The Experts below are selected from a list of 30 Experts worldwide ranked by ideXlab platform
Kamran Shalchian-tabrizi - One of the best experts on this subject based on the ideXlab platform.
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BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Background Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Results Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. Conclusion The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
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BLASTGrabber: A bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
Ralf S. Neumann - One of the best experts on this subject based on the ideXlab platform.
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BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Background Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Results Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. Conclusion The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
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BLASTGrabber: A bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
Thomas Hendricus A. Haverkamp - One of the best experts on this subject based on the ideXlab platform.
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BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Background Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Results Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. Conclusion The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
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BLASTGrabber: A bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
Surendra Kumar - One of the best experts on this subject based on the ideXlab platform.
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BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Background Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Results Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. Conclusion The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
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BLASTGrabber: A bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
BMC Bioinformatics, 2014Co-Authors: Ralf S. Neumann, Thomas Hendricus A. Haverkamp, Surendra Kumar, Kamran Shalchian-tabriziAbstract:Advances in sequencing efficiency have vastly increased the sizes of biological sequence databases, including many thousands of genome-sequenced species. The BLAST algorithm remains the main search engine for retrieving sequence information, and must consequently handle data on an unprecedented scale. This has been possible due to high-performance computers and parallel processing. However, the raw BLAST output from contemporary searches involving thousands of queries becomes ill-suited for direct human processing. Few programs attempt to directly visualize and interpret BLAST output; those that do often provide a mere basic structuring of BLAST data. Here we present a bioinformatics application named BLASTGrabber suitable for high-throughput sequencing analysis. BLASTGrabber, being implemented as a Java application, is OS-independent and includes a User friendly graphical User Interface. Text or XML-formatted BLAST output files can be directly imported, displayed and categorized based on BLAST statistics. Query names and FASTA headers can be analysed by Text-mining. In addition to visualizing sequence alignments, BLAST data can be ordered as an interactive taxonomy tree. All modes of analysis support selection, export and storage of data. A Java Interface-based plugin structure facilitates the addition of customized third party functionality. The BLASTGrabber application introduces new ways of visualizing and analysing massive BLAST output data by integrating taxonomy identification, Text mining capabilities and generic multi-dimensional rendering of BLAST hits. The program aims at a non-expert audience in terms of computer skills; the combination of new functionalities makes the program flexible and useful for a broad range of operations.
Catherine Pawlick - One of the best experts on this subject based on the ideXlab platform.
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SIGDOC - Evaluating guidelines for writing User Interface Text
Proceedings of the 25th annual ACM international conference on Design of communication - SIGDOC '07, 2007Co-Authors: P. J. Schemenaur, Catherine PawlickAbstract:This paper explains the process of developing User Interface Text style guidelines and evaluates the applicability and usefulness of having guidelines for User Interface (UI) developers. The paper also discusses the effectiveness of the book model for documentation and how writers and editors can positively impact the User Interface process.
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Evaluating guidelines for writing User Interface Text
2007Co-Authors: P. J. Schemenaur, Catherine PawlickAbstract:This paper explains the process of developing User Interface Text style guidelines and evaluates the applicability and usefulness of having guidelines for User Interface (UI) developers. The paper also discusses the effectiveness of the book model for documentation and how writers and editors can positively impact the User Interface process.
