SimTK: Predicting Cell Deformation from Body Level Mechanical Loads: Downloads

Predicting Cell Deformation from Body Level Mechanical Loads

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Automated Cell Scale Meshes

This package provides scripts, meshes, and models utilized in the manuscript "Automated Generation of Tissue-Specific Three-Dimensional Finite Element Meshes Containing Ellipsoidal Cellular Inclusions". The scripts provide the capacity to build meshes of prismatic tissue volumes with spherical and/or ellipsoidal inclusions of cells surrounded with a pericellular matrix. The tool requires Python (http://www.python.org) and Salome v6.3.1 (http://www.salome-platform.org/) to operate. Multiple example meshes, all described in the manuscript, are also provided.

version 1.0.0

Jul 19, 2013

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AutoTetMesh_scripts.zip

Jul 19, 2013

28 KB

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Other

Python scripts to built meshes of tissue blocks with arbitrary size, cell organization, and ellipsoidal cell shapes.

ALL_FEATURES_model.zip

Jul 19, 2013

6 MB

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Other

An example mesh illustrating the capabilities of different tissue block meshes including ellipsoidal cellular inclusions.

3D_CLSM_model.zip

Jul 19, 2013

19 MB

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A mesh generated from explicit geometry obtained from confocal laser scanning microscopy of a cell-seeded construct.

CARTILAGE_models.zip

Jul 19, 2013

157 MB

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Other

Multiple meshes generated for the transitional zone of knee cartilage utilizing statistical cell information from literature.

hex_vs_tet.zip

Jul 19, 2013

41 MB

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Other

Raw simulation results to compare model predictions of tetrahedral meshes (generated using the scripts) against those of hexahedral meshes.

PLEASE CITE THESE PAPERS

Bennetts, C. J., Sibole, S. and Erdemir, A. Automated generation of tissue-specific three-dimensional finite element meshes containing ellipsoidal cellular inclusions, Computer Methods in Biomechanics and Biomedical Engineering, 18, 1293-1304. (2015)

Autonomous Pipeline

This package contains i) macroscopic finite element representation of the tibiofemoral joint, ii) two different microscopic finite element representations of chondrocyte environment (single cell vs 11 cell), iii) simulation results for the macroscopic model, iv) simulations result of microscopic models post-processed by macro level solution. The study is conducted through an autonoumous multiscale analysis pipeline described in publications referred below.

version 1.0.0

Oct 25, 2012

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dissemination-v1_0_0.zip

Oct 25, 2012

152 MB

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Source code

Contains all scripts and files to reproduce the study with instructions on how to do this on a cluster or locally.

PLEASE CITE THESE PAPERS

Sibole, S. C. and Erdemir, A. (2012) Chondrocyte deformations as a function of tibiofemoral joint loading predicted by a generalized high-throughput pipeline of multi-scale simulations, PLoS ONE, 7, e37538. (2012) View

Biphasic Multiscale Analysis

This package contains materials to explore data passing assumptions to conduct cell scale biphasic simulations from the results of biphasic tissue simulations. Four cases of tissue loading and boundary conditions were implemented in tissue scale models (four combinations of uniform/nonuniform displacement and symmetric/asymmetric permeability). Two cases of data passing assumptions were tested to drive cell scale models (first order and second order data passing).

version 1.0.0

Oct 25, 2012

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biphasic_coupling.zip

Oct 25, 2012

6 MB

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Source code

Contains all scripts and files to reproduce the study with instructions on how to do this on a cluster or locally.

models.zip

Oct 25, 2012

344 MB

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Source code

Pre-generated FEBio models for every case.

results.zip

Oct 25, 2012

359 KB

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Data/images/video

CSV files containing chondrocyte metrics for each simulation and Taylor series tensor coefficients for 1st or 2nd order coupling.

PLEASE CITE THESE PAPERS

Sibole, S. C., Maas, S., Halloran, J. P., Weiss, J. A. and Erdemir, A. Evaluation of a post-processing approach for multiscale analysis of biphasic mechanics of chondrocytes, Computer Methods in Biomechanics and Biomedical Engineering, 16, 1112-1126. (2013) View

Multiscale data set

This package provides a comprehensive specimen-specific multiscale anatomical and mechanical testing data set for the tibiofemoral joint. For macro and micro scale geometry, magnetic resonance images and histology images are provided respectively. Mechanical testing data at the joint level consists of laxity tests and a combined loading scenario. 12 tissue samples (cartilage, ligaments and menisci) were tested in either compression or tension under stress relaxation conditions to characterize the tissue properties. This data can be useful in developing multi-resolution specimen-specific models of the tibiofemoral joint.

version 1.0.0

Mar 20, 2015

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J2C-MRI.zip

Mar 25, 2015

55 MB

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Data/images/video

This folder contains magnetic resonance images for the knee joint. Please see README-MRI.pdf for content description.

Joint mechanical testing (URL)

Mar 25, 2015

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Data/images/video

This folder contains the joint mechanical testing data. Please see README-JOINT.pdf for content description.

Histology (URL)

Mar 25, 2015

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Data/images/video

This folder contains the histology data.Please see README-HIST.pdf for content description.

J2C-Tissue Mechanical Testing.zip

Mar 25, 2015

194 MB

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Data/images/video

This folder contains all the tissue mechanical testing data. Please see README-TISSUE.pdf for content description.

Documentation Links

Mar 05, 2015

Mar 20, 2015

Mar 20, 2015

Mar 05, 2015

PLEASE CITE THESE PAPERS

Chokhandre, S., Colbrunn, R., Bennetts, C. and Erdemir, A. A comprehensive specimen-specific multiscale data set for anatomical and mechanical characterization of the tibiofemoral Joint, PLoS ONE, 10, e013826. (2015) View

Single vs. Eleven Cell Study

This package provides scripts, meshes, and models utilized in the manuscript "The Potential for Intercellular Mechanical Interaction - Simulations of Single Chondrocyte Versus Anatomically Based Distribution" (currently ahead of print). The scripts provide the capacity to build meshes, run simulations, and process results for models of biphasic, transition zone chondrocyte mechanics for single and anatomically based eleven cell distributions. The tool requires Python (http://www.python.org) and FEBio v1.5.0 (http://febio.org/) to operate.

1.0.0

Aug 17, 2017

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SCv11C_DownloadPackage.tar.gz

Aug 17, 2017

7 MB

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Data/images/video

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

Version 4.2.2. Website design by Viewfarm. Icons created by SimTK team using art by GraphBerry from www.flaticon.com under a CC BY 3.0 license. Forked from FusionForge 6.0.5.

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