SeqExpress is provided 'as is', and is free to use by all. This work is not affiliated with any academic institution, funding body or commercial organisation. If you are having trouble downloading the software contact john@seqexpress.com and a copy can be supplied to you on CD.

SeqExpress is developed by John Boyle, and is written in C#. SeqExpress is supplied as a Windows executable only, although development is continuing on a Linux version.

The Author



Eight years of senior and project management experience in companies specializing in the development of software for the life science industry. The majority of the work has involved the managing of projects developing and deploying enterprise informatics applications in a number of major pharmaceutical companies.

Background in commercial software development. Software development experience encompasses both enterprise and application software development (using both J2EE and .NET).

Background in research. Have lead a research team and published in a variety of life science and computer science journals (including Bioinformatics, Journal of Visual Languages and Computing, European Journal of Biochemistry, Nature and Journal of Healthcare Informatics). Hold a PhD in Computational Biology. MSc in Information Technology, and BSc in Biotechnology.

Employment Experience

Senior Research Scientist (2006-) and Director of the Informatics Core at the Institute for Systems Biology.

Founder and Director of Life Science Informatics Solutions (2000-2005). Wide range of business activities involving contract negotiation, project management and business development. Managed software projects involved in development of enterprise wide analysis software or specialised algorithm development for the life science industries. Customers include Aventis, Bayer, BMS and Incyte.

Senior Consultant at Incyte Pharmaceuticals (2000). Architecture and design of database products for the life science industry. Frequent invited speaker on software design at industrial symposia (Miami, Monte Carlo, Palo Alto and New York).

Senior Manager at Synomics (1997-2000). Role involved the development of long and short term project plans, resource allocation, designing training courses and line management for the software engineering department. Managed teams developing J2EE based products for a number of pharmaceutical clients, principally in the development of software for the integration and linking of heterogeneous data sources.

Computer Science Lecturer at Robert Gordon University (1995-1997). Led the medical informatics research group, principle investigator on grants from Wellcome Trust, Tenovus and EPSRC. Lectured to postgraduates on database theory and multimedia programming.

Postdoctoral Research Fellow at European Molecular Biology Laboratory EMBL. (1994-1995) Postdoctoral fellow conducting research on nucleotide sequence analysis.

Brief synopsis of experience and qualifications are given above

Release Details

1.2.2 available: includes graph based clustering, new ontology import and Seqexpress desktop only version. View change log.
1.2.1 available: includes cluster comparison tool and (EM based) mixture modelling. View change log
1.2 released: includes integration with Gene Expression Omnibus (GEO) and client/server versions. View change log
1.1.8 released: includes cluster visualization/analysis tool.View change log.
1.1.7 released: includes report generation tools. View change log.


SeqExpress and all associated documents are provided "as is" without any warranty of any kind, either expressed, implied, or statutory, including, but not limited to, any implied warranties of merchantability, fitness for a particular purpose and freedom from infringement, or that SeqExpress and all associated documents will be error free. The author makes no representations that the use of SeqExpress or any associated documents will not infringe any patent or proprietary rights of third parties. In no event will the author be liable for any damages, including but not limited to direct, indirect, special or consequential damages, arising out of, resulting from, or in any way connected with the use of SeqExpress or any associated documents.


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