High-throughput bioinformatics research is complex and requires the combination of multiple experimental approaches each producing large amounts of diverse data. The analysis and evaluation of these data are equally complex requiring specific integrations of various software components into complex workflows. The challenge is to provide less technically involved bioinformaticians with simple interfaces to specify the workflow of commands they need while at the same time scale up to hundreds of jobs to get the terabytes of genetic data processed by recent methods. Here, we present a computational framework for bioinformatics which enables data and workflow management in a distributed computational environment. Firstly, we propose a new data model to specify workflow execution logic on available network resources and components. Our model extends existing generic workflow and bioinformatics models to describe workflows compactly and unambiguously. Secondly, we present the implementation of our computational framework, which is constructed as a computational cloud for bioinformatics using open source off-the-shelf components. Finally, we demonstrate applications of the framework on complex real-world bioinformatics tasks.

UNLABELLED: Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts. Here, we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours. This service provides the warping function, the sample chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of overlapping peak area rearranged with hierarchical clustering, allowing the quality control of the time alignment procedure. Taverna workflow and command line tool are provided for remote processing of local user data. AVAILABILITY: online data processing service is available at http://www.nbpp.nl/warp2d.html. Taverna workflow is available at myExperiment with title '2D Time Alignment-Webservice and Workflow' at http://www.myexperiment.org/workflows/1283.html. Command line tool is available at http://www.nbpp.nl/Warp2D_commandline.zip. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We present a new method for the combined visualization of software architecture diagrams, such as UML class diagrams or component diagrams, and software metrics defined on groups of diagram elements. Our method extends an existing rendering technique for the so-called areas of interest in system architecture diagrams to visualize several metrics, possibly having missing values, defined on overlapping areas of interest. For this, we use a solution that combines texturing, blending, and smooth scattered-data point interpolation. Our new method simplifies the task of visually correlating the distribution and outlier values of a multivariate metric dataset with a system's structure. We demonstrate the application of our method on component and class diagrams extracted from real-world systems.

Software tools supporting the design and analysis of complex software-intensive systems are highly desirable, since they enable earlier decision making about system realization. This paper presents a tooling environment that supports the design and performance analysis of time-critical component-based software architectures deployed on complex multiprocessor platforms. The tooling environment contains a set of integrated tools for (a) component storage and retrieval, (b) graphics-based design of software and hardware architectures, (c) performance analysis of the defined architectures and, (d) automated code generation. The cornerstone of the toolkit is a performance analyzer that provides efficient simulation of the designed architectures and enables design-time prediction of key performance properties like response time, data throughout, and usage of hardware resources (processor, memory and bus). For every architecture alternative, the performance predictions can be quickly obtained, thereby enabling a fast and yet broad design space exploration. We demonstrate the efficiency and robustness of this toolkit on a Car Radio Navigation benchmark case.