("Serialization to std::vector failed: %s", e.what());
     }
 }
 
@@ -369,19 +374,22 @@ std::vector<char> serializeToStdVec(T const& data) {
 
 template <typename T>
 T deserializeFromString(std::string const& serialized) {
+    namespace ba = ::boost::archive;
+    namespace bio = ::boost::iostreams;
+
+    bio::basic_array_source<char> device(serialized.data(), serialized.size());
+    bio::stream<bio::basic_array_source<char>> os(device);
+    T deserialized;
+
     try{
-        ::boost::iostreams::basic_array_source<char> device(serialized.data(),
-                                                          serialized.size());
-        ::boost::iostreams::stream<::boost::iostreams::basic_array_source<char>> s(
-            device);
-        ::boost::archive::binary_iarchive iar(s);
-        T deserialized;
+        ba::binary_iarchive iar(os);
 
         iar >> deserialized;
 
         return deserialized;
-    } catch(::boost::archive::archive_exception const& e) {
-        throw AmiException("Deserialization from StdVec failed: %s", e.what());
+    } catch(ba::archive_exception const& e) {
+        throw AmiException("Deserialization from std::string failed: %s",
+                           e.what());
     }
 }
 
diff --git a/include/amici/steadystateproblem.h b/include/amici/steadystateproblem.h
index 3629a4702a..bd7efe47c4 100644
--- a/include/amici/steadystateproblem.h
+++ b/include/amici/steadystateproblem.h
@@ -248,7 +248,6 @@ class SteadystateProblem {
         return x_;
     };
 
-
     /**
      * @brief Returns state sensitivity at steadystate
      * @return sx
@@ -321,6 +320,12 @@ class SteadystateProblem {
      */
     void getAdjointUpdates(Model &model, const ExpData &edata);
 
+    /**
+     * @brief Return the adjoint state
+     * @return xB adjoint state
+     */
+    AmiVector const& getAdjointState() const { return xB_; }
+
     /**
      * @brief Accessor for xQB
      * @return xQB
@@ -372,7 +377,7 @@ class SteadystateProblem {
     AmiVector xQ_;
     /** quadrature state vector */
     AmiVector xQB_;
-    /** quadrature state vector */
+    /** time-derivative of quadrature state vector */
     AmiVector xQBdot_;
 
     /** maximum number of steps for Newton solver for allocating numlinsteps */
diff --git a/python/amici/petab_import.py b/python/amici/petab_import.py
index 68fb53e3d5..bfbbf744ad 100644
--- a/python/amici/petab_import.py
+++ b/python/amici/petab_import.py
@@ -459,6 +459,21 @@ def import_model_sbml(
     sbml_importer = amici.SbmlImporter(sbml_model)
     sbml_model = sbml_importer.sbml
 
+    allow_n_noise_pars = \
+        not petab.lint.observable_table_has_nontrivial_noise_formula(
+            observable_df
+        )
+    if measurement_table is not None and \
+            petab.lint.measurement_table_has_timepoint_specific_mappings(
+        measurement_table,
+        allow_scalar_numeric_noise_parameters=allow_n_noise_pars
+    ):
+        raise ValueError(
+            'AMICI does not support importing models with timepoint specific '
+            'mappings for noise or observable parameters. Please flatten '
+            'the problem and try again.'
+        )
+
     if observable_df is not None:
         observables, noise_distrs, sigmas = \
             get_observation_model(observable_df)
@@ -574,10 +589,10 @@ def import_model_sbml(
 import_model = import_model_sbml
 
 
-def get_observation_model(observable_df: pd.DataFrame
-                          ) -> Tuple[Dict[str, Dict[str, str]],
-                                     Dict[str, str],
-                                     Dict[str, Union[str, float]]]:
+def get_observation_model(
+        observable_df: pd.DataFrame,
+) -> Tuple[Dict[str, Dict[str, str]], Dict[str, str],
+           Dict[str, Union[str, float]]]:
     """
     Get observables, sigmas, and noise distributions from PEtab observation
     table in a format suitable for
@@ -596,13 +611,13 @@ def get_observation_model(observable_df: pd.DataFrame
     observables = {}
     sigmas = {}
 
+    nan_pat = r'^[nN]a[nN]$'
     for _, observable in observable_df.iterrows():
-        oid = observable.name
+        oid = str(observable.name)
         # need to sanitize due to https://github.com/PEtab-dev/PEtab/issues/447
-        pat = r'^[nN]a[nN]$'
-        name = re.sub(pat, '', str(observable.get(OBSERVABLE_NAME, '')))
-        formula_obs = re.sub(pat, '', str(observable[OBSERVABLE_FORMULA]))
-        formula_noise = re.sub(pat, '', str(observable[NOISE_FORMULA]))
+        name = re.sub(nan_pat, '', str(observable.get(OBSERVABLE_NAME, '')))
+        formula_obs = re.sub(nan_pat, '', str(observable[OBSERVABLE_FORMULA]))
+        formula_noise = re.sub(nan_pat, '', str(observable[NOISE_FORMULA]))
         observables[oid] = {'name': name, 'formula': formula_obs}
         sigmas[oid] = formula_noise
 
