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Iain Milne

Information and Computational Sciences
Information and Computational Sciences
Research Software Engineer
iain.milne@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

Most research would be impossible without software, and my research is about providing intuitive, professional software applications – often with a strong visualization component – that underpin many sequencing, genotyping and analysis projects both within the institute and further afield. To this end, I lead the development of a range of extensively used programs with a worldwide install base of over 150,000 users. These programs use a combination of traditional desktop interfaces along with back-end components that rely heavily on our high-performance scientific computing cluster and infrastructure.

For more information on these applications, please visit the website for the Information and Computational Sciences group.

I also manage and maintain the Institute's Linux-based scientific-computing resources, including the HPC cluster and associated storage and network services. This resource provides almost 500 CPU cores of computing power to researchers at the James Hutton Institute, along with access to over 2 TB of memory and just shy of half a petabyte of storage.

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.

Bibliography

  • Guo, W.; Tzioutziou, N.A.; Stephen, G.; Milne, I.; Calixto, C.P.G.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2021) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists., RNA Biology, 18, 1574-1587.
  • Raubach, S.; Kilian, B.; Dreher, K.; Amri, A.; Bassi, F.M.; Boukar, O.; Cook, D.; Cruickshank, A.; Fatokun, C.; El Haddad, N.; Humphries, A.; Jordan, D.; Kehel, Z.; Kumar, S.; Labarosa, S.J.; Nguyen, L.H.; Mace, E.; McCouch, S.; McNally, K.; Marshall, D.F.; Mikwa, E.O.; Milne, I.; Odeny, D.A.; Plazas, M.; Prohens, J.; Rieseberg, L.H.; Schafleitner, R.; Sharma, S.; Stephen, G.; Quang Tin, H.; Togola, A.; Warschefsky, E.; Werner, P.; Shaw, P. (2021) From bits to bites: advancement of the Germinate platform to support prebreeding informatics for crop wild relatives., Crop Science, 61, 1538-1566.
  • Sansaloni, C.; Franco, J.; Santos, B.; Percival-Alwyn, L.; Singh, S.; Petroli, C.; Campos, J.; Dreher, K.; Payne, T.; Marshall, D.; Kilian, B.; Milne, I.; Raubach, S.; Shaw, P.; Stephen, G.; Carling, J.; Saint Pierre, C.; Burgueño, J.; Crosa, J.; Li, H.; Guzman, C.; Kehel, Z.; Amri, A.; Kilian, A.; Wenzl, P.; Uauy, C.; Banziger, M.; Caccamo, M.; Pixley, K. (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints., Nature Communications, 11, Article No. 4572.
  • Selby, P.; Abbeloos, R.; Backlund, J.E.; Basterrechea Salido, M.; Bauchet, G.; Benites-Alfaro, O.; Birkett, C.; Calaminos, V.C.; Carceller, P.; Cornut, G.; Costa, B.V.; Edwards, J.D.; Finkers, R.; Gao, S.Y.; Ghaffar, M.; Glaser, P.; Guignon, V.; Hok, P.; Kilian, A.; König, P; Lagare, J.E.B.; Lange, M.; Laporte, M.-A.; Larmande, P.; LeBauer, D.; Lyon, D.; Marshall, D.; Matthews, D.; Milne, I.; Mistry, N.; Morales, N.; Mueller, L.; Neveu, P.; Papoutsoglou, E.; Pearce, B.; Perez-Masias, I.; Pommier, C.; Ramirez-Gonzalez, R.H.; Rathore, A.; Raquel, A.M.; Raubach, S; Rife, T.; Robbins, K.; Rouard, R.; Sarma, C.; Scholz, U.; Selby, P.; Sempere, G.; Shaw, P.; Simon, R.; Soldevilla, N.; Stephen, G.; Sun, Q.; Tovar, C.; Uszynski, G.; Verouden, M. (2019) BrAPI - an Application Programming Interface for plant breeding applications., Bioinformatics, 35, 4147-4155.
  • Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B.A.; Rowe, J.; Tomkins-Tinch, C.H.; Valieris, R.; Caprez, A.; Batut, B.; Haudgaard, M.; Cokelaer, T.; Beauchamp, K.A.; Pedersen, B.S.; Hoogstrate, Y.; Bretaudeau, A.; Ryan, D.; Le Corguillé, G.; Yusuf, D.; Luna-Valero, S.; Kirchner, R.; Brinda, K.; Wollmann, T.; Raden, M.; Pantano, L.; Soranzo, N.; van Heeringen, S.J.; Charlop-Powers, Z.; Unneberg, P.; de Smet, M.; Martin, M.; Von Kuster, G.; Antao, T.; Miladi, M.; Brueffer, C.; Thornton, K.; van den Beek, M.; Maticzka, D.; Blank, C.; Will, S.; Gravouil, K.; Wolff, J.; Holtgrewe, M.; Fallmann, J.; Piro, V.C.; Shlyakhter, I.; Yousif, A.; Mabon, P.; Zhang, X-O.; Cabral, J.; Shen, W.; Thomas, C.; Brown, J.; Enns, E.; de Hollander, M.; Boekel, J.; Kelleher, J.; Bouvier, D.; Turaga, N.; de Ruiter, J.R.; Choudhary, S.; Harding, N.; Kratz, A.; Fang, Z.; Kleinkauf, R.; Timm, H.; Khan, A.; Cock, P.J.A.; Seiler, E.; Nguyen, H.; Brislawn, C.; Stovner, E.B.; Johnson, J.E.; Hägglund, E.; Ewels, P.; Chambers, M.; Pruesse, E.; Guimera, R.V.; Ye, S.; Dunn, W.A.; Parsons, L.; Cornwell, M.; Reynolds, A.; Bargull, M.; Grassi, E.; Koppstein, D.; Patro, R.; Wohlers, I.; Stoler, N.; Blankenberg, D.; He, G.; Freeberg, M.; Farouini, R.; Junge, A.; Bogema, D.R.; Singh, S.; Cumbo, F.; Larson, D.E.; Wang, L.; Workentine, M.L.; Devisetty, U.K.; Laurent, S.; Garnier, X.; Agren, R.; Roger, P.; Eppley, J.M.; Li, W.; Rausch, R.; Chande, A.T.; Taylor, J.; Stöcker, B.K.; Milne, I.; Wright, P.R.; Taranto, A.P.; Chicco, D.; Abdennur, N.; Sennblad, B.; Baaijens, J.A.; Gopez, M.; Enache, O.M.; Pinello, L.; Srivastava, A.; de Bruijn, I.; Kensche, P.R.; Blin, K.; Pirola, Y.; Preussner, J.; Knudsen, M.; Bendall, M.L.; rai, V.; Gonnella, G.; Stahl, C.; Miles, A.; Waters, N.R.; Hiltemann, S.; Boursin, Y.; Perez-Riverol, Y.; Schmeier, S.; Clarke, E.; Arvai, K.; Jung, M.; Stephen, G.; Domenico, T.; seiler, J.; Rasche, E.; Kornobis, E.; Beisser, D.; Rahmann, S.; Mikheyev, A.S.; Tran, C.; Capellades, J.; Moskalenko, O.; Schröder, C.; Dirmeier, S.; Webster, T.H.; Salatino, A.E.; Urgese, G.; Köster, J. (2018) Bioconda: A sustainable and comprehensive software distribution for the life sciences., Nature Methods, 15, 475-476.
  • Hackett, C.A.; Boskamp, B.; Vogogias, A.; Preedy, K.F.; Milne, I. (2017) TetraploidSNPMap: Software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data., Journal of Heredity, 108, 438-442.
  • Shaw, P.D.; Raubach, S.; Hearne, S.J.; Dreher, K.; Bryan, G.; McKenzie, G.; Milne, I.; Stephen, G.; Marshall, D.F. (2017) Germinate 3: Development of a common platform to support the distribution of experimental data on crop wild relatives., Crop Science, 57, 1259-1273.
  • Russell, J.; Mascher, M.; Dawson, I.K.; Kyriakidis, S.; Calixto, C.; Freund, F.; Bayer, M.; Milne, I.; Marshall-Griffiths, T.; Heinen, S.; Hofstad, A.; Sharma, R.; Himmelbach, A.; Knauft, M.; van Zonneveld, M.; Brown, J.W.S.; Schmid, K.; Kilian, B.; Muehlbauer, G.J.; Stein, N.; Waugh R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation., Nature Genetics, 48, 1024-1030.
