Celestial3D: a novel method for 3D visualization of familial data

Summary: Traditional two-dimensional (2D) software programsfor drawing pedigrees are limited when dealing with extendedpedigrees. In successive generations, the number of individualsgrows exponentially, leading to an unworkable amount of spacerequired in the horizontal direction for 2D displays. In addition,it is not always possible to place closely related individualsnear each other due to the lack of space in 2Ds. To addressthese issues we have developed three-dimensional (3D) pedigreedrawing techniques to enable clearer visualization of extendedpedigrees. Currently no other methods are available for displayingextended pedigrees in 3Ds. We have made freely available a softwaretool—‘Celestial3D’—that implements thesenovel techniques. Availability: Freely available to non-commercial users Contact: celestial3d{at}genepi.org.au Supplementary information: www.genepi.org.au/celestial3d Associate Editor: Martin Bishop ¹A more extensive list of software tools appears in the SupplementaryMaterial.     

A system architecture for genomic data analysis

MOTIVATION: Most of diseases are caused by a set of gene defects, which occur in a complex association. The association scheme of expressed genes can be modelled by genetic networks. Genetic networks are efficiently facilities to understand the dynamic of pathogenic processes by modelling molecular reality of cell conditions. In this sense a genetic network consists of first, a set of genes of specified cells, tissues or species and second, causal relations between these genes determining the functional condition of the biological system, i. e. under disease. A relation between two genes will exist if they both are directly or indirectly associated with disease [8]. Our goal is to characterize diseases (especially autoimmune diseases like chronic pancreatitis CP, multiple sclerosis MS, rheumatoid arthritis RA) by genetic networks generated by a computer system. We want to introduce this practice as a bioinformatic approach for finding targets.     

CRAVE: a database, middleware and visualization system for phenotype ontologies

MOTIVATION: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. RESULTS: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.     

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

Background  

Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.     

myKaryoView: a light-weight client for visualization of genomic data

The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoView's ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com.     

A GIS-based tool for storage,selection and visualization of time series 4D marine datasets

We present an initial attempt for the development of a distributed and scalable GIS-like tool for the storage, selection and visualization of 4D marine datasets. The aim of this tool is to standardize the variety of data available for the water column and support non-technical marine biologists in manipulating 4D marine datasets. The tool is developed towards answering specific environmental and biological questions regarding ocean processes and essential fish habitat mapping in three dimensions. Guest editor: V. D. Valavanis Essential Fish Habitat Mapping in the Mediterranean     

A framework for querying a database for structural information on 3D images of macromolecules: A web-based query-by-content prototype on the BioImage macromolecular server

Nowadays we are experiencing a remarkable growth in the number of databases that have become accessible over the Web. However, in a certain number of cases, for example, in the case of BioImage, this information is not of a textual nature, thus posing new challenges in the design of tools to handle these data. In this work, we concentrate on the development of new mechanisms aimed at "querying" these databases of complex data sets by their intrinsic content, rather than by their textual annotations only. We concentrate our efforts on a subset of BioImage containing 3D images (volumes) of biological macromolecules, implementing a first prototype of a "query-by-content" system. In the context of databases of complex data types the term query-by-content makes reference to those data modeling techniques in which user-defined functions aim at "understanding" (to some extent) the informational content of the data sets. In these systems the matching criteria introduced by the user are related to intrinsic features concerning the 3D images themselves, hence, complementing traditional queries by textual key words only. Efficient computational algorithms are required in order to "extract" structural information of the 3D images prior to storing them in the database. Also, easy-to-use interfaces should be implemented in order to obtain feedback from the expert. Our query-by-content prototype is used to construct a concrete query, making use of basic structural features, which are then evaluated over a set of three-dimensional images of biological macromolecules. This experimental implementation can be accessed via the Web at the BioImage server in Madrid, at http://www.bioimage.org/qbc/index.html.     

A high-level 3D visualization API for Java and ImageJ

Background  

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.     

DiagHunter and GenoPix2D: programs for genomic comparisons,large-scale homology discovery and visualization

The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.     

GenomeDiagram: a python package for the visualization of large-scale genomic data

SUMMARY: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.     

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules. A new version of BRAGI has been developed that is supported on Windows, Linux and SGI. The user interface has been rewritten to give the standard 'look and feel' of the chosen operating system and to provide a more intuitive, easier usage. A large number of new features have been added. Information from public databases such as SWISS-PROT, InterPro, DALI and OMIM can be displayed in the 3D viewer. Structures can be searched for homologous sequences using the NCBI BLAST server.     

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

Background  

Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types.     

Multi-channel data collection and visualization system for intramyocardial electrograms]

The aim of the project was to develop a multichannel data acquisition system for the recording and visualisation of intramyocardial electrograms (IEGM) from both the spontaneously beating and the artificially paced heart. Signal processing comprises multi-step amplification, filtering (0.05-800 Hz), and AD conversion (12 Bit max. 6.25 kHz). IEGMs can be obtained either in unipolar or bipolar mode. Stimulation of the heart is achieved by an incorporated programmable dual-chamber pacemaker that can be selectively switched to the input channels. A LabView-based graphical user interface permits the programming of all system parameters via a microcontroller, and supports data acquisition and visualisation. The system can be used in animal experiments to monitor the spread of excitation across the heart, to measure propagation velocity, or to measure the impact of drugs and pathological changes on the morphology of IEGMs.     

A computer system for the storage and retrieval of clinical pharmacokinetic data

A computer system is described which stores patient data relating to clinical pharmacokinetic assessments made by clinical pharmacists, who are participating in a clinical pharmacokinetics service. The system was developed to assist in the documentation of service activities and storage of patients' pharmacokinetic data. An additional component of the system is the ability for retrospective review of the stored data. Applications of this system to the derivation of new information on drug pharmacokinetics and drug efficacy/toxicity in various patient groups is discussed. The implications for Phase IV drug studies and toxicity screening studies is also described.