@@ -617,7 +632,8 @@ def get_observation_model(observable_df: pd.DataFrame
     return observables, noise_distrs, sigmas
 
 
-def petab_noise_distributions_to_amici(observable_df: pd.DataFrame) -> Dict:
+def petab_noise_distributions_to_amici(observable_df: pd.DataFrame
+                                       ) -> Dict[str, str]:
     """
     Map from the petab to the amici format of noise distribution
     identifiers.
@@ -689,6 +705,10 @@ def parse_cli_args():
     parser.add_argument('--no-compile', action='store_false',
                         dest='compile',
                         help='Only generate model code, do not compile')
+    parser.add_argument('--flatten', dest='flatten', default=False,
+                        action='store_true',
+                        help='Flatten measurement specific overrides of '
+                             'observable and noise parameters')
 
     # Call with set of files
     parser.add_argument('-s', '--sbml', dest='sbml_file_name',
@@ -740,6 +760,9 @@ def main():
     # First check for valid PEtab
     petab.lint_problem(pp)
 
+    if args.flatten:
+        petab.flatten_timepoint_specific_output_overrides(pp)
+
     import_model(model_name=args.model_name,
                  sbml_model=pp.sbml_model,
                  condition_table=pp.condition_df,
diff --git a/python/amici/petab_import_pysb.py b/python/amici/petab_import_pysb.py
index f5aa22dd5d..3d33906e5b 100644
--- a/python/amici/petab_import_pysb.py
+++ b/python/amici/petab_import_pysb.py
@@ -47,8 +47,10 @@ def __init__(self, pysb_model: 'pysb.Model' = None, *args, **kwargs):
         :param args: See :meth:`petab.Problem.__init__`
         :param kwargs: See :meth:`petab.Problem.__init__`
         """
-
+        flatten = kwargs.pop('flatten', False)
         super().__init__(*args, **kwargs)
+        if flatten:
+            petab.flatten_timepoint_specific_output_overrides(self)
 
         self.pysb_model: 'pysb.Model' = pysb_model
         self._add_observation_model()
@@ -108,17 +110,33 @@ def from_files(condition_file: str = None,
                    visualization_files: Union[str, Iterable[str]] = None,
                    observable_files: Union[str, Iterable[str]] = None,
                    pysb_model_file: str = None,
-                   ) -> 'PysbPetabProblem':
+                   flatten: bool = False) -> 'PysbPetabProblem':
         """
         Factory method to load model and tables from files.
 
-        Arguments:
-            condition_file: PEtab condition table
-            measurement_file: PEtab measurement table
-            parameter_file: PEtab parameter table
-            visualization_files: PEtab visualization tables
-            observable_files: PEtab observables tables
-            pysb_model_file: PySB model file
+        :param condition_file:
+            PEtab condition table
+
+        :param measurement_file:
+            PEtab measurement table
+
+        :param parameter_file:
+            PEtab parameter table
+
+        :param visualization_files:
+            PEtab visualization tables
+
+        :param observable_files:
+            PEtab observables tables
+
+        :param pysb_model_file:
+            PySB model file
+
+        :param flatten:
+            Flatten the petab problem
+
+        :return:
+            Petab Problem
         """
 
         condition_df = measurement_df = parameter_df = visualization_df = None
@@ -152,18 +170,27 @@ def from_files(condition_file: str = None,
             measurement_df=measurement_df,
             parameter_df=parameter_df,
             observable_df=observable_df,
-            visualization_df=visualization_df)
+            visualization_df=visualization_df,
+            flatten=flatten
+        )
 
     @staticmethod
-    def from_yaml(yaml_config: Union[Dict, str]) -> 'PysbPetabProblem':
+    def from_yaml(yaml_config: Union[Dict, str],
+                  flatten: bool = False) -> 'PysbPetabProblem':
         """
         Factory method to load model and tables as specified by YAML file.
 
         NOTE: The PySB model is currently expected in the YAML file under
         ``sbml_files``.
 
