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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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	<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
	<head>
	<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
	<title>Interview: NetBeans Platform Helps Advance Biomechanics Research</title>
	<link rel="stylesheet" type="text/css" HREF="../../../netbeans.css">
	</head>
	<body>
	<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 & 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
	& 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 the users 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>

	</body>
	</html>