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Center for Computational Biology at UCLA

Summary:

The Center for Computational Biology (CCB) is focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales.

The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge.

Affiliations:

Resources:

Software

  • ASAP ( Software )

    "After transcription of a gene, the resulting pre-mRNA is spliced before exiting the nucleus. Alternative splicing of a single pre-mRNA can give rise to different mRNA transcripts. Consequently, alternative splicing is an important mechanism for generating protein diversity from a single gene. It has been suggested that large numbers of human genes are alternatively spliced (1, 2, 3). Alternative splicing is observed all across metazoa, and has been implicated in various biological processes."

    License: CCB License

    Development stage: Development with public user base

    Release date: 6/28/1905

    Keywords: alternative splicing, biological process, alternatively spliced isoforms

  • Automated Image Registration ( Software )

    "A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities."

    License: CCB License

    Development stage: Mature

  • BLASTgres ( Software )

    License: CCB License

    Development stage: Development with public user base

    Release date: Dec-06

    Keywords: PostgreSQL, data management of biological sequences, bioinformatics.

  • Brain Surface Extractor ( Software )

    "Brain Surface Extraction: Designed to automatically extract the brain from a set of T1 weighted Magnetic Resonance (MR) images of the human head."

    Development stage: Development with public user base

    License: CCB License

  • BrainSuite2 ( Software )

    "BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head."

    Development stage: Development with public user base

    Release date: 6/1/2005

    License: CCB License

  • Charged Fluid Model for Brain Image Segmentation ( Software )

    "CCFMBIS is a computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model."

    Development stage: Development with public userbase

    Release date: 1/20/2007

    License: CCB License

  • Charged Fluid Model for Vascular Segmentation ( Software )

    "A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model."

    Development stage: Development with public user base

    Release date: 5/30/2006

    License: CCB License

  • DualSurfaceMin ( Algorithmic software component )

    "The dualsurfacemin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces [1]. The method is developed for automatic surface extraction from noisy volumetric images."

    Development stage: Development with public userbase

    Release date: 5/31/2005

    License: CCB License

  • DXJava ( Software )

    "The DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files."

    Development stage: Development with public userbase

    Released date: 5/1/2006

    License: CCB License

  • Extract4DUcfAttributes ( Software )

    "The Extract4DUcfAttributes application extracts data attributes associated with each vertex of a Ucf file."

    Development stage: Development with public userbase

    Release date: 5/10/2006

    License: CCB License

  • FFT Library ( Software )

    "An FFT library in Java."

    Development stage: Development with public userbase

    Release date: 2/24/2005

    License: CCB License

  • InterpolateUcf ( Software )

    "InterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file."

    Development stage: Development with public userbase

    Release date: 10/10/2005

    License: CCB License

  • jViewbox ( Software )

    "A portable software framework for medical imaging research."

    Development stage: Development with public userbase

    Release date: 3/1/2003

    License: CCB License

  • LONI De-identification Debablet ( Software )

    "A simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files."

    Development stage: Development with public userbase

    Release date: 10/13/2005

    License: CCB License

  • LONI Debabeler ( Software )

    "The LONI Debabeler enables researchers to manage the conversion of imaging data from one file format to another using a graphical user interface."

    Development stage: Development with public userbase

    Release date: 11/13/2006

    License: CCB License

  • LONI It's Close Enuf ( Software )

    "LONI ICE is a Java application that generates seed points for other image processing applications."

    Development stage: Development with public userbase

    Release date: 11/1/2006

    License: CCB License

  • LONI Java Image I/O Plugins ( Software )

    "Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats."

    Development stage: Development with public userbase

    Release date: 11/13/2006

    License: CCB License

  • LONI Pipeline Processing Environment ( Software )

    Protocol Execution Environment.

    Development stage: Beta

    Release date: 2/28/2006

    License: CCB License

    Keywords: Protocol Execution Environment

  • LONI ShapeDistance ( Software )

    "A tool for calculating the distance between vertices of two shape files."

    Development stage: Development with public user base

    Release date: 10/31/2005

    License: CCB License

  • LONI ShapeTools ( Software )

    "The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values."

    Development stage: Development with public user base

    Release date: 5/10/2006

    License: CCB License

  • LONI ShapeViewer ( Software )

    "The LONI ShapeViewer is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java,it can run on a wide variety of computers."

    Development stage: Development with public user base

    Release date: 5/10/2006

    License: CCB License

  • LONI ShapeViewerApplet ( Software )

    "The ShapeViewerApplet displays three dimensional shapes in a web page."

    Development stage: Development with public user base

    Release date: 10/28/2005

    License: CCB License

  • LONI Visualization Tool ( Software )

    "An interactive tool for stereotaxic brain data visualization."

    Development stage: Development with public user base

    Release date: 5/23/2006

    License: CCB License

  • MultiPhase-SEG ( Software )

    "MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model."

    Development stage: Development with public user base

    Release date: 3/1/2005

    License: CCB License

  • MultiTracer ( Software )

    "Tracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision."

    Development stage: Development with public user base

    License: CCB License

  • Pygr ( Software )

    "Pygr is an open source software project used to develop graph database interfaces."

    Development stage: Development with public user base

    Release date: 3/10/2006

    License: CCB License

  • ShapeCurvature ( Software )

    "The ShapeCurvature application allows researchers to calculate the curvature of a surface mesh that is stored in a shape file. These curvature values may be written to disk files in a variety of file formats."

    Development stage: Development with public user base

    Release date: 5/10/2006

    License: CCB License

  • ShapeToDX ( Software )

    "The ShapeToDX application is a Java application that translates data files that can be read by the ShapeTools library into an OpenDX genreal format data file."

    License: CCB License

    Development stage: Development with public user base

    Release date: 5/10/2006

  • ShapeTransform ( Software )

    "The ShapeTransform application facilitates the moveof a shape file from one coordinate system to another."

    Development stage: Development with public user base

    Release date: 5/3/2006

    License: CCB License

  • Statistical Online Computational Resource ( Software )

    "The SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications."

    Development stage: Mature

    Release date: 8/1/2003

    License: CCB License

  • Sub-Volume Thresholding Analysis ( Software )

    "A tool for Statistical Analysis of Stereotactic Functional Brain Data."

    Development stage: Development with public user base

    Release date: 8/1/2003

    License: CCB License

  • Synchronized Histological Image Viewing Architecture ( Software )

    "The Synchronized Histological Image Viewing Architecture is a Java-based visualization and analysis application."

    Development stage: Development with public user base

    Release date: 10/16/2005

    License: CCB License

  • Virtual File System Browser ( Software )

    "The Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols."

    Development stage: Development with public user base

    Release date: 5/10/2006

    License: CCB License

  • Wavelet Analysis of Image Registration ( Software )

    "A tool for quantitative analysis of various n-dimensional (n-D) image registration techniques."

    Development stage: Development with public user base

    License: CCB License


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Last updated: 2013-10-01T16:07:58.503-05:00

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