Alan J. Bleasby

CLUSTAL V: improved software for multiple sequence alignment.

The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided.

DNAPlotter: circular and linear interactive genome visualization

Summary: DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages. Availability: DNAPlotter is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/ Contact: artemis@sanger.ac.uk

The design of Jemboss: a graphical user interface to EMBOSS

DESIGN Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a users workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the users account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. RESULTS This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. AVAILABILITY The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/

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

The bioinformatics resource

The collaborative computing project in biosequence and structure analysis (CCP11) was established to foster bioinformatics in the broad community and the UK research community in particular. Its purpose is to facilitate the transfer of knowledge and expertise through conferences, workshops, a newsletter and the use of the World Wide Web.The CCP11 website is called ‘The Bioinformatics Resource’ (TBR) and contains a comprehensive set of information resources of use to the bioinformatician. TBR includes listings of conferences, workshops, WWW-based courses and graduate-level courses run in the UK. Links to online tutorials, lecture notes and various glossaries of biocomputing terms are given, and details for PhD programmes and other schemes to support research in bioinformatics are provided. Job lists, with separate resources for postdoctoral, lectureship and industrial vacancies, are also available. A directory of bioinformatics research groups contains contact details, links and descriptions of research interests. Similar resources are available for worldwide institutes and companies involved in research or service provision. Bioinformatics programs are organized by category of analysis and all the major programming libraries and software suites are listed, along with primary data sources and integrated databases. Finally, TBR provides a moderated archive of news articles, excerpts of which are distributed approximately every fortnight to subscribers of this service.TBR is available at http://www.hgmp.mrc.ac.uk/CCP11/, where details of forthcoming CCP11 meetings, conferences and newsletter subscription are available. TBR is maintained on a full-time basis and should therefore be comprehensive and up to date. However, the success of the project relies on the support and involvement of the broad bioinformatics community, and we welcome contributions to our resource and suggestions for additions and training courses. All correspondence should be sent to Jon Ison (jison@hgmp.mrc.ac.uk).