Projects

Current software development in the lab:
autoPACK is an open-source general packing algorithm that positions 3D objects on surfaces and into/around volumes with zero to minimal overlap depending on the method used and the accuracy vs speed parameters selected by the user. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPack can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the "loose packing problem" which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.)
http://www.cellpack.org
cellPACK is a specialized version of autoPack designed to pack biological components together. The current version is optimized to pack molecules into cells with biologically relevant interactions to populate massive cell models with atomic or near-atomic details. Components of the algorithm pack transmembrane proteins and lipids into bilayers, globular molecules into compartments defined by the bilayers (or as exteriors), and fibrous components like microtubules, actin, and DNA.
 
Lead developer: Ludovic Autin @ MGL
ePMV, the embedded Python Molecular Viewer, runs free molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and molecular toolkit functionalities into a single interface, allows illustrators to quickly create common representations of molecular models and to perform computational simulations, like molecular dynamics, directly inside of a host’s viewport with relative ease.
Available free at http://epmv.scripps.edu, ePMV currently supports Blender, Cinema4D, Maya, 3D Studio Max & SoftImage
 
Lead developer: Ludovic Autin @ MGL
uPy, the ubiquitous Python API,extends the Python programming language to wrap most common functions of the APIs of several computer graphics programs called hosts. With uPy, computer programmers can develop graphical user interfaces and sophisticated plugins once and use them in any uPy wrapped host. Hosts currently include Cinema4D, Maya, 3D Studio Max, Soft Image, Blender, PyQT, & Tkinter.
Medical Illustration & Animation Graham Johnson's professional medical illustration and animation service. Available to generate cover images, teaching slides, animations and for consultation on game development, art installations and other teaching or edutainment purposes.
 sigViz (early stages) sigVIZ aims to develop software,  sigViz,  that researchers can use to create interactive dynamic representations of cell signaling pathways that contain accurate structural details for improved communication,  hypothesis generation,  and systems simulation. , The sigViz app will function in a variety of popular interfaces,  including web browsers,  to enable researchers from any background to easily access and use the tools with no special training. A graphic user interface designed for quantitative biologists will produce outputs that target diverse audiences and purposes (e.g., journals, slides, websites, and thought/virtual experiment tools).
 ASCB2 coming soon  ASCB2, Coming soon
 ImmuneAttack2 coming soon  ImmuneAttack, Coming soon
autoPACK Challenges serve to:
  • attract users & open-source programmers
  • expand the impact of software developed in the lab
  • unite experts from diverse fields to solve new and complex problems associated with the software
  • unite talents from diverse fields to generate novel and engaging visualizations of subjects studied with the lab software for peer communication, education, and outreach audiences
The first autoPACK Visualization Challenge was sponsored by Autodesk, hosted on CG Society, and ended March 18, 2013. View the entries HIV in Blood Plasma

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