Pittsburgh Supercomputing Center

National Resource for Biomedical Supercomputing

Carnegie Mellon University

The Salk Institute
Howard Hughes Medical Institute

National Institute of Health

National Center for Research Resources

National Institute of General Medical Sciences

National Science Foundation

DReAMM Overview


This flow chart (click here for larger image) outlines the principal DReAMM Operations and Control Panels (menus). Note that:

  • DReAMM can import a variety of mesh objects, including polylines, surfaces, and volumes in any combination.
    • Most often, mesh objects will be triangulated surfaces or tetrahedral or cuboidal volumes.
    • File formats for meshes can be OpenDX (.dx suffix), 3df (.3df, from CAD software), or ASCII VRML 1.0 (.wrl).
    • Meshes output by MCell for DReAMM are in OpenDX format. MCell also exports molecule and effector site positions and states in OpenDX format for visualization with DReAMM.
  • Imported objects (meshes, molecules, and/or effector sites) are chosen for operations by name.
    • For MCell simulations, the names are defined in the MDL (Model Description Language) files used for the simulations.
    • In cases of other mesh input files, existing object names are used whenever possible. Otherwise DReAMM will assign default names (object_1, object_2, & ).
    • You can use UNIX-style wildcard characters to filter names (see Filtering Objects) and dramatically speed up operations on thousands of objects.
    • You can use very long object names without dramatic speed penalties (up to 1024 characters per name).
  • Imported meshes can be edited in various ways and subsequently saved again in OpenDX or MDL format (see Advanced DReAMM tutorials).
  • Data Clipping can be used to reduce the amount of visualized data, passing through only the amount included within user-specified (±)x, y, and z limits.
  • Mesh, molecule, and effector site objects can be rendered using separate Default or Custom settings.
    • In Default mode, all of the selected objects receive the same color, opacity, and shading, as well as other rendering properties (e.g., choice of glyph for molecules or effector sites).
    • In Custom mode, each object is looked up by name in a user-editable table (see the Overview of Lookup Tables tutorials). If the matching object name is found in the table, the corresponding properties are applied, otherwise the object is omitted (not rendered). Custom settings include the option of user-editable Color and Opacity Maps on an object-by-object basis (see Advanced DReAMM tutorials).
    • As when selecting objects, wildcard filtering can be used when assigning custom properties to speed up operations on thousands of objects.
  • Mesh objects imported from OpenDX files may include pre-existing color and shading information. If so it is used in Default rendering mode, and can be overridden in Custom mode.
  • Depth Cueing can be applied with separate settings for different types of objects. Depth Cueing makes objects easier to perceive in 3-D, typically by progressive darkening as a function of distance from the viewpoint.
  • Image Clipping can be used to produce an arbitrarily oriented, smoothly cut section through the rendered objects. This is distinct from Data Clipping, which removes parts of objects before they are rendered. Thus Data Clipping reduces work, while Image Clipping increases work because the data must be interpolated to produce the arbitrary smooth cut edges.
  • DReAMM's default lighting is well-suited to almost all conditions, but ambient and distant Lights can be controlled by the user if necessary.
  • DReAMM includes both Software and Hardware rendering.
    • Software rendering is performed by the computer's CPU (central processing unit), while hardware rendering is performed by the video card's GPU (graphical processing unit).
    • If DReAMM is running with PSC_DX (required for DReAMM v.3.x), hardware rendering matches software rendering. If DReAMM is running with OpenDX, hardware rendering does not include two-sided lighting and also suffers from some shading bugs.
    • Hardware rendering can be much faster than software rendering but is limited to objects that can fit in the memory on the video card.
    • Software rendering is slower than hardware rendering but may be advantageous or required for large objects, and is also used for additional flexibility and features when Saving Images and/or rendering Stereo pairs.
  • Sequence Control, Frame Control, and Animation Sequence settings provide interleaved control of time series data, Image Clipping and Keyframe Animations (see Advanced DReAMM tutorials).
  • All settings and customization tables can be saved in a DReAMM project for subsequent reuse.

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    • MCell 3.3 and DReAMM 3.3.0 Now Available

    New versions for Linux and Mac OS X now available on our Downloads page.

    MCell Used in New Vesicle Fusion Findings

    Researchers at the National Institute of Neurological Disorders and Stroke use MCell to simulate "kiss-and-run" fusion at calyx-type synapses. See He, L., et al. Two modes of fusion pore opening revealed by cell-attached recordings at a synapse. Nature 444, 102-105 (2006).

    MCell and DReAMM Demographics and Teaching Statistics

    Check out CQBS's most recent usage statistics. [Read more]