skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


This content will become publicly available on April 1, 2026

Title: MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco
MocoExtendProblem (MEP) is a framework to rapidly develop novel goals for biomechanical optimal control problems using OpenSim Moco (Dembia et al., 2020) and MATLAB (The MathWorks, Inc., Natick, MA, USA). MEP features several templates for testing and prototyping novel MocoGoals as well as a build tool to create a MEX function using OpenSim’s API for MATLAB in lieu of rebuilding OpenSim from source or building a plugin and generating an .omoco file from C++ to load the problem into MATLAB. Instead, users structure and design custom goals in C++, build them with the provided tool, and call custom goals from within MATLAB scripts. This repository features: • A build.m script that compiles goals in the custom_goals directory and procedurally constructs the C++/MATLAB class implementations and compiles the MEX interface. • Compatibility tested with OpenSim 4.2-4.5. – Support for OpenSim versions 4.2-4.4 require unique considerations to custom goal development and build pipeline since Booleans for division by duration, distance and mass were migrated to the abstract MocoGoal. • The ability to include MEP as a submodule, build, and use valid custom goals. • Three example custom goals in the custom_goals and custom_goals_compat directories.  more » « less
Award ID(s):
2018436 2018523
PAR ID:
10587526
Author(s) / Creator(s):
; ; ;
Publisher / Repository:
Journal of Open Source Software
Date Published:
Journal Name:
Journal of Open Source Software
Volume:
10
Issue:
108
ISSN:
2475-9066
Page Range / eLocation ID:
7110
Subject(s) / Keyword(s):
OpenSim Musculoskeletal Modeling Simulation Moco Human Direct Collocation
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. null (Ed.)
    A reliable, accurate, and yet simple dynamic model is important to analyzing, designing, and controlling hybrid rigid–continuum robots. Such models should be fast, as simple as possible, and user-friendly to be widely accepted by the ever-growing robotics research community. In this study, we introduce two new modeling methods for continuum manipulators: a general reduced-order model (ROM) and a discretized model with absolute states and Euler–Bernoulli beam segments (EBA). In addition, a new formulation is presented for a recently introduced discretized model based on Euler–Bernoulli beam segments and relative states (EBR). We implement these models in a Matlab software package, named TMTDyn, to develop a modeling tool for hybrid rigid–continuum systems. The package features a new high-level language (HLL) text-based interface, a CAD-file import module, automatic formation of the system equation of motion (EOM) for different modeling and control tasks, implementing Matlab C-mex functionality for improved performance, and modules for static and linear modal analysis of a hybrid system. The underlying theory and software package are validated for modeling experimental results for (i) dynamics of a continuum appendage, and (ii) general deformation of a fabric sleeve worn by a rigid link pendulum. A comparison shows higher simulation accuracy (8–14% normalized error) and numerical robustness of the ROM model for a system with a small number of states, and computational efficiency of the EBA model with near real-time performances that makes it suitable for large systems. The challenges and necessary modules to further automate the design and analysis of hybrid systems with a large number of states are briefly discussed. 
    more » « less
  2. Abstract SummaryMolecular mechanisms of biological functions and disease processes are exceptionally complex, and our ability to interrogate and understand relationships is becoming increasingly dependent on the use of computational modeling. We have developed “BioModME,” a standalone R-based web application package, providing an intuitive and comprehensive graphical user interface to help investigators build, solve, visualize, and analyze computational models of complex biological systems. Some important features of the application package include multi-region system modeling, custom reaction rate laws and equations, unit conversion, model parameter estimation utilizing experimental data, and import and export of model information in the Systems Biology Matkup Language format. The users can also export models to MATLAB, R, and Python languages and the equations to LaTeX and Mathematical Markup Language formats. Other important features include an online model development platform, multi-modality visualization tool, and efficient numerical solvers for differential-algebraic equations and optimization. Availability and implementationAll relevant software information including documentation and tutorials can be found at https://mcw.marquette.edu/biomedical-engineering/computational-systems-biology-lab/biomodme.php. Deployed software can be accessed at https://biomodme.ctsi.mcw.edu/. Source code is freely available for download at https://github.com/MCWComputationalBiologyLab/BioModME. 
    more » « less
  3. null (Ed.)
    The detection of abnormal moving objects over high-volume trajectory streams is critical for real-time applications ranging from military surveillance to transportation management. Yet this outlier detection problem, especially along both the spatial and temporal dimensions, remains largely unexplored. In this work, we propose a rich taxonomy of novel classes of neighbor-based trajectory outlier definitions that model the anomalous behavior of moving objects for a large range of real-time applications. Our theoretical analysis and empirical study on two real-world datasets—the Beijing Taxi trajectory data and the Ground Moving Target Indicator data stream—and one generated Moving Objects dataset demonstrate the effectiveness of our taxonomy in effectively capturing different types of abnormal moving objects. Furthermore, we propose a general strategy for efficiently detecting these new outlier classes called the minimal examination (MEX) framework. The MEX framework features three core optimization principles, which leverage spatiotemporal as well as the predictability properties of the neighbor evidence to minimize the detection costs. Based on this foundation, we design algorithms that detect the outliers based on these classes of new outlier semantics that successfully leverage our optimization principles. Our comprehensive experimental study demonstrates that our proposed MEX strategy drives the detection costs 100-fold down into the practical realm for applications that analyze high-volume trajectory streams in near real time. 
    more » « less
  4. In this comprehensive study, a novel MATLAB to Python (M-to-PY) conversion process is showcased, specifically tailored for an intricate image skeletonization project involving fifteen MATLAB files and a large dataset. The central innovation of this research is the adept use of ChatGPT-4 as an AI assistant, pivotal in crafting a prototype M-to-PY converter. This converter’s capabilities were thoroughly evaluated using a set of test cases generated by the Bard bot, ensuring a robust and effective tool. The culmination of this effort was the development of the Skeleton App, adept at image sketching and skeletonization. This live and publicly available app underscores the enormous potential of AI in enhancing the transition of scientific research from MATLAB to Python. The study highlights the blend of AI’s computational prowess and human ingenuity in computational research, making significant strides in AI-assisted scientific exploration and tool development. 
    more » « less
  5. The Maximum Entropy Production (MEP) method for modeling surface energy budget has been developed and validated at local, regional and global scale including the Arctic regions. The MEP model has solid theoretical foundation built on the Bayesian probability theory, information theory, non-equilibrium thermodynamics and boundary layer turbulence theory. Its formulation has advantageous features including closing energy budget at any space-time scales, independence of moisture and temperature gradient, wind speed and surface roughness, and free of tunable empirical parameters. Application of the MEP model has been covering all types of land covers including Arctic permafrost tundra, sea ice and snow surfaces. Recent tests using field experimental observations suggest that the MEP model using fewer input data and model parameters is able to simulate surface energy budget accurately. It is a more efficient alternative to the classical Penman-Monteith model of potential evapotranspiration. The MEP method has potential to influence the study of Arctic water-energy cycles and climate change. 
    more » « less