PN 2

SimTech EXC 2075 Project Network 2 "In silico models of coupled biological systems"

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1 to 10 of 36 Results

Kinetic modeling of enzymatic cephalexin synthesis with neural ODEs and surrogate-accelerated Bayesian inference Dec 9, 2025 - PN 2-6 Range, Jan Peter; Pleiss, Jürgen; Bommarius, Andreas, 2025, "Kinetic modeling of enzymatic cephalexin synthesis with neural ODEs and surrogate-accelerated Bayesian inference", https://doi.org/10.18419/DARUS-5539, DaRUS, V1, UNF:6:l47sIu5Gd2e6cn3HDM5h6g== [fileUNF] α-Amino ester hydrolases (AEHs) offer a promising route to the stereoselective synthesis of β-lactams such as cephalexin. However, published kinetic studies have encountered difficulty when extended beyond fitting of the data, indicating practical non-identifiability of the underlying kinetic models. Here, we address this issue using Bayesian infer...
arm26 Version for: Closed-Loop Coupling of Both Physiological Spindle Model and Spinal Pathways for Sensorimotor Control of Human Center-Out Reaching Aug 27, 2025 - demoa Santana Chacon, Pablo Filipe; Wochner, Isabell; Hammer, Maria; Schmitt, Syn, 2025, "arm26 Version for: Closed-Loop Coupling of Both Physiological Spindle Model and Spinal Pathways for Sensorimotor Control of Human Center-Out Reaching", https://doi.org/10.18419/DARUS-4765, DaRUS, V1 Version of the arm26 model (https://doi.org/10.18419/DARUS-2871) used in the study 'Closed-loop coupling of both physiological spindle model and spinal pathways for sensorimotor control of human center-out reaching', including additional scripts to run with python, muscle spindle module and NEST simulator. The file contains an archive including all...
gspine: A Human Spine Model Built Using Literature Data Jul 24, 2025 - demoa Hammer, Maria; Riede, Julia Maria; Meszaros-Beller, Laura; Schmitt, Syn, 2022, "gspine: A Human Spine Model Built Using Literature Data", https://doi.org/10.18419/DARUS-2814, DaRUS, V5 A fully articulating human spine model parametrised using generic literature data for the geometry of the skeleton including attachment points for ligaments and muscles. The model is prepared to run muscle-driven simulations using a simple biological motor control model. The file contains an archive including all relevant data to run the simulation...
demoa-base: a biophysics simulator for muscle-driven motion Jul 16, 2025 - demoa Schmitt, Syn, 2022, "demoa-base: a biophysics simulator for muscle-driven motion", https://doi.org/10.18419/DARUS-2550, DaRUS, V7 For more information, such as installation, requirements and user guide, please see the demoa manual. The development of this package was supported by “Deutsche Forschungsgemeinschaft” (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2075 - 390740016.
allmin: A Reduced Human All-Body Model Jun 3, 2025 - demoa Walter, Johannes R.; Wochner, Isabell; Jacob, Marc; Stollenmaier, Katrin; Lerge, Patrick; Schmitt, Syn, 2022, "allmin: A Reduced Human All-Body Model", https://doi.org/10.18419/DARUS-2982, DaRUS, V3 A reduced all-body model parametrised using generic literature data for the geometry of the skeleton including attachment points for ligaments and muscles. This allmin model consists of a musculoskeletal model of the human body with 20 degrees of freedom actuated by 36 muscles. The model is prepared to run muscle-driven simulation. The file contain...
PN 2-8 Siebert(Universität Stuttgart) Nov 19, 2024 SimTech Project PN 2-8 Siebert "Modelling of architectural-informed and activation-driven contractions of the human M. tibialis anterior"
Replication Code for: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference Mar 14, 2024 - PN 2-7 Reiser, Philipp; Aguilar, Javier Enrique; Guthke, Anneli; Bürkner, Paul-Christian, 2024, "Replication Code for: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference", https://doi.org/10.18419/DARUS-4093, DaRUS, V1 This code allows to replicate key experiments from our paper: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference. For further details, please refer to the README.md.
PN 2-7(Universität Stuttgart) Mar 13, 2024 SimTech Project PN 2-7 "Data-integrated training of surrogate models for uncertainty quantification and diagnostics of complex biological systems models"
Replication Data for: A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers Dec 15, 2023 - PN 2-3B Santana Chacon, Pablo Filipe; Hammer, Maria; Wochner, Isabell; Walter, Johannes R.; Schmitt, Syn, 2023, "Replication Data for: A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers", https://doi.org/10.18419/DARUS-3796, DaRUS, V1 This code/data allows you reproduce the results of the paper: "A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers" by P. F. S. Chacon, M. Hammer, I. Wochner, J. R. Walter and S. Schmitt. Always cite the paper together with this dataset because this dataset is not self-exp...
PN 2-3B(Universität Stuttgart) Nov 9, 2023 Open-Source structurally physiological Hill-type model of the muscle spindle for forward-dynamic simulations in biophysics and biomechanics.

