An object-oriented framework to organize genomic data

Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data

Current usage of Component based Principles for Developing Web Applications with Frameworks: A Literature Review

Component based software development has become a very popular paradigm in many software engineering branches. In the early phase of Web 2.0 appearance, it was also popular for web application development. From the analyzed papers, between this period and today, use of component based techniques for web application development was somewhat slowed down, however, the recent development indicates a comeback. Most of all it is apparent with W3C’s component web working group. In this article we want to investigate the current state of web application development with component approach. Most of all we are interested in which way components are used, which web development frameworks are being used, for which domains is component based web development most popular and successful, etc. How many current web development frameworks explicitly refer to component-based approach? To answer this question, we performed a literature review

Version Control in Online Software Repositories

Software version control repositories provide a uniform and stable interface to manage documents and their version histories. Unfortunately, Open Source systems, for example, CVS, Subversion, and GNU Arch are not well suited to highly collaborative environments and fail to track semantic changes in repositories. We introduce document provenance as our Description Logic framework to track the semantic changes in software repositories and draw interesting results about their historic behaviour using a rule-based inference engine. To support the use of this framework, we have developed our own online collaborative tool, leveraging the fluency of the modern WikiWikiWeb

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine

Antidote application: an educational system for treatment of common toxin overdose

Poisonings account for almost 1% of emergency room visits each year. Time is a critical factor in dealing with a toxicologic emergency. Delay in dispensing the first antidote dose can lead to life-threatening sequelae. Current toxicological resources that support treatment decisions are broad in scope, time-consuming to read, or at times unavailable. Our review of current toxicological resources revealed a gap in their ability to provide expedient calculations and recommendations about appropriate course of treatment. To bridge the gap, we developed the Antidote Application (AA), a computational system that automatically provides patient-specific antidote treatment recommendations and individualized dose calculations. We implemented 27 algorithms that describe FDA (the US Food and Drug Administration) approved use and evidence-based practices found in primary literature for the treatment of common toxin exposure. The AA covers 29 antidotes recommended by Poison Control and toxicology experts, 19 poison classes and 31 poisons, which represent over 200 toxic entities. To the best of our knowledge, the AA is the first educational decision support system in toxicology that provides patient-specific treatment recommendations and drug dose calculations. The AA is publicly available at http://projects.met- hilab.org/antidote/

JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases

BACKGROUND: Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. RESULTS: We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. CONCLUSION: We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily

GMODWeb: a web framework for the generic model organism database

ABSTRACT: The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of Model Organism Database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from http://turnkey.sourceforge.net

Bioclipse: an open source workbench for chemo- and bioinformatics

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at

RegulonIT - A web based tool for regulon, gene, and co-expression data

One of the greatest challenges in the field of biology today is the determination of unknown gene function. A number of web applications are currently being developed which aim at providing gene related information, such as gene expression and co-expression data for individual genes. Integrating gene expression networks with external data sources may give researchers additional information about these genes. A regulon is a collection of highly co-expressed genes which can be identified by clustering a network of genes obtained from transcriptomic analysis. Regulon analysis offers a potential way to evaluate functions of genes in a given gene family or for developing hypothesis about the function of unknown genes. Hence, it is important that information about regulons, genes, and co-expression data be available to all biologists in a user friendly manner. Currently, information about regulons and its associated genes are not easily accessible, and in order to view regulon information, manual look up into flat files such as text files is required. In order to avoid this, we come up with an application which aim at providing regulon, gene, and co-expression data for three important species in a user-friendly manner using a web interface. RegulonIT is a web based tool that aims at providing information about regulons and other gene related information. Currently, the tool provides regulon, gene and co-expression information for three species (Arabidopsis thaliana, Saccharomyces cerevisiae and Homo sapiens) for very large transcriptomic datasets using a web interface. RegulonIT is a user friendly platform independent web tool and is available at http://metnetdb.org:9090/regulonit

Software Architectures and Efficient Data Sharing for Promoting Continuous Drug Re-purposing

The proposed layered and component based architectural style enables data sharing and accessibility of computational software components across problem domains in Biomedical Science. However, it also opens door to translational informatics, which bridges the gap between knowledge generated in biomedical science and clinical practices. Software applications generated from such an architectural style, are able to support continues drug repurposing. They exploit the semantic which exists, and is available across biomedical problem domains, between drug chemical compounds, their biological targets, particularly unintentional targets and drug therapeutic effects. The excerpt from the proposed software architectures has already been deployed in computationally light-weight software applications which based drug repurposing on reasoning upon collected available semantic. However a full scale implementation of the ideas of data sharing across the spectrum of biomedical research and disciplines, would require some changes in the way therapeutic drugs are discovered, tested and approved