From 0a174ad50583fbcc591e4d38ffb8fa76073f4ccc Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 14 Jan 2025 11:37:57 +0000
Subject: [PATCH 1/6] add omex_file_name to remote simulation dictionary
instead of generic 'test'
---
utils/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/utils/__init__.py b/utils/__init__.py
index caec12d..225e14d 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -696,7 +696,7 @@ def run_biosimulators_remote(engine, sedml_filepath, sbml_filepath):
engine_version = biosimulations.get_simulator_versions(engine)
sim_dict = {
- "name": "test",
+ "name": omex_file_name,
"simulator": engine,
"simulatorVersion": engine_version[engine][-1], # get the latest version
"cpus": 1,
From 3e849dd21380df9a64b4050a0a11dac66988d1ae Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 14 Jan 2025 11:39:25 +0000
Subject: [PATCH 2/6] set use_original_files to False to use ammended sedml
files and remove unnecessary comment
---
BioModels/test_biomodels_compatibility_biosimulators.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py
index a75bb1a..695c295 100644
--- a/BioModels/test_biomodels_compatibility_biosimulators.py
+++ b/BioModels/test_biomodels_compatibility_biosimulators.py
@@ -165,7 +165,6 @@ def main():
print(f"Changed to {new_directory}")
engine_ids = list(engines.keys())
- # engine_ids = engine_list if engine_list is not None else engine_ids
test_folder = "tests"
utils.run_biosimulators_remotely_and_locally(
@@ -181,7 +180,7 @@ def main():
if __name__ == "__main__":
- use_original_files = True
+ use_original_files = False
biomodel_id_list = [
"BIOMD0000000001",
"BIOMD0000000138",
From f82e682421f3d678b50569bf03e47b97b70faf93 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 14 Jan 2025 11:58:24 +0000
Subject: [PATCH 3/6] adjust sedml files to replicate curated BioModels
figures
---
.../BIOMD0000000001/BIOMD0000000001_url.sedml | 28 +++++++++----------
.../BIOMD0000000138/BIOMD0000000138_url.sedml | 4 +--
2 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml
index 03dd1b4..bf61678 100644
--- a/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml
+++ b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml
@@ -4,7 +4,7 @@
-
+
@@ -613,21 +613,21 @@
-
+
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml
index 13802d1..4f531fb 100644
--- a/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml
+++ b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml
@@ -4,7 +4,7 @@
-
+
@@ -422,4 +422,4 @@
-
+
\ No newline at end of file
From b1936d0147d4fc5cf93b440667d4f27c555d0f3a Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Tue, 14 Jan 2025 11:59:39 +0000
Subject: [PATCH 4/6] add created omex files
---
.../BIOMD0000000001/BIOMD0000000001_url.omex | Bin 0 -> 8269 bytes
.../BIOMD0000000138/BIOMD0000000138_url.omex | Bin 0 -> 5637 bytes
.../BIOMD0000000724/Theinmozhi_2018.omex | Bin 0 -> 13790 bytes
.../Adlung2021 _model_jakstat_pa.omex | Bin 0 -> 9542 bytes
.../Adlung2021__model_jakstat_pa.omex | Bin 9542 -> 9542 bytes
5 files changed, 0 insertions(+), 0 deletions(-)
create mode 100644 BioModels/BIOMD0000000001/BIOMD0000000001_url.omex
create mode 100644 BioModels/BIOMD0000000138/BIOMD0000000138_url.omex
create mode 100644 BioModels/BIOMD0000000724/Theinmozhi_2018.omex
create mode 100644 BioModels/BIOMD0000001077/Adlung2021 _model_jakstat_pa.omex
diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.omex b/BioModels/BIOMD0000000001/BIOMD0000000001_url.omex
new file mode 100644