-        Arguments:
-            yaml_config: PEtab configuration as dictionary or YAML file name
+        :param yaml_config:
+            PEtab configuration as dictionary or YAML file name
+
+        :param flatten:
+            Flatten the petab problem
+
+        :return:
+            Petab Problem
         """
         from petab.yaml import (load_yaml, is_composite_problem,
                                 assert_single_condition_and_sbml_file)
@@ -210,7 +237,8 @@ def from_yaml(yaml_config: Union[Dict, str]) -> 'PysbPetabProblem':
                 for f in problem0.get(VISUALIZATION_FILES, [])],
             observable_files=[
                 os.path.join(path_prefix, f)
-                for f in problem0.get(OBSERVABLE_FILES, [])]
+                for f in problem0.get(OBSERVABLE_FILES, [])],
+            flatten=flatten
         )
 
 
diff --git a/python/amici/petab_objective.py b/python/amici/petab_objective.py
index 7b4d4fcf6b..2039d68033 100644
--- a/python/amici/petab_objective.py
+++ b/python/amici/petab_objective.py
@@ -262,7 +262,12 @@ def create_parameter_mapping(
 
     prelim_parameter_mapping = \
         petab_problem.get_optimization_to_simulation_parameter_mapping(
-            warn_unmapped=False, scaled_parameters=scaled_parameters)
+            warn_unmapped=False, scaled_parameters=scaled_parameters,
+            allow_timepoint_specific_numeric_noise_parameters=
+            not petab.lint.observable_table_has_nontrivial_noise_formula(
+                petab_problem.observable_df
+            )
+        )
 
     parameter_mapping = ParameterMapping()
     for (_, condition), prelim_mapping_for_condition in \
diff --git a/python/sdist/setup.cfg b/python/sdist/setup.cfg
index 735b68e748..8e8fdbaeaf 100644
--- a/python/sdist/setup.cfg
+++ b/python/sdist/setup.cfg
@@ -41,7 +41,7 @@ include_package_data = True
 zip_safe = False
 
 [options.extras_require]
-petab = petab>=0.1.11
+petab = petab>=0.1.17
 pysb = pysb>=1.11.0
 
 [options.package_data]
diff --git a/src/hdf5.cpp b/src/hdf5.cpp
index 12ef25cf7a..2dc974bb8d 100644
--- a/src/hdf5.cpp
+++ b/src/hdf5.cpp
@@ -1,3 +1,12 @@
+/**
+ * Functions for HDF5 I/O
+ *
+ * NOTE: Use only `const char*` versions of any HDF5 functions, not the
+ * `std::string` version. On many systems, HDF5 libraries are still not compiled
+ * with C++11 support, but use the old C++03 ABI, which will lead to linking
+ * issues.
+ */
+
 #include "amici/hdf5.h"
 #include "amici/amici.h"
 
@@ -97,7 +106,7 @@ void createGroup(H5::H5File const& file,
 std::unique_ptr<ExpData> readSimulationExpData(std::string const& hdf5Filename,
                                                std::string const& hdf5Root,
                                                Model const& model) {
-    H5::H5File file(hdf5Filename, H5F_ACC_RDONLY);
+    H5::H5File file(hdf5Filename.c_str(), H5F_ACC_RDONLY);
 
     hsize_t m, n;
 
@@ -495,7 +504,7 @@ void createAndWriteInt1DDataset(H5::H5File const& file,
                                 gsl::span<const int> buffer) {
     hsize_t size = buffer.size();
     H5::DataSpace dataspace(1, &size);
-    auto dataset = file.createDataSet(datasetName, H5::PredType::NATIVE_INT,
+    auto dataset = file.createDataSet(datasetName.c_str(), H5::PredType::NATIVE_INT,
                                       dataspace);
     dataset.write(buffer.data(), H5::PredType::NATIVE_INT);
 }
@@ -505,7 +514,7 @@ void createAndWriteDouble1DDataset(const H5::H5File &file,
                                    gsl::span<const double> buffer) {
     hsize_t size = buffer.size();
     H5::DataSpace dataspace(1, &size);
-    auto dataset = file.createDataSet(datasetName, H5::PredType::NATIVE_DOUBLE,
+    auto dataset = file.createDataSet(datasetName.c_str(), H5::PredType::NATIVE_DOUBLE,
                                       dataspace);
     dataset.write(buffer.data(), H5::PredType::NATIVE_DOUBLE);
 }
@@ -516,7 +525,7 @@ void createAndWriteDouble2DDataset(const H5::H5File &file,
                                    hsize_t n) {
     const hsize_t adims[] {m, n};
     H5::DataSpace dataspace(2, adims);
-    auto dataset = file.createDataSet(datasetName, H5::PredType::NATIVE_DOUBLE,
+    auto dataset = file.createDataSet(datasetName.c_str(), H5::PredType::NATIVE_DOUBLE,
                                       dataspace);
     dataset.write(buffer.data(), H5::PredType::NATIVE_DOUBLE);
 }
@@ -527,7 +536,7 @@ void createAndWriteInt2DDataset(H5::H5File const& file,
                                 hsize_t n) {
     const hsize_t adims[] {m, n};
     H5::DataSpace dataspace(2, adims);
-    auto dataset = file.createDataSet(datasetName, H5::PredType::NATIVE_INT,
+    auto dataset = file.createDataSet(datasetName.c_str(), H5::PredType::NATIVE_INT,
                                       dataspace);
     dataset.write(buffer.data(), H5::PredType::NATIVE_INT);
 }
@@ -538,7 +547,7 @@ void createAndWriteDouble3DDataset(H5::H5File const& file,
                                    hsize_t n, hsize_t o) {
     const hsize_t adims[] {m, n, o};
     H5::DataSpace dataspace(3, adims);
-    auto dataset = file.createDataSet(datasetName, H5::PredType::NATIVE_DOUBLE,
+    auto dataset = file.createDataSet(datasetName.c_str(), H5::PredType::NATIVE_DOUBLE,
                                       dataspace);
     dataset.write(buffer.data(), H5::PredType::NATIVE_DOUBLE);
 }
@@ -871,14 +880,14 @@ void readSolverSettingsFromHDF5(H5::H5File const& file, Solver &solver,
 
