The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).

A visibility ordering of a set of objects from some viewpoint is an ordering such that if object a obstructs object b, then b precedes a in the ordering. An algorithm is presented that generates a visibility ordering of an acyclic convex set of meshed convex polyhedra. This algorithm takes time linear in the size of the mesh. Modifications to this algorithm and/or preprocessing techniques are described that permit nonconvex cells, nonconvex meshes (meshes with cavities and/or voids), meshes with cycles, and sets of disconnected meshes to be ordered. Visibility ordering of polyhedra is applicable to scientific visualization, particularly direct volume rendering, It is shown how the ordering algorithms can be used for domain decomposition of finite element meshes for parallel processing, and how the data structures used by these algorithms can be used to solve the spatial point location problem. The effects of cyclically obstructing polyhedra are discussed and methods for their elimination are described, including the use of the Delaunay triangulation.Methods for converting nonconvex meshes into convex meshes are described.

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This paper describes a volume rendering system for unstructured data, especially finite element data, that creates images with very high accuracy. The system will currently handle meshes whose cells are either linear or quadratic tetrahedra. Compromises or approximations are not introduced for the sake of efficiency. Whenever possible, exact mathematical solutions for the radiance integrals involved and for interpolation are used. The system will also handle meshes with mixed cell types: tetrahedra, bricks, prisms, wedges, and pyramids, but not with high accuracy. Accurate semitransparent shaded isosurfaces may be embedded in the volume rendering. For very small cells, subpixel accumulation by splatting is used to avoid sampling error. A revision to an existing accurate visibility ordering algorithm is described, which includes a correction and a method for dramatically increasing its efficiency. Finally, hardware assisted projection and compositing are extended from tetrahedra to arbitrary convex polyhedra.