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Pegasys: software for executing and integrating analyses of biological sequences

Sohrab P Shah, David Y M He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace X Y Zheng, Tao Xu, B F Francis Ouellette
2004 BMC Bioinformatics  
We present Pegasys--a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.  ...  We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results.  ...  We also thank Miroslav Hatas and Graeme Campbell for systems and software installation and maintenance for the Pegasys server.  ... 
doi:10.1186/1471-2105-5-40 pmid:15096276 pmcid:PMC406494 fatcat:nlg5rwy27vdxvjyymfwmts54xu

Pegasys [chapter]

Sohrab Shah, David He, Jessica Sawkins, Jeffrey Druce, Gerald Quon, Drew Lett, Grace Zheng, Tao Xu, B Ouellette
2011 Data Structure and Software Engineering  
We present Pegasys -a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.  ...  We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results.  ...  We also thank Miroslav Hatas and Graeme Campbell for systems and software installation and maintenance for the Pegasys server.  ... 
doi:10.1201/b13126-15 fatcat:efiblfv7sjeavcigrqeb6r6cgy

Pegasys: software for executing and integrating analyses of biological sequences [article]

Sohrab P Shah, David Y He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace X Zheng, Tao Xu, BF F Ouellette
2015
Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.  ...  We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results.  ...  We also thank Miroslav Hatas and Graeme Campbell for systems and software installation and maintenance for the Pegasys server.  ... 
doi:10.14288/1.0228391 fatcat:ibabzhaxdfd27jfwtmpwyz6amy

High-throughput bioinformatics with the Cyrille2 pipeline system

Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot, Roeland CHJ van Ham
2008 BMC Bioinformatics  
These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases.  ...  , which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3) the Executor, which searches for scheduled  ...  Acknowledgements The development of Cyrille2 was supported by the Centre for BioSystems Genomics (CBSG).  ... 
doi:10.1186/1471-2105-9-96 pmid:18269742 pmcid:PMC2268656 fatcat:d6daijaz4rfw5gmprxm3ipacxu

Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences

Sung Lee, Taowei David Wang, Nada Hashmi, Michael P. Cummings
2007 Future generations computer systems  
of the connecting service.  ...  This process of constructing a workflow is complex.  ...  Acknowledgments We thank Adam Bazinet, Matthew Conte, Ryusuke Masuoka, and Zhexuan Song for their help.  ... 
doi:10.1016/j.future.2006.07.011 fatcat:hpqaj35qdnekzjy4b4wykphtte

Ruffus: a lightweight Python library for computational pipelines

Leo Goodstadt
2010 Computer applications in the biosciences : CABIOS  
Its lightweight and unobtrusive design recommends it for use even for the most trivial of analyses.  ...  However, most of the resources for constructing pipelines are heavyweight systems with graphical user interfaces. Ruffus is a library for the creation of computational pipelines.  ...  ACKNOWLEDGEMENTS Many thanks to Andreas Heger for advice on the design of Ruffus; Chris Nellåker and T.  ... 
doi:10.1093/bioinformatics/btq524 pmid:20847218 fatcat:t4yutbvnxvaihh6cie27qsxm3q

Atlas - a data warehouse for integrative bioinformatics

Sohrab P Shah, Yong Huang, Tao Xu, Macaire M S Yuen, John Ling, B F Francis Ouellette
2005 BMC Bioinformatics  
We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological  ...  The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development.  ...  Smoot, for his contributions and enhancements to his Templatized C++ Command Line Processor [51] . Special thanks to Joanne Fox and Graeme Campbell for their help in reviewing and editing this paper.  ... 
doi:10.1186/1471-2105-6-34 pmid:15723693 pmcid:PMC554782 fatcat:pfhx5xq65jhtlnl5ldl2kblvbq

Open source tools and toolkits for bioinformatics: significance, and where are we?

