This hands-on workshop will introduce users of the R software environment to the techniques involved in generating reproducible, dynamic data analyses and reports. Using literate programming approaches, participants will learn to build automated reusable reports in R.
ArachnoServer, the world’s first manually curated resource for protein spider toxins
BRIEF DESCRIPTION OF THE PROJECT
QFAB has worked in collaboration with Professor Glenn King to create Arachnoserver, the online data repository for spider toxin research.
BACKGROUND AND AIM OF THE PROJECT
High impact research requires the wide and clear distribution of results. This can be hampered by bioinformatics web applications, which often suffer from a lack of maintenance, leading to a decline in data currency and subsequent accuracy. These databases also require that their structure, data, and utility be appropriately modified over time with new discoveries and changes in information priority.
The aim of this project was to develop a robust, extensible and maintainable software architecture that would make ArachnoServer the world’s gold standard online data repository for spider toxin research for years to come.
WHAT WERE THE OUTCOMES
A web application was developed to enable two key functions:
1) Allowing secure manual curation of the toxin records by the expert team led by Professor Glenn King using available literature and patent information.
2) Providing easy and powerful advanced search, browse and view capabilities. ArachnoServer enables neuroscientists, pharmacologists, and toxinologists to explore high quality toxin information and rapidly answer their research questions. Each toxin record is displayed in a single page and, where available, a toxin’s structure can be dynamically displayed.
The solution chosen for ArachnoServer was to develop a Java Spring Model View Controller (MVC) application that uses a Hibernate Object Relational Mapping (ORM) layer to a MySQL database. Using this architecture, the application and data model can be easily extended or modified, as changes to the data model do not require SQL changes.
Two powerful bioinformatics tools have been made available through the web interface. First, similarity searches can be made using BLAST. Secondly, signal peptide and propeptide regions in spider-toxin precursors can be predicted using SpiderP, a new tool developed for ArachnoServer.
ArachnoServer has become an international resource that is cross-referenced by the European Bioinformatics Institute’s UniProt knowledge base (UniProtKB).
Volker Herzig, David L. A. Wood, Felicity Newell, Pierre-Alain Chaumeil, Quentin Kaas, Greta J. Binford; Graham M. Nicholson; Dominique Gorse; Glenn F. King (2011) ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. Nucleic Acids Research 39, D653-D657
David LA Wood, Tomas Miljenović, Shuzhi Cai, Robert J Raven, Quentin Kaas, Pierre Escoubas, Volker Herzig, David Wilson and Glenn F King (2009) BMC Genomics 10:375
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