A Service Giving a Case-Based Instruction of Bioinformatics Workflow Running on High Performance Computer for Engineering Design and Education

The role of bioinformatics workflows to support the Life Sciences has become fundamental for the comprehensive analysis of large amount of biological data concerning different bioinformatics tools and databases. In this paper, we design and develop a web service giving a case-based instruction of bioinformatics workflow running on high performance computer for engineers and educators. The service is designed for interactive usage and the possibility to learn from the case in a straightforward way. It will help to integrate bioinformatics software tools to address questions in life science by providing the designer, student, or educator specific questions in bioinformatics workflow design and hands-on experience. It is publicly accessible at http://bioinfo.hust.edu.cn:8080/bio-estexplore/.

[1]  David M. Grant,et al.  ESTminer: a suite of programs for gene and allele identification , 2005, Bioinform..

[2]  Ken Barker,et al.  Helping Biologists Effectively Build Workflows, without Programming , 2010, DILS.

[3]  P. Pevzner,et al.  Computing Has Changed Biology—Biology Education Must Catch Up , 2009, Science.

[4]  Marion M. Zatz.  Bioinformatics Training in the USA , 2002, Briefings Bioinform..

[5]  Shawn Bowers,et al.  An approach for pipelining nested collections in scientific workflows , 2005, SGMD.

[6]  Allen R. Hanson,et al.  Analytic webs support the synthesis of ecological data sets. , 2006, Ecology.

[7]  Tin Wee Tan,et al.  Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges , 2009, PLoS Comput. Biol..

[8]  Shawn Bowers,et al.  The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere , 2006 .

[9]  Mark A. Ragan,et al.  Genome-Scale Computational Biology and Bioinformatics in Australia , 2008, PLoS Comput. Biol..

[10]  Dong-Wook Kim,et al.  PESTAS: a web server for EST analysis and sequence mining , 2009, Bioinform..

[11]  Ina Koch,et al.  A review of bioinformatics education in Germany , 2008, Briefings Bioinform..

[12]  Robin B. Gasser,et al.  A hitchhiker's guide to expressed sequence tag (EST) analysis , 2006, Briefings Bioinform..

[13]  Bertram Ludäscher,et al.  Kepler: an extensible system for design and execution of scientific workflows , 2004 .

[14]  William K. Michener,et al.  The EcoGrid and the Kepler Workflow System: a New Platform for Conducting Ecological Analyses , 2005 .

[15]  Yolanda Gil,et al.  Pegasus: Mapping Scientific Workflows onto the Grid , 2004, European Across Grids Conference.

[16]  F M Hoffman,et al.  The do it yourself supercomputer. , 2001, Scientific American.

[17]  Ting Wang,et al.  The UCSC Genome Browser Database: update 2009 , 2008, Nucleic Acids Res..

[18]  Sonia Cattley.  A review of bioinformatics degrees in Australia , 2004, Briefings Bioinform..

[19]  Damian Counsell,et al.  A Review of Bioinformatics Education in the UK , 2003, Briefings Bioinform..

[20]  Shoba Ranganathan,et al.  ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform , 2007, Nucleic Acids Res..

[21]  Philip E. Bourne,et al.  A case study of high-throughput biological data processing on parallel platforms , 2004, Bioinform..

[22]  Masanori Suzuki,et al.  EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments , 2006, Nucleic Acids Res..

[23]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[24]  John Quackenbush,et al.  TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets , 2003, Bioinform..

[25]  Jonathan W. Arthur,et al.  BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training , 2007, Briefings Bioinform..

[26]  Byungwook Lee,et al.  ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences , 2007, Nucleic Acids Res..

[27]  Peter Ernst,et al.  ESTAnnotator: a tool for high throughput EST annotation , 2003, Nucleic Acids Res..

[28]  Nunzio D'Agostino,et al.  ParPEST: a pipeline for EST data analysis based on parallel computing , 2005, BMC Bioinformatics.

[29]  Alexander Sczyrba,et al.  Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server , 2008, Briefings Bioinform..

[30]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[31]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.