A Simple GUI-based Sequencing Format Conversion Tool for the Three NGS Platforms

To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In this respect, a format conversion tool, as well as quality conversion tool would be the minimum requirements to integrate reads from different platforms. We have developed the Pyrus NGS Sequencing Format Converter, a simple software toolkit which allows to convert three kinds of Next Generation Sequencing reads, into commonly used fasta or fastq formats. The converter modules are all implemented, uniformly, in Java GUI modules that can be integrated in software applications for displaying the data content in the same format.

Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.

J2.5dPathway: A 2.5D Visualization Tool to Display Selected Nodes in Biological Pathways, in Parallel Planes

The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in twoand- a-half dimensions (2.5D) as an alternative to three dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.

J2dpathway: A Global Metabolic Pathway Viewer with Node-Abstracting Features

The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to this thorny issue, we propose J2dpathway, a metabolic pathway atlas viewer that has node-abstracting features.

Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.

Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.