index 0000000000000000000000000000000000000000..01e982da437630d5083fd80c21fd8aa92007c195
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Date: Tue, 14 Jan 2025 12:00:29 +0000
Subject: [PATCH 5/6] update detailed biomodels tables and d1 plots
---
.../amici_autogen_plot_for_task1.pdf | Bin 11104 -> 11738 bytes
.../copasi_autogen_plot_for_task1.pdf | Bin 11133 -> 12278 bytes
.../pysces_autogen_plot_for_task1.pdf | Bin 11174 -> 12368 bytes
.../tellurium_autogen_plot_for_task1.pdf | Bin 11134 -> 12352 bytes
.../vcell_autogen_plot_for_task1.pdf | Bin 15029 -> 15102 bytes
.../amici_autogen_plot_for_task1.pdf | Bin 11110 -> 11744 bytes
.../copasi_autogen_plot_for_task1.pdf | Bin 11139 -> 12284 bytes
.../masspy_autogen_plot_for_task1.pdf | Bin 5954 -> 5954 bytes
.../pysces_autogen_plot_for_task1.pdf | Bin 11180 -> 12374 bytes
.../tellurium_autogen_plot_for_task1.pdf | Bin 11113 -> 12331 bytes
.../vcell_autogen_plot_for_task1.pdf | Bin 11381 -> 11422 bytes
.../results_compatibility_biosimulators.md | 42 +--
.../BIOMD0000000001/tests/results_local.json | 118 ++++----
.../BIOMD0000000001/tests/results_remote.json | 216 +++++++--------
.../amici_autogen_plot_for_task1.pdf | Bin 5948 -> 5948 bytes
.../copasi_autogen_plot_for_task1.pdf | Bin 8709 -> 11663 bytes
.../pysces_autogen_plot_for_task1.pdf | Bin 5948 -> 5948 bytes
.../tellurium_autogen_plot_for_task1.pdf | Bin 8708 -> 11672 bytes
.../vcell_autogen_plot_for_task1.pdf | Bin 12268 -> 16477 bytes
.../amici_autogen_plot_for_task1.pdf | Bin 5954 -> 5954 bytes
.../copasi_autogen_plot_for_task1.pdf | Bin 8715 -> 11669 bytes
.../masspy_autogen_plot_for_task1.pdf | Bin 5954 -> 5954 bytes
.../pysces_autogen_plot_for_task1.pdf | Bin 5954 -> 5954 bytes
.../tellurium_autogen_plot_for_task1.pdf | Bin 8714 -> 11678 bytes
.../vcell_autogen_plot_for_task1.pdf | Bin 8937 -> 13133 bytes
.../results_compatibility_biosimulators.md | 42 +--
.../BIOMD0000000138/tests/results_local.json | 116 ++++----
.../BIOMD0000000138/tests/results_remote.json | 212 +++++++-------
.../d1_plots_local/amici_plot_10_task2.pdf | Bin 5948 -> 5948 bytes
.../d1_plots_local/amici_plot_6_task2.pdf | Bin 5948 -> 5948 bytes
.../d1_plots_local/amici_plot_7_task2.pdf | Bin 5948 -> 5948 bytes
.../d1_plots_local/amici_plot_8_task2.pdf | Bin 5948 -> 5948 bytes
.../d1_plots_local/amici_plot_9_task2.pdf | Bin 5948 -> 5948 bytes
.../d1_plots_local/copasi_plot_10_task2.pdf | Bin 10320 -> 10314 bytes
.../d1_plots_local/copasi_plot_6_task2.pdf | Bin 13690 -> 13687 bytes
.../d1_plots_local/copasi_plot_7_task2.pdf | Bin 13661 -> 13662 bytes
.../d1_plots_local/copasi_plot_8_task2.pdf | Bin 15540 -> 15532 bytes
.../d1_plots_local/copasi_plot_9_task2.pdf | Bin 10204 -> 10213 bytes
.../d1_plots_local/pysces_plot_10_task2.pdf | Bin 10312 -> 10312 bytes
.../d1_plots_local/pysces_plot_6_task2.pdf | Bin 13684 -> 13684 bytes
.../d1_plots_local/pysces_plot_7_task2.pdf | Bin 13677 -> 13677 bytes
.../d1_plots_local/pysces_plot_8_task2.pdf | Bin 15525 -> 15525 bytes
.../d1_plots_local/pysces_plot_9_task2.pdf | Bin 10210 -> 10210 bytes
.../tellurium_plot_10_task2.pdf | Bin 9563 -> 9563 bytes
.../d1_plots_local/tellurium_plot_6_task2.pdf | Bin 12915 -> 12915 bytes
.../d1_plots_local/tellurium_plot_7_task2.pdf | Bin 12982 -> 12982 bytes
.../d1_plots_local/tellurium_plot_8_task2.pdf | Bin 14935 -> 14935 bytes
.../d1_plots_local/tellurium_plot_9_task2.pdf | Bin 9519 -> 9519 bytes
