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    <title>Interview: NetBeans Platform Helps Advance Biomechanics Research</title>
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    <H1>Interview: NetBeans Platform Helps Advance Biomechanics Research</H1>
    <p><img src="../../../images_www/articles/interviews/bio-mechanics/ayman-3.png" alt="" align="right">
Ayman Habib (pictured, right) is a software engineer working for the <a href="http://nmbl.stanford.edu/">Neuromuscular Biomechanics Lab</a> (led by Prof. Scott Delp) and a staff member of the <a href="http://simbios.stanford.edu/">National Center for Biomedical Computation at Stanford University</a>.</p>

<p>His main job in the lab is writing and supporting the code used by
researchers and students, to perform modeling and simulation of the
musculoskeletal system, known collectively as <a href="https://simtk.org/home/opensim">OpenSim</a>,
and also disseminating the software to make it available to students
and researchers elsewhere. Ayman is the lead developer of the OpenSim
User Interface; in addition he supports the user community, and
participates in the design and development of a (C++) API to increase
the utility of the software. He has been programming for more than 20
years and has a Ph.D. in Computer Science from Rice University.</p>

<p><strong>In a nutshell, what is OpenSim?</strong></p>

<p>OpenSim is a set of tools that enable users to develop models of
musculoskeletal structures, build and refine simulations that utilize
these models and analyze the results of these simulations to gain
insight into muscle function and other aspects of the musculoskeletal
system. The models built using OpenSim range in complexity from simple
models used for educational purposes to subject specific models of
humans with movement disorders. OpenSim has also been used to model
animals, robots and orthotics. </p>

<p>The OpenSim application is the
Graphical User Interface that sits on top of the modeling and
simulation tools to make them accessible to a wide spectrum of users.</p>

<p><img src="../../../images_www/articles/interviews/bio-mechanics/ayman-1-smaller.png" alt=""> </p>

<p><strong>How long has it existed, how did it initially come about, how has it been funded and developed?</strong> </p>

<p>It started by an initiative from the NIH (<a href="http://www.nih.gov/">National Institute of Health</a>)
to launch a set of National Centers for Biomedical Computation.
Stanford won the national competition to host the center supporting
Physics Based Simulation of Biological Structures (<a href="http://simbios.stanford.edu/">Simbios</a>)
and secured the grant in 2004. NIH continues to fund the center. OpenSim is one of the projects supported by this center.</p>

<p><strong>It seems to be very widely used. Can you say something about what kind of
users it has, how many, and what users have found to be of particular
interest in the application, as well as compared to its competing
products?</strong> </p>

<p>OpenSim caters to a variety of users from
students (as a teaching tool in biomedical/mechanical engineering
departments and in some medical schools), to researchers performing
cutting edge research in movement science, rehabilitation, and design
of orthotics. It is also used by some clinicians in gait labs studying
gait-abnormalities. </p>

<p>The first public release of OpenSim was in Aug. 07, since then we have added more than 4500 new users and growing strong.  </p>
<p>Users like the intuitive Graphical User Interface:</p>
<p><img src="../../../images_www/articles/interviews/bio-mechanics/ayman-2-smaller.png" alt=""> </p>
<p>They
also like the extensibility of the system, so that they can add their
own modeling objects &amp; analyses and also availability of the latest
algorithms used to produce some of the most accurate simulations
around. </p>
<p>The main competing products in this area are
proprietary and commercial so users can’t have access to the algorithms
used in order to validate them and can’t plug in their own to
experiment with new ideas/algorithms. Many competing products come from
makers of motion capture systems, so they have different priorities.</p>

<p><strong>What are some of the main technical challenges that OpenSim has had to deal with?</strong></p>

<p>One of the main technical challenges to OpenSim is the wide
spectrum of users from high school kids learning the basics to involved
researchers who would want to have access to and be able to modify core
algorithms to fit their needs. </p>
<p>That's where a modular
architecture as the NetBeans Platform comes in handy, as you can
envision multiple products building on a shared set of modules
targeting users at different levels. Because the OpenSim API layer and
supporting libraries have been evolving over the last couple of years,
we have not had the chance to leverage the NetBeans Platform as much as
I'd like, but we’re moving in this direction and so the vision is
starting to materialize. </p>

<p><strong>Looking under the hood, what
are the main libraries/frameworks/languages/etc used by OpenSim, i.e.,
what are its technical specifics?</strong> </p>

<p>The OpenSim application is built on top of a stack of C++ libraries developed under the SimTK project (<a href="http://netbeans.dzone.com/simtk.org">htttp://simtk.org</a>) to perform neural/musculoskeletal modeling, multibody dynamics, and numerical methods. We use <a href="http://www.swig.org/">SWIG</a> for wrapping to call these libraries from Java. OpenSim also uses <a href="http://www.vtk.org/">VTK</a> for 3D visualization, <a href="http://www.jfree.org/jfreechart/">JFreechart</a> for plotting and is built on top of the <a href="http://platform.netbeans.org/">NetBeans Platform</a>.  </p>

<p><strong>When and how was the decision made to use the NetBeans Platform?</strong></p>

<p> When I started writing the GUI for OpenSim in 2005, the
NetBeans Platform was not available as a solid platform for writing
Java applications as it is today, and I looked around for existing Java
&amp; Cross-platform C++ frameworks but didn’t find something that fits
our needs (I didn’t want to use Eclipse since I wanted to stay with
Swing rather than use SWT for easier integration with other tools), so
I started to write my own framework, and I got something going quickly,
but the progress was slow as there was so much code that I had to write
and document to enable modular/collaborative development which has
always been the vision for OpenSim. </p><p>Then a colleague came on
board around the time when NetBeans 5.0 became available and started
using it as an IDE for development. That’s when we took a serious look
into the NetBeans Platform, and then the switch was an easy decision,
since I found so many issues that I had been thinking about being built
into the platform (e.g., modules/plugins, windows management and
docking, Matisse to begin with). </p><p>The switch over took less than
a couple of months and it’s been reassuring to see our needs being met
by the NetBeans Platform since then. (<a href="http://wiki.simtk.org/opensim/NetbeansUI">Here</a> is our NetBeans Platform related Wiki.)</p><p><strong>How has it been to learn to use the NetBeans Platform and do you have any tips and tricks to share about the NetBeans Platform?</strong>
</p><p>Starting up was not hard as there were many tutorials and code
examples to begin with. I have also used the user forum a few times and
it continues to be a great resource for me. The book “Rich Client
Programming: Plugging into the NetBeans Platform” has also been helpful
as a backup plan for things I couldn’t find elsewhere. </p><p>One tip that I found useful (especially because we do not expose the Plugin 
  Manager as of yet) is that we can distribute modules as NBM files and that 
  they get installed automatically if&nbsp;the users&nbsp;put those NBM files in 
  a directory (update/download/) below our “cluster” directory. I have used this 
  a few times to deliver special purpose modules and was impressed by how 
  smoothly that went. </p>
  <p><strong>Anything else you'd like to say?</strong>

</p><p>Well, keep up the good work, it’s been a great ride so far and
I’m excited about the opportunities that are opening up for us and for
the biomechanics community at large through the use of the NetBeans
Platform. I'd also want to acknowledge the collaborative effort behind
OpenSim, including the great body of work provided by the simtk staff
and many current and former members of the NMBL lab at Stanford along
with our funding sources at the NIH (Roadmap for Medical Research,
Grant U54 GM072970). Thanks. </p>

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