 void readSolverSettingsFromHDF5(const std::string &hdffile, Solver &solver,
                                 const std::string &datasetPath) {
-    H5::H5File file(hdffile, H5F_ACC_RDONLY, H5P_DEFAULT);
+    H5::H5File file(hdffile.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
 
     readSolverSettingsFromHDF5(file, solver, datasetPath);
 }
 
 void readModelDataFromHDF5(const std::string &hdffile, Model &model,
                            const std::string &datasetPath) {
-    H5::H5File file(hdffile, H5F_ACC_RDONLY, H5P_DEFAULT);
+    H5::H5File file(hdffile.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
 
     readModelDataFromHDF5(file, model, datasetPath);
 }
@@ -958,12 +967,12 @@ H5::H5File createOrOpenForWriting(const std::string &hdf5filename)
 {
     AMICI_H5_SAVE_ERROR_HANDLER;
     try {
-        H5::H5File file(hdf5filename, H5F_ACC_RDWR);
+        H5::H5File file(hdf5filename.c_str(), H5F_ACC_RDWR);
         AMICI_H5_RESTORE_ERROR_HANDLER;
         return file;
     } catch(...) {
         AMICI_H5_RESTORE_ERROR_HANDLER;
-        return H5::H5File(hdf5filename, H5F_ACC_EXCL);
+        return H5::H5File(hdf5filename.c_str(), H5F_ACC_EXCL);
     }
 }
 
@@ -977,13 +986,13 @@ bool locationExists(const H5::H5File &file, const std::string &location)
 
 bool locationExists(const std::string &filename, const std::string &location)
 {
-    H5::H5File file(filename, H5F_ACC_RDONLY);
+    H5::H5File file(filename.c_str(), H5F_ACC_RDONLY);
     return locationExists(file, location);
 }
 
 std::vector<int> getIntDataset1D(const H5::H5File &file,
                                  std::string const& name) {
-    auto dataset = file.openDataSet(name);
+    auto dataset = file.openDataSet(name.c_str());
     auto dataspace = dataset.getSpace();
 
     int rank = dataspace.getSimpleExtentNdims();
@@ -1002,7 +1011,7 @@ std::vector<int> getIntDataset1D(const H5::H5File &file,
 std::vector<double> getDoubleDataset1D(const H5::H5File &file,
                                        const std::string &name)
 {
-    auto dataset = file.openDataSet(name);
+    auto dataset = file.openDataSet(name.c_str());
     auto dataspace = dataset.getSpace();
 
     int rank = dataspace.getSimpleExtentNdims();
@@ -1025,7 +1034,7 @@ std::vector<double> getDoubleDataset2D(const H5::H5File &file,
 {
     m = n = 0;
 
-    auto dataset = file.openDataSet(name);
+    auto dataset = file.openDataSet(name.c_str());
     auto dataspace = dataset.getSpace();
 
     int rank = dataspace.getSimpleExtentNdims();
@@ -1050,7 +1059,7 @@ std::vector<double> getDoubleDataset3D(const H5::H5File &file,
 {
     m = n = o = 0;
 
