Recurring Meeting of Cleveland Clinic Core Team

Date: November 18, 2014

Time: 10:30 AM EST

Means: In person meeting


  1. Ahmet Erdemir
  2. Craig Bennetts
  3. Snehal Chokhandre
  4. Tara Bonner


  1. Discuss immediate action items from the last meeting.
  2. Discuss how to run simulations on in-house high performance cluster.
  3. Decide immediate action items for the next meeting.
  4. Other.

Immediate Action Items:


  1. Discuss immediate action items from the last meeting.
    • Ahmet found the Introduction to Robotics book by John J. Craig. The material Jason Halloran was referring to was from this book. The team members can utilize this book to learn more about transformation matrices and robot kinematics and kinetics.
    • Ahmet provided the goals and input-output variables in the specifications page of joint kinematics-kinetics modeling.
    • Ahmet updated the specifications to reflect the notes in the oks002 wiki page.
    • Snehal had a hard time to find a bone cement supplier already approved by Cleveland Clinic purchasing. The team may need to order this personally and get reimbursed later.
    • Snehal informed Science Care (specimen supplier) to acquire additional knee specimens. The company is currently looking for two knees (from healthy elderly donors).
    • Snehal has conducted more re-testing of the oks004 tissue samples. The work will continue in the upcoming week.
    • Snehal also provided soft copies of donor sheets in the in-house data management system in appropriate specimen folders.
    • Tara provided laxity plots for oks001, oks002, and oks004. These will help quickly evaluate the tibiofemoral mechanics of a given specimen.
  2. Discuss how to run simulations on in-house high performance cluster.
    • Ahmet provided a brief tutorial on how to use the high performance computing cluster at the Cleveland Clinic for conducting simulations with Open Knee(s) - Generation 1.
    • Any registered user can connect the cluster using an SSH client (for terminal access, e.g., Putty) and with secure FTP (to transfer files, e.g., psftp).
    • To run a simulation one needs to transfer four files to the cluster: FEBio executable (optional if pre-installed version exists), FEBio configuration file (optional if pre-installed version exists), the model file, and a job submission script (relying on SLURM, scheduler used in the cluster).
    • Once all the files are uploaded, the user can submit the simulation by invoking the job submission script using the sbatch command. The job submission script has many configurable variables indicating desired number of nodes, cpus, memory, etc. Once a job is submitted, squeue command can show where the job is in the queue. The user can disconnect after submitting the job, e-mails will be sent when the job starts and ends.
    • The user can transfer the results files back to his/her local computer for further post-processing or visualization.
    • One can use the module command to see what software is available and to load/unload the environment to use a desired software package.
  3. Decide immediate action items for the next meeting.
    • See Immediate Action Items above.
  4. Other.
    • Snehal noted that oks005 may have some health issues, which may make the team uneasy to work on it. The group emphasized that universal precautions should be in place at all times. Nonetheless, Snehal will contact science care and the physicians of the Advisory Board to inquire about the potential implications of oks005 health issues (if they exist).
    • Robb will explore if there are existing designs for the current tissue thickness testing system. If so, the team may have another built to keep in the laboratory, where tissue testing is done, for easier access.
    • Ahmet reminded all to provide any experimentation images that may be left in or in personal devices.
    • The group briefly discussed organization of tibiofemoral joint data collected in a previous project. A separate meeting including Robb will be arranged to further elaborate on this issue.

RecurringMeetings/2014-11-18 (last edited 2016-05-04 22:09:50 by localhost)