.../d1_plots_remote/amici_plot_10_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/amici_plot_6_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/amici_plot_7_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/amici_plot_8_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/amici_plot_9_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/copasi_plot_10_task2.pdf | Bin 10316 -> 10322 bytes
.../d1_plots_remote/copasi_plot_6_task2.pdf | Bin 13691 -> 13699 bytes
.../d1_plots_remote/copasi_plot_7_task2.pdf | Bin 13669 -> 13663 bytes
.../d1_plots_remote/copasi_plot_8_task2.pdf | Bin 15532 -> 15527 bytes
.../d1_plots_remote/copasi_plot_9_task2.pdf | Bin 10212 -> 10218 bytes
.../d1_plots_remote/masspy_plot_10_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/masspy_plot_6_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/masspy_plot_7_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/masspy_plot_8_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/masspy_plot_9_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/pysces_plot_10_task2.pdf | Bin 10318 -> 10318 bytes
.../d1_plots_remote/pysces_plot_6_task2.pdf | Bin 13690 -> 13690 bytes
.../d1_plots_remote/pysces_plot_7_task2.pdf | Bin 13683 -> 13683 bytes
.../d1_plots_remote/pysces_plot_8_task2.pdf | Bin 15531 -> 15531 bytes
.../d1_plots_remote/pysces_plot_9_task2.pdf | Bin 10216 -> 10216 bytes
.../tellurium_plot_10_task2.pdf | Bin 9569 -> 9569 bytes
.../tellurium_plot_6_task2.pdf | Bin 12921 -> 12921 bytes
.../tellurium_plot_7_task2.pdf | Bin 12988 -> 12988 bytes
.../tellurium_plot_8_task2.pdf | Bin 14970 -> 14970 bytes
.../tellurium_plot_9_task2.pdf | Bin 9524 -> 9524 bytes
.../d1_plots_remote/vcell_plot_10_task2.pdf | Bin 9677 -> 9677 bytes
.../d1_plots_remote/vcell_plot_6_task2.pdf | Bin 13056 -> 13056 bytes
.../d1_plots_remote/vcell_plot_7_task2.pdf | Bin 13135 -> 13135 bytes
.../d1_plots_remote/vcell_plot_8_task2.pdf | Bin 14647 -> 14647 bytes
.../d1_plots_remote/vcell_plot_9_task2.pdf | Bin 9658 -> 9658 bytes
.../results_compatibility_biosimulators.md | 42 +--
.../BIOMD0000000724/tests/results_local.json | 148 +++++-----
.../BIOMD0000000724/tests/results_remote.json | 260 +++++++++---------
.../d1_plots_local/amici_plot_2_task2.pdf | Bin 5948 -> 5948 bytes
.../d1_plots_local/copasi_plot_2_task2.pdf | Bin 12792 -> 12792 bytes
.../d1_plots_local/pysces_plot_2_task2.pdf | Bin 12797 -> 12797 bytes
.../d1_plots_local/tellurium_plot_2_task2.pdf | Bin 12796 -> 12796 bytes
.../d1_plots_remote/amici_plot_2_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/copasi_plot_2_task2.pdf | Bin 12798 -> 12798 bytes
.../d1_plots_remote/masspy_plot_2_task2.pdf | Bin 5954 -> 5954 bytes
.../d1_plots_remote/pysces_plot_2_task2.pdf | Bin 12803 -> 12803 bytes
.../tellurium_plot_2_task2.pdf | Bin 12822 -> 12822 bytes
.../d1_plots_remote/vcell_plot_2_task2.pdf | Bin 12762 -> 12762 bytes
.../results_compatibility_biosimulators.md | 42 +--
.../BIOMD0000001077/tests/results_local.json | 116 ++++----
.../BIOMD0000001077/tests/results_remote.json | 216 +++++++--------
94 files changed, 785 insertions(+), 785 deletions(-)
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf
index 48d9399d780b73d896081802dbc1d238bbdc42f9..26b4c729e6324c3266c4daed7e3985eb3d16803f 100644
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diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf
index a12a44b91b6a3fe3532c67d2be871854845e0b32..32519528424e433963ba5224ae1bb71f6ee279d2 100644
GIT binary patch
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