-    auto dataset = file.openDataSet(name);
+    auto dataset = file.openDataSet(name.c_str());
     auto dataspace = dataset.getSpace();
 
     int rank = dataspace.getSimpleExtentNdims();
diff --git a/src/rdata.cpp b/src/rdata.cpp
index 9b7f944611..6e78a4b83d 100644
--- a/src/rdata.cpp
+++ b/src/rdata.cpp
@@ -414,7 +414,7 @@ void ReturnData::processBackwardProblem(ForwardProblem const &fwd,
     auto xQB = bwd.getAdjointQuadrature();
 
     if (preeq && preeq->hasQuadrature()) {
-        handleSx0Backward(model, *preeq, xQB);
+        handleSx0Backward(model, *preeq, llhS0, xQB);
     } else {
         handleSx0Forward(model, llhS0, xB);
     }
@@ -433,6 +433,7 @@ void ReturnData::processBackwardProblem(ForwardProblem const &fwd,
 
 void ReturnData::handleSx0Backward(const Model &model,
                                    SteadystateProblem const &preeq,
+                                   std::vector<realtype> &llhS0,
                                    AmiVector &xQB) const {
     /* If preequilibration is run in adjoint mode, the scalar product of sx0
        with its adjoint counterpart (see handleSx0Forward()) is not necessary:
@@ -441,9 +442,23 @@ void ReturnData::handleSx0Backward(const Model &model,
        and so is the scalar product. Instead of the scalar product, the
        quadratures xQB from preequilibration contribute to the gradient
        (see example notebook on equilibration for further documentation). */
-    auto xQBpreeq = preeq.getAdjointQuadrature();
+    const auto &xQBpreeq = preeq.getAdjointQuadrature();
     for (int ip = 0; ip < model.nplist(); ++ip)
-        xQB[ip] += xQBpreeq[ip];
+        xQB[ip] += xQBpreeq.at(ip);
+
+    /* We really need references here, as sx0 can be large... */
+    const auto& sx0preeq = preeq.getStateSensitivity();
+    const auto& xBpreeq = preeq.getAdjointState();
+
+    /* Add the contribution for sx0 from preequilibration. If backward
+     * preequilibration was done by simulation due to a singular Jacobian,
+     * xB is not necessarily 0 and we may get a non-zero contribution here. */
+    for (int ip = 0; ip < model.nplist(); ++ip) {
+        llhS0[ip] = 0.0;
+        for (int ix = 0; ix < model.nxtrue_solver; ++ix) {
+            llhS0[ip] += xBpreeq.at(ix) * sx0preeq.at(ix, ip);
+        }
+    }
 }
 
 void ReturnData::handleSx0Forward(const Model &model,
diff --git a/src/steadystateproblem.cpp b/src/steadystateproblem.cpp
index 6d75c469fd..969c5723f8 100644
--- a/src/steadystateproblem.cpp
+++ b/src/steadystateproblem.cpp
@@ -101,9 +101,6 @@ void SteadystateProblem::workSteadyStateBackwardProblem(Solver *solver,
     clock_t starttime = clock();
     computeSteadyStateQuadrature(newtonSolver.get(), solver, model);
     cpu_timeB_ = (double)((clock() - starttime) * 1000) / CLOCKS_PER_SEC;
-
-    /* Finalize by setting adjoint state to zero (its steady state) */
-    xB_.zero();
 }
 
 void SteadystateProblem::findSteadyState(Solver *solver,
@@ -285,6 +282,9 @@ void SteadystateProblem::getQuadratureByLinSolve(NewtonSolver *newtonSolver,
         computeQBfromQ(model, xQ_, xQB_);
         /* set flag that quadratures is available (for processing in rdata) */
         hasQuadrature_ = true;
+        
+        /* Finalize by setting adjoint state to zero (its steady state) */
+        xB_.zero();
     } catch (NewtonFailure const &) {
         hasQuadrature_ = false;
     }
diff --git a/tests/benchmark-models/benchmark_models.yaml b/tests/benchmark-models/benchmark_models.yaml
index a84afe34f3..d290171e82 100644
--- a/tests/benchmark-models/benchmark_models.yaml
+++ b/tests/benchmark-models/benchmark_models.yaml
@@ -5,7 +5,9 @@ Bachmann_MSB2011:
 Becker_Science2010:
   llh: -364.118614198023
 
-#Beer_MolBioSystems2014    None
+Beer_MolBioSystems2014:
+  llh: 58622.9145631413
+  note: benchmark collection reference parameters do not match petab, but reference llh has been confirmed for parameters reported there up to sign
 
 Boehm_JProteomeRes2014:
   llh: -138.22199693517703
@@ -16,8 +18,7 @@ Borghans_BiophysChem1997:
   note: benchmark collection reference value matches up to sign when applying log10-correction +sum(log(meas*log(10)) / 2
 
 Brannmark_JBC2010:
-  llh: 283.778227541074
-  note: unchecked
+  llh: -141.889113770537
 
 #Bruno_JExpBio2016:    None
 
@@ -34,8 +35,7 @@ Elowitz_Nature2000:
   note: benchmark collection reference value matches up to sign when applying log10-correction +sum(log(meas*log(10))) / 2
 
 Fiedler_BMC2016:
-  llh: -117.16780323362
-  note: unchecked
+  llh: 58.58390161681
 
