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<div class=WordSection1>
<p class=MsoNormal><b>Simbios Update…</b><o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>1)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>1)
OpenSim Jamboree brings together researchers from around the world<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>2)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>2)
OpenMM 2.0 enables molecular dynamics acceleration on ATI and NVIDIA GPUs<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>3)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>3)
AMBER/Sander-compatible interface to OpenMM just released<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>4)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>4)
Special issue from Royal Society Publishing - The virtual physiological
human: computer simulation for integrative biomedicine<o:p></o:p></p>
<p class=MsoNormal><i> </i><o:p></o:p></p>
<div class=MsoNormal align=center style='text-align:center'><i>
<hr size=2 width="100%" align=center>
</i></div>
<p class=MsoNormal><i> </i><o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l1 level1 lfo4'><![if !supportLists]><i><span style='mso-list:Ignore'>1)<span
style='font:7.0pt "Times New Roman"'> </span></span></i><![endif]><b><i>1)
OpenSim Jamboree Brings Together Researchers from Around the World</i></b><br>
The OpenSim Developer Jamboree, an intense working session that brought
together researchers from 14 institutions around the world, was held from July
12-14. The<span class=apple-converted-space> </span><a
href="http://simtk.org/home/opensim" target="_blank">OpenSim</a> software
enables computer modeling and dynamic simulations of movement. During
these three days, participants worked with the newest version of OpenSim and
received help from the OpenSim team on individual research projects.
Exciting progress was made on biomechanical research questions and useful
plugins for the OpenSim community. In addition, participants were
introduced to a <span style='color:#1F497D'><a
href="http://simtk.org/home/opensim_matlab">Matlab/Simulink interface</a></span><span
class=apple-converted-space> </span>to OpenSim, developed by Prof.
Reinbolt as part of a Simbios seed grant.<span style='font-size:12.0pt;
font-family:"Times New Roman","serif"'> </span><o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l1 level1 lfo4'><![if !supportLists]><span class=MsoHyperlink><i><span
style='color:windowtext;text-decoration:none'><span style='mso-list:Ignore'>2)<span
style='font:7.0pt "Times New Roman"'> </span></span></span></i></span><![endif]><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p> </o:p></span></span></p>
<p class=MsoNormal><b><i>2) OpenMM 2.0 Enables Molecular Dynamics
Acceleration on ATI and NVIDIA GPUs</i></b><br>
Simbios is excited to announce the release of OpenMM 2.0, <span
class=apple-converted-space> </span>a major update of this library for
accelerating molecular dynamics. This version supports accelerated calculations
on NVIDIA GPU cards (using either CUDA or OpenCL), as well as ATI GPU cards
(using OpenCL). It also includes pressure coupling, more custom force
types, and significant performance increases. You can download OpenMM
from<span class=apple-converted-space> </span><span
style='color:#1F497D'><a href="http://simtk.org/home/openmm">http://simtk.org/home/openmm</a></span>.
OpenMM 2.0 has been made available to GROMACS users (via
OpenMM-Accelerated GROMACS) and to AMBER users (via an AMBER/Sander-compatible
interface to OpenMM, available at <span style='color:#1F497D'><a
href="http://simtk.org/home/sander_openmm">http://simtk.org/home/sander_openmm</a></span>).<span
class=MsoHyperlink><i><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></i></span></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span style='font-size:12.0pt;font-family:
"Times New Roman","serif"'><span style='mso-list:Ignore'>5)<span
style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span class=MsoHyperlink><b><span
style='color:windowtext;text-decoration:none'><span style='mso-list:Ignore'>6)<span
style='font:7.0pt "Times New Roman"'> </span></span></span></b></span><![endif]><b><i><a
href="http://simtk.org/home/opensim" target="_blank"><span style='color:windowtext;
text-decoration:none'>3) AMBER/Sander-compatible interface to OpenMM Just
Released</span></a></i><span class=MsoHyperlink><span style='color:windowtext;
text-decoration:none'><o:p></o:p></span></span></b></p>
<p class=MsoListParagraph style='margin-left:0in;text-indent:-.25in;mso-list:
l0 level1 lfo2'><![if !supportLists]><span class=MsoHyperlink><i><span
style='color:windowtext;text-decoration:none'><span style='mso-list:Ignore'>7)<span
style='font:7.0pt "Times New Roman"'> </span></span></span></i></span><![endif]>AMBER
users are now able to use the power of OpenMM to run accelerated molecular
dynamics with their existing Sander input files. The code for the
AMBER/Sander-compatible interface to OpenMM and exciting benchmark numbers for
systems including the villin headpiece, lambda repressor, and alpha spectrin
are available for download from <a href="https://simtk.org/home/sander_openmm">http://simtk.org/home/sander_openmm</a>.<span
class=MsoHyperlink><i><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></i></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><b><i><a href="https://simtk.org/home/sander_openmm"><span
style='color:windowtext;text-decoration:none'>4) Special issue from Royal
Society Publishing - The virtual physiological human: computer simulation
for integrative biomedicine</span></a></i><span class=MsoHyperlink><span
style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></b></p>
<p class=MsoNormal>Simbios EU collaborators have been actively involved in a
special issue from Royal Society Publishing on “The virtual physiological
human: computer simulation for integrative biomedicine.” <span
class=apple-converted-space> </span><span lang=EN-GB style='font-size:
10.0pt;font-family:"Arial","sans-serif"'>See<span class=apple-converted-space> </span><span
style='color:#1F497D'><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml">http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml</a></span><span
class=apple-converted-space> </span>for further details. </span><span
lang=EN-GB>All articles in this double issue (along with all content back to
1665) are<span class=apple-converted-space> </span><b>free<span
class=apple-converted-space> </span></b>to access up until the end of July
2010.</span><span class=MsoHyperlink><span style='color:windowtext;text-decoration:
none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a href="https://simtk.org/home/sander_openmm"><span
style='color:windowtext;text-decoration:none'> </span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a href="https://simtk.org/home/sander_openmm"><span
style='color:windowtext;text-decoration:none'>______________________________________________________</span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>Joy P. Ku</span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>Director of Dissemination</span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>Simbios, Stanford University</span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>(W) 650.736.8434 </span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>(F) 650.723.7461</span></a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>Email: </span>joyku@stanford.edu</a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
<p class=MsoNormal><a
href="http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-human.xhtml"><span
style='color:windowtext;text-decoration:none'>Website: </span>http://simbios.stanford.edu</a><span
class=MsoHyperlink><span style='color:windowtext;text-decoration:none'><o:p></o:p></span></span></p>
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