Accelerating in silico research with workflows: A lesson in Simplicity

Bioinformatics is the application of computer science and related disciplines to the field of molecular biology. While there are currently several web based and desktop tools available for biologists to perform routine bioinformatics tasks, these tools often require users to manually and repeatedly co-ordinate multiple applications before reaching a result. In an effort to reduce time and error, workflow tools have been developed to automate these tasks. However, many of these tools require expert knowledge of the techniques and supporting databases which more often than not lies outside the scope of most biologists. Herein, we describe the development of sequence information management platform (Simplicity), a workflow-based bioinformatics management tool, which allows non-bioinformaticians to rapidly annotate large amounts of DNA and protein sequence data.

[1]  Joel Dudley,et al.  MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences , 2008, Briefings Bioinform..

[2]  T. Manning,et al.  Naturally selecting solutions , 2013, Bioengineered.

[3]  Paul Walsh,et al.  An overview of in silico protein function prediction , 2010, Archives of Microbiology.

[4]  Giovanni Toffetti Carughi,et al.  Engineering rich internet applications with a model-driven approach , 2010, TWEB.

[5]  Alan M. Davis,et al.  Operational prototyping: a new development approach , 1992, IEEE Software.

[6]  Andreas Holzinger,et al.  Usability engineering methods for software developers , 2005, CACM.

[7]  Abhishek Tiwari,et al.  Workflow based framework for life science informatics , 2007, Comput. Biol. Chem..

[8]  Jano I. van Hemert,et al.  Scientific Workflow: A Survey and Research Directions , 2007, PPAM.

[9]  Alan Bridge,et al.  New and continuing developments at PROSITE , 2012, Nucleic Acids Res..

[10]  Roy D. Sleator.  A Beginner’s Guide to Phylogenetics , 2013, Microbial Ecology.

[11]  Roy D Sleator,et al.  Proteins: form and function. , 2012, Bioengineered bugs.

[12]  Wolfgang Blochinger,et al.  E-Biology Workflows with Calvin , 2009, WISE.

[13]  Aidan Coffey,et al.  In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil. , 2010, Gene.

[14]  H. Kitano,et al.  Software for systems biology: from tools to integrated platforms , 2011, Nature Reviews Genetics.

[15]  Rolf Daniel,et al.  Metagenomics , 2010, Methods in Molecular Biology.

[16]  Paolo Fontana,et al.  Bioinformatic approaches for functional annotation and pathway inference in metagenomics data , 2012, Briefings Bioinform..

[17]  Kei-Hoi Cheung,et al.  Bringing Web 2.0 to bioinformatics , 2008, Briefings Bioinform..

[18]  Ann E. Stapleton,et al.  Codifying bioinformatics processes without programming , 2004 .

[19]  Carole A. Goble,et al.  Taverna: a tool for building and running workflows of services , 2006, Nucleic Acids Res..

[20]  Jack A. M. Leunissen,et al.  Evolution of web services in bioinformatics , 2005, Briefings Bioinform..

[21]  Roy D. Sleator,et al.  An overview of the current status of eukaryote gene prediction strategies. , 2010, Gene.

[22]  Carole A. Goble,et al.  Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt , 2004, SEMWEB.

[23]  Roy D Sleator,et al.  The Evolution of Elearning Background, Blends and Blackboard … , 2010, Science progress.

[24]  Mark Johnson,et al.  NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..