 Fujita_SciSignal2010:
   llh: 53.08749124997969
diff --git a/tests/benchmark-models/test_benchmark_collection.sh b/tests/benchmark-models/test_benchmark_collection.sh
index ea3dbbfbed..0422dd3e23 100755
--- a/tests/benchmark-models/test_benchmark_collection.sh
+++ b/tests/benchmark-models/test_benchmark_collection.sh
@@ -7,15 +7,18 @@
 
 # Confirmed to be working
 models="
+Beer_MolBioSystems2014
 Boehm_JProteomeRes2014
 Borghans_BiophysChem1997
+Brannmark_JBC2010
+Crauste_CellSystems2017
 Elowitz_Nature2000
-Schwen_PONE2014
+Fiedler_BMC2016
 Fujita_SciSignal2010
+Schwen_PONE2014
 Sneyd_PNAS2002
-Zheng_PNAS2012
 Weber_BMC2015
-Crauste_CellSystems2017"
+Zheng_PNAS2012"
 
 #
 # Not matching reference for unclear reasons
@@ -29,19 +32,12 @@ Crauste_CellSystems2017"
 #
 # no reference value:
 # Alkan_SciSignal2018
-# Beer_MolBioSystems2014
 # Blasi_CellSystems2016
 # Hass_PONE2017
 # Korkut_eLIFE2015
 # Perelson_Science1996
 # Bruno_JExpBio2016
 #
-# Timepoint-specific parameter overrides
-# Fiedler_BMC2016
-# Brannmark_JBC2010
-# Isensee_JCB2018
-# Sobotta_Frontiers2017
-#
 # yaml missing:
 # Casaletto_PNAS2019
 #
@@ -59,6 +55,9 @@ Crauste_CellSystems2017"
 #
 # Evaluation is known to be inconsistent:
 # Chen_MSB2009
+#
+# Integration Failure:
+# Isensee_JCB2018
 
 set -e
 
@@ -91,7 +90,7 @@ for model in $models; do
   yaml="${model_dir}"/"${model}"/"${model}".yaml
   amici_model_dir=test_bmc/"${model}"
   mkdir -p "$amici_model_dir"
-  cmd_import="amici_import_petab --verbose -y ${yaml} -o ${amici_model_dir} -n ${model}"
+  cmd_import="amici_import_petab --verbose -y ${yaml} -o ${amici_model_dir} -n ${model} --flatten"
   cmd_run="$script_path/test_petab_model.py --verbose -y ${yaml} -d ${amici_model_dir} -m ${model} -c"
 
   printf '=%.0s' {1..40}
diff --git a/tests/benchmark-models/test_petab_model.py b/tests/benchmark-models/test_petab_model.py
index 370b38df6b..692a7aadd6 100755
--- a/tests/benchmark-models/test_petab_model.py
+++ b/tests/benchmark-models/test_petab_model.py
@@ -75,6 +75,7 @@ def main():
 
     # load PEtab files
     problem = petab.Problem.from_yaml(args.yaml_file_name)
+    petab.flatten_timepoint_specific_output_overrides(problem)
 
     # load model
     if args.model_directory:
diff --git a/tests/cpputest/testfunctions.cpp b/tests/cpputest/testfunctions.cpp
index b24fdd1bee..382e7fa43d 100644
--- a/tests/cpputest/testfunctions.cpp
+++ b/tests/cpputest/testfunctions.cpp
@@ -73,7 +73,7 @@ void simulateVerifyWrite(const std::string& hdffileOptions, const std::string& h
 
     // write
     // delete destination group
-    H5::H5File in(hdffileOptions, H5F_ACC_RDONLY);
+    H5::H5File in(hdffileOptions.c_str(), H5F_ACC_RDONLY);
     auto out = amici::hdf5::createOrOpenForWriting(hdffilewrite);
     if(hdf5::locationExists(out, path))
         H5Ldelete(out.getId(), path.c_str(), H5P_DEFAULT);
@@ -169,7 +169,7 @@ void verifyReturnData(std::string const& hdffile, std::string const& resultPath,
     }
 
     // compare to saved data in hdf file
-    H5::H5File file(hdffile, H5F_ACC_RDONLY);
+    H5::H5File file(hdffile.c_str(), H5F_ACC_RDONLY);
 
     hsize_t m, n;
 
diff --git a/tests/performance/reference.yml b/tests/performance/reference.yml
index b641ac92a5..085363b6ae 100644
--- a/tests/performance/reference.yml
+++ b/tests/performance/reference.yml
@@ -2,7 +2,10 @@
 create_sdist: 5
 install_sdist: 150
 petab_import: 2100
-install_model: 350
+install_model: 120
+install_model_O0: 40
+install_model_O1: 90
+install_model_O2: 120
 forward_simulation: 2
 forward_sensitivities: 2
 adjoint_sensitivities: 2
diff --git a/tests/performance/test.py b/tests/performance/test.py
index 0f853c4a66..cf58c116b8 100755
--- a/tests/performance/test.py
+++ b/tests/performance/test.py
@@ -5,47 +5,73 @@
 import petab
 import subprocess
 import os
+import re
+import shutil
 