J. E. Stajich
2006 Briefings in Bioinformatics  
standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.  ...  This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years.  ...  The development of open and freely available infrastructure for bioinformatics analyses across the web is bringing the algorithms and tools closer to scientists and enabling new ways of integrating data  ... 
doi:10.1093/bib/bbl026 pmid:16899494 fatcat:x2dugkcc2vdv7j3b4ry6jkpiba

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

Mohamed Abouelhoda, Shadi Issa, Moustafa Ghanem
2012 BMC Bioinformatics  
Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It also allows the integration of existing Taverna and Galaxy workflows in a single environment  ...  Results In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns.  ...  We thank Sondos Seif from Nile University for helping us in software engineering tasks.  ... 
doi:10.1186/1471-2105-13-77 pmid:22559942 pmcid:PMC3583125 fatcat:arnykmuzbnehnnk73kmfroe36a

XML schemas for common bioinformatic data types and their application in workflow systems

Philipp N Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich
2006 BMC Bioinformatics  
These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless  ...  Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions  ...  Acknowledgements We thank Martin Szugat (Teaching and Research Unit Bioinformatics of the LMU Munich), initiator and maintainer of BioTypes, for his work and all other HOBIT members for helpful discussions  ... 
doi:10.1186/1471-2105-7-490 pmid:17087823 pmcid:PMC2001303 fatcat:gybyjuukqvdqrpii7xgrtbzvvi

A novel approach to sequence validating protein expression clones with automated decision making

Elena Taycher, Andreas Rolfs, Yanhui Hu, Dongmei Zuo, Stephanie E Mohr, Janice Williamson, Joshua LaBaer
2007 BMC Bioinformatics  
Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation.  ...  The software dramatically reduced the amount of time and labor required to evaluate clone sequences and decreased the number of missed sequence discrepancies, which commonly occur during manual evaluation  ...  used to test and develop this software.  ... 
doi:10.1186/1471-2105-8-198 pmid:17567908 pmcid:PMC1914086 fatcat:ocfblez5o5gjxj5bdv3heahvve

Towards an ontology-based recommender system for relevant bioinformatics workflows [article]

Ahmed Halioui, Petko Valtchev, Abdoulaye Banire Diallo
2016 bioRxiv   pre-print
With the large and diverse type of biological data, bioinformatic solutions are being more complex and computationally intensive.  ...  The large amount of heterogenous data and the lack of knowledge in using bioinformatics tools could mislead the users during their analyses.  ...  These workflows may not properly execute since a part of the analysis requires several specific software versions and dependencies.  ... 
doi:10.1101/082776 fatcat:e2dfw6fn4vbxdgzqrj6uouqdwu

Modal Analysis of Electric sail

Todd D. Lillian
2021 Acta Astronautica  
Gerald Karr and Brooke Graham of the University of Alabama, Huntsville for facilitating the no-Cost extension that allowed the completion of this report.  ...  Many thanks also go to Melina Zaharias, Dawn Phillips, and Robert Wingate for conducting the tests and providing critical PAF information.  ...  integrator, and how to run a single model executable.  ... 
doi:10.1016/j.actaastro.2021.05.003 fatcat:haxb75tn2bd7xp43hw6hv4mlya

Workflow management systems

2004 8th International Conference on Computer Supported Cooperative Work in Design CSCWD-04  
Pegasys is a software for executing and integrating analyses of biological sequences, developed by the University of British Columbia.Taverna Workbenchis an open source workflow system that enables scientists  ...  It also provides services for communicating with software outside the workflow. The host process hosts the WWF runtime engine and any workflow it executes.  ...  Starting work units in activities The WMS executes activities in a workflow based on the code in program listing 2. Notice the little amount of code for activity execution.  ... 
doi:10.1109/cacwd.2004.1349048 fatcat:q65kmdefofbzpehmqzqcylrtc4

Integrating Mutations Data of the TP53 Human Gene in the Bioinformatics Network Environment [chapter]

Domenico Marra, Paolo Romano
Bioinformatics Research and Development  
Automatically carry out analyses and/or searches involving more databases and software o Effectively perform analyses involving large data sets o Achieve a better and wider view of all available information  ...  integration of dbs Computerised workflows for the definition and execution of analysis processes We showed how: o Databases can effectively be uploaded/imported to/in powerful integration tools, like  ... 
doi:10.1007/978-3-540-71233-6_35 dblp:conf/bird/MarraR07 fatcat:x2aafprpobh2vcn3lxx57ubqf4
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