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1.  Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers 
Briefings in Bioinformatics  2011;13(3):383-389.
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.
doi:10.1093/bib/bbr064
PMCID: PMC3357490  PMID: 22110242
Bioinformatics; training; end users; bioinformatics courses; learning bioinformatics
2.  Fast and efficient searching of biological data resources—using EB-eye 
Briefings in Bioinformatics  2010;11(4):375-384.
The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines. In this article we describe in detail how to exploit its powerful capabilities.
doi:10.1093/bib/bbp065
PMCID: PMC2905521  PMID: 20150321
text search; biological databases; integration; interoperability; web services; Apache Lucene

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