 from amici.petab_import import import_model
 
 
-def main():
+def parse_args():
     arg = sys.argv[1]
+    if '_' in arg and re.match(r'O[0-2]', arg.split("_")[-1]):
+        optim = arg.split("_")[-1]
+        os.environ['AMICI_CXXFLAGS'] = f'-{optim}'
+        suffix = f'_{optim}'
+        arg = '_'.join(arg.split("_")[:-1])
+    else:
+        suffix = ''
 
-    if arg == 'compilation':
-        git_dir = os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT')
-        if not os.path.exists(git_dir):
-            subprocess.run([
-                'git', 'clone', '--depth', '1',
-                'https://github.com/ICB-DCM/CS_Signalling_ERBB_RAS_AKT']
-            )
-        os.chdir(os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT'))
-
-        pp = petab.Problem.from_yaml('FroehlichKes2018/PEtab/FroehlichKes2018.yaml')
-        petab.lint_problem(pp)
-        os.chdir(os.path.dirname(os.path.abspath(os.curdir)))
-        import_model(model_name='CS_Signalling_ERBB_RAS_AKT_petab',
-                     sbml_model=pp.sbml_model,
-                     condition_table=pp.condition_df,
-                     observable_table=pp.observable_df,
-                     measurement_table=pp.measurement_df,
-                     compile=False,
-                     verbose=True)
-        os.chdir(os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT_petab'))
-
-        subprocess.run(['python', 'setup.py', 'install'])
+    return arg, suffix
 
-        return
-    else:
-        import CS_Signalling_ERBB_RAS_AKT_petab as model_module
-        model = model_module.getModel()
-        solver = model.getSolver()
-        # TODO
-        edata = amici.ExpData(model)
-        edata.setTimepoints([1e8])
-        edata.setObservedData([1.0])
-        edata.setObservedDataStdDev([1.0])
 
+def check_results(rdata):
+    diagnostics = ['numsteps', 'numstepsB', 'numrhsevals', 'numrhsevalsB',
+                   'numerrtestfails', 'numerrtestfailsB',
+                   'numnonlinsolvconvfails', 'numnonlinsolvconvfailsB',
+                   'preeq_cpu_time', 'preeq_cpu_timeB',
+                   'cpu_time', 'cpu_timeB',
+                   'posteq_cpu_time', 'posteq_cpu_timeB']
+    for d in diagnostics:
+        print(d, rdata[d])
+    assert rdata['status'] == amici.AMICI_SUCCESS
+
+
+def run_import(model_name):
+    git_dir = os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT')
+    if not os.path.exists(git_dir):
+        subprocess.run([
+            'git', 'clone', '--depth', '1',
+            'https://github.com/ICB-DCM/CS_Signalling_ERBB_RAS_AKT']
+        )
+    os.chdir(os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT'))
+
+    pp = petab.Problem.from_yaml(
+        'FroehlichKes2018/PEtab/FroehlichKes2018.yaml'
+    )
+    petab.lint_problem(pp)
+    import_model(model_name=model_name,
+                 sbml_model=pp.sbml_model,
+                 condition_table=pp.condition_df,
+                 observable_table=pp.observable_df,
+                 measurement_table=pp.measurement_df,
+                 compile=False,
+                 verbose=True)
+
+
+def compile_model(model_name, model_dir):
+    if model_name != os.path.basename(model_dir):
+        shutil.copytree(
+            os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT',
+                         model_name),
+            model_dir
+        )
+
+    subprocess.run(['python', 'setup.py',
+                    'build_ext', f'--build-lib=.', '--force'],
+                   cwd=model_dir)
+
+
+def prepare_simulation(arg, model, solver, edata):
     if arg == 'forward_simulation':
         solver.setSensitivityMethod(amici.SensitivityMethod.none)
         solver.setSensitivityOrder(amici.SensitivityOrder.none)
@@ -57,41 +83,60 @@ def main():
         solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)
         solver.setSensitivityOrder(amici.SensitivityOrder.first)
     elif arg == 'forward_simulation_non_optimal_parameters':
-        tmpPar = model.getParameters()
-        model.setParameters([0.1 for _ in tmpPar])
+        tmp_par = model.getParameters()
+        model.setParameters([0.1 for _ in tmp_par])
         solver.setSensitivityMethod(amici.SensitivityMethod.none)
         solver.setSensitivityOrder(amici.SensitivityOrder.none)
     elif arg == 'adjoint_sensitivities_non_optimal_parameters':
-        tmpPar = model.getParameters()
-        model.setParameters([0.1 for _ in tmpPar])
+        tmp_par = model.getParameters()
+        model.setParameters([0.1 for _ in tmp_par])
         solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)
         solver.setSensitivityOrder(amici.SensitivityOrder.first)
     elif arg == 'forward_steadystate_sensitivities_non_optimal_parameters':
-        tmpPar = model.getParameters()
-        model.setParameters([0.1 for _ in tmpPar])
+        tmp_par = model.getParameters()
+        model.setParameters([0.1 for _ in tmp_par])
         solver.setSensitivityMethod(amici.SensitivityMethod.forward)
         solver.setSensitivityOrder(amici.SensitivityOrder.first)
         edata.setTimepoints([float('inf')])
     elif arg == 'adjoint_steadystate_sensitivities_non_optimal_parameters':
-        tmpPar = model.getParameters()
-        model.setParameters([0.1 for _ in tmpPar])
+        tmp_par = model.getParameters()
+        model.setParameters([0.1 for _ in tmp_par])
         solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)
         solver.setSensitivityOrder(amici.SensitivityOrder.first)
         edata.setTimepoints([float('inf')])
     else:
         print("Unknown argument:", arg)
         sys.exit(1)
+
+
+def main():
+    arg, suffix = parse_args()
+
+    model_dir = os.path.join(os.curdir, 'CS_Signalling_ERBB_RAS_AKT',
+                             'CS_Signalling_ERBB_RAS_AKT_petab' + suffix)
+    model_name = 'CS_Signalling_ERBB_RAS_AKT_petab'
+
+    if arg == 'import':
+        run_import(model_name)
+        return
+    elif arg == 'compile':
+        compile_model(model_name, model_dir)
+        return
+    else:
+        model_module = amici.import_model_module(model_name, model_dir)
+        model = model_module.getModel()
+        solver = model.getSolver()
+        # TODO
+        edata = amici.ExpData(model)
+        edata.setTimepoints([1e8])
+        edata.setObservedData([1.0])
+        edata.setObservedDataStdDev([1.0])
+
+    prepare_simulation(arg, model, solver, edata)
+
     rdata = amici.runAmiciSimulation(model, solver, edata)
 
