SUMMARY: We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps. AVAILABILITY AND IMPLEMENTATION: http://genomics.isi.edu/rnaseq CONTACT: [email protected]; [email protected]; [email protected]; [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. RESULTS: This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. CONCLUSIONS: The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators--experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community.

A technique for the estimation of the sampled impulse response of an HF radio link was developed several years ago and was shown by computer simulation tests to have a substantial potential advantage in performance over more conventional systems. A number of further developments have led to new channel estimators. In some of these, a Kalman filter is incorporated into the system in such a way that the filter operates on only a few variable quantities and is therefore considerably less complex than a conventional Kalman filter. Three different Kalman filters are studied, two of these being designed for a channel varying linearly (at a constant rate) with time, and the third being a conventional Kalman filter that is designed for a time-invariant or very slowly time-varying channel. All of these employ an exponential window and therefore operate with a fading memory. A description is given of the various estimators, the results of a series of computer simulation tests are presented, and the accuracies of the channel estimates given by the different systems are compared.>

A simple estimator designed for a 2400-b/s modem is a development of the conventional gradient estimator and uses a polynomial filter that gives a prediction of the channel response. A description is given of new estimators that are developments of the simple estimator but make no use of any knowledge of the number of different paths. The new estimators have performances intermediate between those of the simple and improved estimators, but are only a little more complex than the simple estimator. The new estimators are studied for a particular QPSK modem that operates at 4800 b/s over voiceband HF radio links. Results of computer simulation tests are presented, comparing the accuracies of the channel estimates given by different estimators, and hence suggesting the most suitable of these.>