Current Software Applications

Tablet - next generation sequence assembly visualization

Flapjack - high performance visualization of genotype data

TOPALi - statistical and evolutionary analysis of multiple sequence alignments

OPTIRas III - web-based decision support systems for starch potato farmers in the EU.

TetraploidMap - linkage map construction and QTL mapping in autotetraploid species

Biography

• 1st Class BSc (Hons) Computer Science.
• PhD (Software Visualization).
• Bioinformatics Programmer with BioSS at SCRI.
• Bioinformatics Systems and Webservices Developer in the Scottish Bioinformatics Research Network.

Areas of Expertise

• Object oriented programming (Java, C#, C++).
• Software visualization.
• Interface design and programming.
• Web technologies/application programming (frontend and middleware).
• J2EE (web services, JDBC, JavaBeans, JavaMail, Servlets, JSP, JSF).
• Parallel programming and high-performance computing technologies.
• Network programming.
• Windows/Linux systems administration.

Publications and Posters

• Chen, X., Hackett, C., Niks, R., Hedley, P., Booth, C., Druka, A., Marcel, T., Vels, A., Bayer M., Milne, I., Morris, J., Ramsay, L., Marshall, D., Cardle, L. and Waugh, R. 2010. An eQTL Analysis of Partial Resistance to Puccinia hordei in Barley, PLoS One 5(1).
• Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F. and Marshall, D. 2009. Tablet - Next Generation Sequence Assembly Visualization, Bioinformatics 26 (3), 401-402.
• Milne, I., Lindner, D., Bayer, M., Husmeier, D., McGuire, G., Marshall, D.F. and Wright, F. 2008. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops, Bioinformatics 25 (1), 126-127.
• Hackett, C.A., Milne, I., Bradshaw, J.E. and Luo, Z. 2007. TetraploidMap for Windows: Linkage Map Construction and QTL Mapping in Autotetraploid Species, Journal of Heredity 98(7), 727-729.
• Milne, I., Lindner, D. and Wright, F. 2007. TOPALi v2: Extended multiple sequence alignment analysis software using web services and cluster computing, ISMB 2007 (Vienna).
• Husmeier, D., Wright, F. and Milne, I. 2005. Detecting interspecific recombination with a pruned probabilistic divergence measure, Bioinformatics 21, 1797-1806.
• Milne, I. and Rowe, G. 2005. Interpreting computer code in a computer-based learning system for novice programmers, Software Practise and Experience 35, 1477-1493.
• Milne, I., Wright, F., Rowe, G., Marshall, D.F., Husmeier, D. and McGuire, G. 2004. TOPALi: Software for automatic identification of recombinant sequences within DNA multiple alignments, Bioinformatics 20, 1806-1807.
• Milne, I. and Wright, F. 2004. A simple algorithm to automatically detect recombinants in DNA/RNA sequence alignments, ISMB/ECCB 2004 (Glasgow).
• Husmeier, D., Wright, F. and Milne, I. 2004. Pruning the probabilistic divergence measure for improved detection of interspecific recombination, ISMB/ECCB 2004 (Glasgow).
• Milne, I. and Rowe, G. 2004. OGRE: Three-Dimensional Program Visualization for Novice Programmers, Education and Information Technologies 9(3), 219-237.
• Milne, I., Wright, F., Rowe, G., Marshall, D.F. and Husmeier, D. 2004. TOPALi - Software for detecting recombinants in DNA multiple alignments, Plant and Animals Genomes XII, (San Diego, CA).
• Milne, I. 2003. OGRE: A Software Visualization System for Novice Programmers Learning C++, PhD Thesis, University of Dundee.
• Milne, I. and Rowe, G. 2002. Difficulties in learning and teaching programming - views of students and tutors, Education and Information Technologies 7(1), 55-66.
• Milne, I., Cardle, L., Marshall, D. and Rowe, G. 2000. Java tools for plant genome mapping, Plant and Animal Genomes VIII (San Diego, CA).
• Parkes, S.M., Martin, I. and Milne, I. 1999. Lunar surface simulation-modelling for vision-guided lunar landers, DASI '99 (Lisbon), 369-374.

Posters

(View all posters)

Attachment	Size
Flapjack High performance graphical genotyping	4.15 MB
Bioinformatics Resources at the Scottish Crop Research Institute	1.58 MB
TOPALi v2	444.3 KB
Tablet Flapjack CurlyWhirly and Strudel : SCRI Visualization Tools To Support SNP Discovery	4.74 MB
Germinate 2: Storage Visualization and Analysis of High Volume Genotypic Phenotypic and Pedigree Data	992.31 KB