Jon C. Ison

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk

EMBOSS Developer's Guide: Bioinformatics Programming

The European Molecular Biology Open Software Suite (EMBOSS) is a high quality, well documented package of open source software tools for molecular biology. EMBOSS includes extensive and extensible C programming libraries, providing a powerful and robust toolkit for developing new bioinformatics tools from scratch. The EMBOSS Developers Manual is the official and definitive guide to developing software under EMBOSS. It includes comprehensive reference information and guidelines, including step-by-step instructions and real-world code examples: Learn how to write fully-featured tools guided by the people who developed EMBOSS Step-by-step guide to writing EMBOSS applications, illustrated with functional, deployed code ACD file development - learn how to customise existing tools without coding, or design and write entirely new application interfaces EMBOSS API programming guidelines - quickly master application development Wrapping and porting applications under EMBOSS - learn how to incorporate third-party tools

EMBOSS Administrator's Guide: Bioinformatics Software Management

The European Molecular Biology Open Software Suite (EMBOSS) is a high quality package of open source software tools for molecular biology. It includes over 200 applications integrated with a range of popular third party software packages under a consistent and powerful command line interface. The tools are available from a wide range of graphical interfaces, including easy to use web interfaces and powerful workflow software. The EMBOSS Administrators Guide is the official, definitive and comprehensive guide to EMBOSS installation and maintenance: Find all the information needed to configure, install and maintain EMBOSS, including recent additions for version 6.2 Step-by-step instructions with real-world examples - saves you time and helps you avoid the pitfalls on all the common platforms In-depth reference to database configuration - learn how to set up and use databases under EMBOSS Includes EMBOSS Frequently Asked Questions (FAQ) with answers - quickly find solutions to common problems