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modify_model.cfg  modify_model.cfg:: text file to prescribe target clinical movement (exposed in the input section of the cloud computing interface)
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model.feb  model.feb:: template model (provided in results section of the cloud computing interface)
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modify_model.py  modify_model.py:: Python script to modify the template model using target clinical movement provided in modify_model.cfg
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post_process.py  post_process.py:: Python script to post-process simulation results
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submit_simulation.py  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)
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FEBio executable (distributed at http://febio.org/)  FEBio executable:: Finite element analysis software, required version 2.5 and above (distributed at http://febio.org/)
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model_MOD.feb  model_MOD.feb:: modified model (temporarily provided in results section of the cloud computing interface)
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model_MOD.log  model_MOD.log:: FEBio log file reporting simulation convergence history (temporarily provided in results section of the cloud computing interface)
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model_MOD.xplt  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)
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femur_kinematics.txt  femur_kinematics.txt:: FEBio output file for femur movements used in post-processing
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femur_kinetics.txt  femur_kinetics.txt:: FEBio output file for femur loading used in post-processing
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tibia_kinematics.txt  tibia_kinematics.txt:: FEBio output file for tibia movements
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tibia_kinetics.txt  tibia_kinetics.txt:: FEBio output file for tibia loading
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post_process.txt  post_process.txt

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 version 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 provided in here as reference.

AP

ML

CD

FE

IE

VV

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)
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
femur_kinetics.txt
FEBio output file for femur loading used in post-processing
tibia_kinematics.txt
FEBio output file for tibia movements
tibia_kinetics.txt
FEBio output file for tibia loading post_process.txt

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

Source Code Repository

https://simtk.org/svn/openknee/app/CloudComputing/

Data

https://simtk.org/svn/openknee/app/CloudComputing/dat/

Model Customization

https://simtk.org/svn/openknee/app/CloudComputing/src/

Simulations Results

https://simtk.org/svn/openknee/app/CloudComputing/sol/

Publications

https://simtk.org/svn/openknee/app/CloudComputing/doc/

Cases/CloudComputing (last edited 2016-09-03 01:45:34 by aerdemir)