Cases/CloudComputing

Contents

Synopsis
Files
Licensing
Team Members
Progress
References

Synopsis

This simulation and related scripts are utilized for the demonstration of cloud computing with Open Knee(s) and derivative models. The sample model is a simplified representation of femur-anterior cruciate ligament-tibia based on Open Knee(s) - Generation 1 (version g1-s1-v1.1.0.391). The model includes femur and tibia as rigid bodies and anterior cruciate ligament as a deformable body with same constitutive properties as described for Open Knee(s) - Generation 1 model. Tibia is fixed, femur motion is prescribed using a clinically based joint coordinate system. Finite element analysis, using FEBio (tested with versions 2.4.3 & 2.5.0), predicts resultant tibiofemoral joint forces, from which the anterior cruciate force is calculated. Femur kinematics at the final and intermediate steps of simulation are processed to report the resultant tibiofemoral joint kinematics in a clinically relevant manner. Raw simulation results, including anterior cruciate ligament stresses and strains, can be accessed through the FEBio output file (.xplt) using PostView (distributed at http://febio.org/). Simulations should complete within a few minutes assuming target movement pattern is physiological.

Clinical movement definitions are adapted from Grood and Suntay (1983). Their descriptions are provided in here as reference.

AP: anterior (+) / posterior (-) translation (mm); defines translation of tibia origin relative to femur along a floating axis orthogonal to flexion axis (femur fixed) and internal-external rotation axis (tibia fixed)
ML: medial (+) / lateral (-) translation (mm); defines translation of tibia origin relative to femur along a mediolateral axis fixed on femur
DC: distraction (+) / compression (-) (mm); defines location of femur origin relative to tibia along a superior-inferior axis fixed on tibia
FE: flexion (+) / extension (-) (deg); defines rotation of tibia relative to femur around a mediolateral axis fixed on femur
IE: internal (+) / external (-) rotation (deg); defines rotation of tibia relative to femur around a superior-inferior axis fixed on tibia
VV: varus (+) / valgus (-) (deg); defines rotation of tibia relative to femur around a floating axis orthogonal to femur and tibia fixed axes

The coordinate system of the model at the reference state matches that of Open Knee(s) - Generation 1 model. The femur and tibia coordinate systems are coincident and aligned; x-axis is directed laterally, y-axis is directed anteriorly, z-axis is pointed towards the superior direction (right knee).

For more information on the development of cloud computing infrastructure for Open Knee(s), please refer to Specifications/CloudComputingPrototype

Files

Input

modify_model.cfg: text file to prescribe target clinical movement (exposed in the input section of the cloud computing interface and provided in results section of the cloud computing interface)
model.feb: template model (provided in results section of the cloud computing interface)

Background Computing

modify_model.py: Python script to modify the template model using target clinical movement provided in modify_model.cfg
post_process.py: Python script to post-process simulation results
submit_simulation.py: Python script that does it all; modifies template model (using modify_model.py), runs simulation by calling FEBio executable, post-processes results (using post_process.py)
FEBio executable: Finite element analysis software, required version 2.5 and above (distributed at http://febio.org/)

Output

model_MOD.feb: modified model (temporarily provided in results section of the cloud computing interface)
model_MOD.log: FEBio log file reporting simulation convergence history (temporarily provided in results section of the cloud computing interface)
model_MOD.xplt: FEBio output file, which can be accessed by PostView to visualize tibiofemoral joint movement and stress-strain distribution in the anterior cruciate ligament (temporarily provided in results section of the cloud computing interface)
femur_kinematics.txt: FEBio output file for femur movements used in post-processing (temporarily provided in results section of the cloud computing interface)
femur_kinetics.txt: FEBio output file for femur loading used in post-processing (temporarily provided in results section of the cloud computing interface)
tibia_kinematics.txt: FEBio output file for tibia movements (temporarily provided in results section of the cloud computing interface)
tibia_kinetics.txt: FEBio output file for tibia loading (temporarily provided in results section of the cloud computing interface)
post_process.txt: Post-processed results including trajectories of tibiofemoral joint movements (described in a clinically relevant manner) and anterior cruciate ligament force (provided in results section of the cloud computing interface)

Licensing

Python scripts are distributed under MIT license.

Open Knee(s) models are distributed under Creative Commons Attribution-ShareAlike licensing.

FEBio is freely available for non-commercial use, including academic research and teaching applications (see http://febio.org/about/licensing/).

Use of simulation results need to comply with licensing requirements of script, models, and FEBio, the simulation software.

Use of computing resources need to comply with requirements of respective resource providers.

THE SCRIPTS, MODELS, SOFTWARE, AND SIMULATION RESULTS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Team Members

Ahmet Erdemir (Cleveland Clinic)
Craig Bennetts (Cleveland Clinic)
Joy Ku (Stanford University)
Henry Kwong (Stanford University)

Progress

References

Grood ES, Suntay WJ. A joint coordinate system for the clinical description of three-dimensional motions: application to the knee. J Biomech Eng. 1983 May;105(2):136-44. PubMed

Synopsis

Files

Input

Background Computing

Output

Licensing

Team Members

Progress

Source Code Repository

Data

Model Customization

Simulations Results

Publications

References