Kinetic modeling of enzymatic cephalexin synthesis with neural ODEs and surrogate-accelerated Bayesian inference

Dec 9, 2025 - PN 2-6

Range, Jan Peter; Pleiss, Jürgen; Bommarius, Andreas, 2025, "Kinetic modeling of enzymatic cephalexin synthesis with neural ODEs and surrogate-accelerated Bayesian inference", https://doi.org/10.18419/DARUS-5539, DaRUS, V1, UNF:6:l47sIu5Gd2e6cn3HDM5h6g== [fileUNF]

α-Amino ester hydrolases (AEHs) offer a promising route to the stereoselective synthesis of β-lactams such as cephalexin. However, published kinetic studies have encountered difficulty when extended beyond fitting of the data, indicating practical non-identifiability of the underlying kinetic models. Here, we address this issue using Bayesian infer...

arm26 Version for: Closed-Loop Coupling of Both Physiological Spindle Model and Spinal Pathways for Sensorimotor Control of Human Center-Out Reaching

Aug 27, 2025 - demoa

Santana Chacon, Pablo Filipe; Wochner, Isabell; Hammer, Maria; Schmitt, Syn, 2025, "arm26 Version for: Closed-Loop Coupling of Both Physiological Spindle Model and Spinal Pathways for Sensorimotor Control of Human Center-Out Reaching", https://doi.org/10.18419/DARUS-4765, DaRUS, V1

Version of the arm26 model (https://doi.org/10.18419/DARUS-2871) used in the study 'Closed-loop coupling of both physiological spindle model and spinal pathways for sensorimotor control of human center-out reaching', including additional scripts to run with python, muscle spindle module and NEST simulator. The file contains an archive including all...

gspine: A Human Spine Model Built Using Literature Data

Jul 24, 2025 - demoa

Hammer, Maria; Riede, Julia Maria; Meszaros-Beller, Laura; Schmitt, Syn, 2022, "gspine: A Human Spine Model Built Using Literature Data", https://doi.org/10.18419/DARUS-2814, DaRUS, V5

A fully articulating human spine model parametrised using generic literature data for the geometry of the skeleton including attachment points for ligaments and muscles. The model is prepared to run muscle-driven simulations using a simple biological motor control model. The file contains an archive including all relevant data to run the simulation...

demoa-base: a biophysics simulator for muscle-driven motion

Jul 16, 2025 - demoa

Schmitt, Syn, 2022, "demoa-base: a biophysics simulator for muscle-driven motion", https://doi.org/10.18419/DARUS-2550, DaRUS, V7

For more information, such as installation, requirements and user guide, please see the demoa manual. The development of this package was supported by “Deutsche Forschungsgemeinschaft” (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2075 - 390740016.

allmin: A Reduced Human All-Body Model

Jun 3, 2025 - demoa

Walter, Johannes R.; Wochner, Isabell; Jacob, Marc; Stollenmaier, Katrin; Lerge, Patrick; Schmitt, Syn, 2022, "allmin: A Reduced Human All-Body Model", https://doi.org/10.18419/DARUS-2982, DaRUS, V3

A reduced all-body model parametrised using generic literature data for the geometry of the skeleton including attachment points for ligaments and muscles. This allmin model consists of a musculoskeletal model of the human body with 20 degrees of freedom actuated by 36 muscles. The model is prepared to run muscle-driven simulation. The file contain...

PN 2-8 Siebert(Universität Stuttgart)

Nov 19, 2024

SimTech Project PN 2-8 Siebert "Modelling of architectural-informed and activation-driven contractions of the human M. tibialis anterior"

Replication Code for: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference

Mar 14, 2024 - PN 2-7

Reiser, Philipp; Aguilar, Javier Enrique; Guthke, Anneli; Bürkner, Paul-Christian, 2024, "Replication Code for: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference", https://doi.org/10.18419/DARUS-4093, DaRUS, V1

This code allows to replicate key experiments from our paper: Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference. For further details, please refer to the README.md.

PN 2-7(Universität Stuttgart)

Mar 13, 2024

SimTech Project PN 2-7 "Data-integrated training of surrogate models for uncertainty quantification and diagnostics of complex biological systems models"

Replication Data for: A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers

Dec 15, 2023 - PN 2-3B

Santana Chacon, Pablo Filipe; Hammer, Maria; Wochner, Isabell; Walter, Johannes R.; Schmitt, Syn, 2023, "Replication Data for: A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers", https://doi.org/10.18419/DARUS-3796, DaRUS, V1

This code/data allows you reproduce the results of the paper: "A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers" by P. F. S. Chacon, M. Hammer, I. Wochner, J. R. Walter and S. Schmitt. Always cite the paper together with this dataset because this dataset is not self-exp...

PN 2-3B(Universität Stuttgart)

Nov 9, 2023

Open-Source structurally physiological Hill-type model of the muscle spindle for forward-dynamic simulations in biophysics and biomechanics.

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