-    diagnostics = ['numsteps', 'numstepsB', 'numrhsevals', 'numrhsevalsB',
-                   'numerrtestfails', 'numerrtestfailsB',
-                   'numnonlinsolvconvfails', 'numnonlinsolvconvfailsB',
-                   'preeq_cpu_time', 'preeq_cpu_timeB',
-                   'cpu_time', 'cpu_timeB',
-                   'posteq_cpu_time', 'posteq_cpu_timeB']
-    for d in diagnostics:
-        print(d, rdata[d])
-    assert rdata['status'] == amici.AMICI_SUCCESS
+    check_results(rdata)
 
 
 if __name__ == '__main__':
diff --git a/tests/petab_test_suite/test_petab_suite.py b/tests/petab_test_suite/test_petab_suite.py
index f799c28080..73c7a58db3 100755
--- a/tests/petab_test_suite/test_petab_suite.py
+++ b/tests/petab_test_suite/test_petab_suite.py
@@ -57,11 +57,14 @@ def _test_case(case, model_type):
         case_dir = os.path.join(petabtests.PYSB_DIR, case)
         # import petab problem
         yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
-        problem = PysbPetabProblem.from_yaml(yaml_file)
+        problem = PysbPetabProblem.from_yaml(yaml_file,
+                                             flatten=case.startswith('0006'))
     else:
         raise ValueError(f"Unsupported model_type: {model_type}")
 
     # compile amici model
+    if case.startswith('0006') and model_type != "pysb":
+        petab.flatten_timepoint_specific_output_overrides(problem)
     model_output_dir = f'amici_models/model_{case}'
     model = import_petab_problem(
         problem, model_output_dir=model_output_dir,
@@ -83,6 +86,10 @@ def _test_case(case, model_type):
     gt_chi2 = solution[petabtests.CHI2]
     gt_llh = solution[petabtests.LLH]
     gt_simulation_dfs = solution[petabtests.SIMULATION_DFS]
+    if case.startswith('0006'):
+        # account for flattening
+        gt_simulation_dfs[0].loc[:, petab.OBSERVABLE_ID] = ('obs_a__10__c0',
+                                                            'obs_a__15__c0')
     tol_chi2 = solution[petabtests.TOL_CHI2]
     tol_llh = solution[petabtests.TOL_LLH]
     tol_simulations = solution[petabtests.TOL_SIMULATIONS]
diff --git a/version.txt b/version.txt
index a95c45d4fb..4aa0906934 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-0.11.14
+0.11.15