Tag Archive: projects

PorToL – PHRED Documentation

Program: phred Version: 0.020425.c Copyright (C) 1993-2002 by Phil Green and Brent Ewing. All rights reserved. This software is a beta-test version of the phred package. It should not be redistributed or used for any commercial purpose, including commercially funded sequencing, without written permission from the author and the University of Washington. This software is …

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PorToL – PHRAP Documentation

/***************************************************************************** # Copyright (C) 1994-1999 by Phil Green. # All rights reserved. # # This software is part of a beta-test version of the swat/cross_match/phrap # package. It should not be redistributed or # used for any commercial purpose, including commercially funded # sequencing, without written permission from the author and the # University of …

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PorToL

BRIEF PROJECT DESCRIPTION Features The PorToL – Porifera Tree of Life project is a interdisciplinary, multi-organizational effort to define the family tree for the phylum Porifera (commonly known as sponges), which contains 8,122 valid species with an estimated 4,000 awaiting discovery and/or description. The CCL lab is participating in PorToL by building user interfaces and processing pipelines …

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Glossary of PorToL Processing Pipeline Terms

base call A process by which a program analyzes sequencer data to determine which base (A,C,T or G) is most likely the one which is present at a particular location in a sequence. The sequencer is an analog device which relies on chromatography, which is subject to interference from background noise, adjacent bases, and other …

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PorToL Lifecycle

Lifecycle of a PorToL Project Specimen The “Wet” Phase Collection The first step in sequencing a sponge specimen is to collect the specimen. Specimens are collected around the world and brought back to DNA sequencing labs (e.g. Smithsonian Institute). Sample Preparation Some portion of the sample is chosen for sequencing. This could be a particular gene, or …

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Grid-Flow

Grid-Flow is a scientific workflow infrastructure that assists researchers in specifying scientific experiments using a Petri-net-based interface. The contributions of Grid-Flow are as follows: (1) a new, lightweight, programmable Grid workflow language, Grid-Flow Description Language (GFDL), to describe the workflow process in a Grid environment; (2) a Petri-net-based user interface, based on the Generic Modeling …

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GAUGE

The Grid Automation and Generative Environment (GAUGE) uses concepts of domain-specific modeling (DSM) to build a high-level abstract layer to enable users to create Grid applications without knowledge of specific programming languages or being bound to specific Grid platforms. The goal of GAUGE is to automate the generation of Grid applications to allow inexperienced users …

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Adaptive Parallel Genetic Algorithms

Genetic algorithms are a widely used technique for search and optimization problems and belong to the group of evolutionary algorithms. One of its recent applications has been in image clustering. Serial implementations of the algorithm, customized for image clustering, suffer from slow execution. Also, a genetic algorithm, if run for small number of generations, gets …

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GridAtlas

e.g., Globus Toolkit, GridWay) enables simultaneous access and invocation of application instances across grid resources, complexities involved with the installation properties on selected resources should not be left for the end-user to deal with and manage. GridAtlas is a tool that hides and automates this process by keeping track of resource and application instance details. …

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Application Performance Database (AppDB)

Performance of any one application is more often than not very intimately related to the hardware and software characteristics of a resource the application is being executed on, as well as the use of application parameters during job instantiation. As such, execution of applications and associated user jobs in heterogeneous environments exhibit heterogeneous performance. Users …

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Application Specification Language (ASL)

Language motivation and goals Application deployment process in grid environment is a non-trivial task and the user has to first determine what resources are available and then decide which is the most suitable resource for that particular application. Typically, HPC applications are developed using a specific programming language and parallel programming paradigm (e.g., compiler directive-based, …

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BLAST performance analysis

Performance Characterization of BLAST on the Grid BLAST (Basic Local Alignment Search Tool) is a commonly used bioinformatics application for performing query searches and analysis of biological data. As the amount of search data increases so do job search times. As means of reducing job turnaround times, scientists are resorting to new technologies such as grid …

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DynamicBLAST

Basic Local Alignment Search Tool (BLAST) is a heavily used bioinformatics application that has gotten significant attention from the high performance computing community. In the context of the DynamicBLAST project, BLAST execution was taken a step further by enabling it to execute on grid resources. Adapting BLAST to execute on the grid brings up concerns regarding …

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UABgrid

UABgrid is a distributed campus-wide computing environment that connects HPC resources across campus and offers access to regional resources via SURAgrid, TeraGrid and beyond. UABgrid leverages Globus technologies for system inter-connectivity and Shibboleth for federated identity management. UABgrid enables the construction of automated research workflows by providing consistent user identities and system interfaces across all …

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Designing Parallel Programs using AOP

The most popular approach to developing parallel programs for distributed memory architectures requires adding explicit message passing calls into existing sequential programs for data distribution, coordination, and communication. Aspect oriented programming provides an option to separate programming concerns and weave code into applications instead of directly modifying the original program. This effort aims to use …

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HI-Pal

Hi-PaL A Domain-Specific Language (DSL) for specifying parallel computations has been developed in this research and is called High-Level Parallelization Language (Hi-PaL). Because the specifications for parallel computations can vary from application to application, different application-domains (e.g.,image processing and stencil-based computations) were evaluated to build the key abstractions in the form of a DSL. General Structure The general …

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Domain-Specific Language for Checkpointing

Language motivation and goals DSLs are specialized languages that are written for a particular application-domain. DSLs are more expressive in a given domain than General-Purpose Languages (GPLs) but unlike the GPLs, they have limited features and applicability. Because the DSLs are more specialized and expressive than other GPLs, they are easy to learn and use. …

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FraSPA

In this research, a Framework for Synthesizing Parallel Applications (FraSPA) in a user-guided manner is being developed. The FraSPA would facilitate the synthesis of parallel applications from existing sequential applications and middleware components for multiple-platforms and diverse domains. The framework design is based upon design patterns and generative programming techniques. The main goal of this …

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