Motivation: BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results: In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation: The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

A new method for computing form-factors within a progressive radiosity approach is presented. Previously, the progressive radiosity approach has depended on the use of the hemi-cube algorithm to determine form-factors. However, sampling problems inherent in the hemi-cube algorithm limit its usefulness for complex images. A more robust approach is described in which ray tracing is used to perform the numerical integration of the form-factor equation. The approach is tailored to provide good, approximate results for a low number of rays, while still providing a smooth continuum of increasing accuracy for higher numbers of rays. Quantitative comparisons between analytically derived form-factors and ray traced form-factors are presented.

A reformulated radiosity algorithm is presented that produces initial images in time linear to the number of patches. The enormous memory costs of the radiosity algorithm are also eliminated by computing form-factors on-the-fly. The technique is based on the approach of rendering by progressive refinement. The algorithm provides a useful solution almost immediately which progresses gracefully and continuously to the complete radiosity solution. In this way the competing demands of realism and interactivity are accommodated. The technique brings the use of radiosity for interactive rendering within reach and has implications for the use and development of current and future graphics workstations.

View-independent and view-dependent image synthesis techniques, represented by radiosity and ray tracing, respectively, are discussed. View-dependent techniques are found to have advantages for calculating the specular component of illumination and view-independent techniques for the diffuse component. Based on these observations a methodology is presented for simulating global illumination within complex environments using a two-pass approach. The first pass is view-independent and is based on the hemi-cube radiosity algorithm, with extensions to include the effects of diffuse transmission, and specular to diffuse reflection and transmission. The second pass is view-dependent and is based on an alternative to distributed ray tracing in which a z-buffer algorithm is used to sample the intensities contributing to the specularly reflected or transmitted intensity.