2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001

Showing Our Brains: Image Wins Prize, Made with New VND Software (Jun 2021)

image size: 6.9MB
Made with VND

Modern neuroscience is undergoing a profound evolution due to systematic efforts that provide large, comprehensive datasets on properties of brain cells, their connectivity, and activity. Converting these widening streams of complex data into new knowledge via analysis and modeling is a major challenge for the field. This rendering of a model of the mouse primary visual cortex (V1) with a Neuropixels probe was awarded 2nd Prize in the 2021 NIH BRAIN Initiative "Show Us Your BRAINs!" Photo and Video Contest. The image was created with new software created at the Center: Visual Neuronal Dynamics VND — based on the Center's powerful VMD software, and produced in collaboration with the Allen Institute. The VND software performs visualization of bio-realisitc 3D neuronal network models and aims to provide efficient workflows for large and complex systems of thousands of neurons and beyond. VND integrates the SONATA format, which is used by the Brain Modeling Toolkit (BMTK), with the existing powerful visualization capabilities of VMD to provide a platform for user-friendly, flexible, and highly efficient visualization of bio-realistic neuronal network models and simulations. The initial version of VND reads SONATA file data, displays a new neuroscience-specific interactive GUI, and creates neuronal network visualizations for both exploratory visualization and for generating publication-quality figures for research manuscripts.
VMD ARM Wrestles Apple M1 Macs (Mar 2021)

Made with VMD

VMD supports the broadest possible range of hardware platforms of value to molecular scientists. ARM processors have dominated mobile phone and tablet platforms due to their energy efficiency and customizability. Our investigation of GPU-accelerated ARM platforms for molecular modeling demonstrated their potential, as as we previously reported. Recently ARM platforms have become significantly more performant, with today's state-of-the-art 64-bit ARM CPUs beginning to turn up in top ranked supercomputers, public clouds such as AWS, and both laptop and desktop PCs. Apple has released new Mac laptop and desktop computers based on its own "M1" 64-bit ARM processors. VMD 1.9.4 adds support for the new Apple M1 platform and MacOS 11, a major new version of MacOS that supports hardware based on both Intel x86 and Apple ARM M1 processors. The new VMD builds for Apple M1 platforms uses 64-bit addressing to facilitate efficiently working with very large macromolecular systems and biomolecular complexes limited only by memory capacity. To provide the best possible performance on the new ARM-based platforms by Apple and other vendors, VMD incorporates hand-vectorized loops for NEON SIMD instructions, enabling rapid alignment of atomic structures with cryo-EM densities, and interactive animation of molecular surfaces with QuickSurf, and molecular orbital visualizations from quantum chemistry calculations and hybrid QM/MM simulations. The new VMD builds for Apple M1 Mac hardware are available from the VMD home page.

2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001