  • Milne, I.; Bayer, M.; Stephen, G.; Cardle, L.; Marshall, D. (2016) Tablet: visualizing next-generation sequence assemblies and mappings., In: Edwards, D. (ed.). Plant Bioinformatics: Methods and Protocols, Methods in Molecular Biology. Springer Science+Business Media, New York, 14, pp253-268.
  • Baker, K.; Dhillon, T.; Colas, I.; Cook, N.; Milne, I.; Milne, L.; Bayer, M.; Flavell, A.J. (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance., Plant Journal, 84, 111-124.
  • Ribeiro, A.; Golicz, A.; Hackett, C.A.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J.; Bayer, M. (2015) An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryotic genome., BMC Bioinformatics, 16, Article No.382.
  • Shaw, P.D.; Graham, M.; Kennedy, J.; Milne, I.; Marshall, D.F. (2014) Helium: visualization of large scale plant pedigrees., BMC Bioinformatics, 15, Article No. 259.
  • Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
  • Russell, J.R.; Hedley, P.E.; Cardle, L.; Dancey, S.; Morris, J.; Booth, A.; Odee, D.; Mwaura, L.; Omondi, W.; Angaine, P.; Machua, J.; Muchugi, A.; Milne, I.; Kindt, R.; Jamnadass, R.; Dawson, I.K. (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species., PLoS ONE, 9, Article No. e102502.
  • Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F. (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
  • Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Thomas, W.T.B.; Ramsay, L.; Comadran, J.; Stephen G.; Bayer, M.; Graham, M.; Kennedy J.; Oakey, H.; Marshall, D.F. (2012) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XX, San Diego, California, 14-18 January 2012.
  • Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F. (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
  • Bayer, M.; Liu, H.; Marshall, D.F.; Russell, J.; Hedley, P.E.; Milne, I.; Stephen G.; Waugh, R.; (2011) A GBS data processing pipeline for barley., StatSeq Meeting on Genotyping by Sequencing. Wageningen, Netherlands, 3-4 November 2011 (Talk).
  • Milne, I.; Shaw, P.J.; Stephen, G.; Bayer, M.M.; Cardle, L.; Thomas, W.T.B.; Flavell, A.J.; Marshall, D.F. (2010) Flapjack - graphical genotype visualization., Bioinformatics, 26, 3133-3134.
  • Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Booth, C.; Druka, A.; Marcel, T.C.; Vels, A.; Bayer, M.M.; Milne, I.; Morris, J.; Ramsay, L.; Marshall, D.F.; Cardle, L.; Waugh, R. (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley., PLoS ONE, 5, 1-15.
  • Milne, I.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F. (2010) Tablet - next generation sequence assembly visualization., Bioinformatics, 26, 401-402.
  • Moragues, M.; Comadran, J.; Waugh, R.; Milne, I.; Flavell, A.J.; Russell, J.R. (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data., Theoretical and Applied Genetics, 120, 1525-1534.
  • Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F. (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.
  • Milne, I.; Lindner, D.; Bayer, M.M.; Husmeier, D.; McGuire, G.; Marshall, D.F.; Wright, F. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops., Bioinformatics, 25, 126-127.
  • Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
  • Russell, J.R.; Moragues, M.; Dawson, I.K.; Waugh, R.; Marshall, D.F.; Milne, I.; Grando, S.; Tondelli, A.; Cattivelli, L.; Hubner, S.; Fridman, E.; Flavell, A.J. (2009) Genetic diversity analysis of wild and landrace barleys using the BODA1 Illumina genotyping platform., 19th International Triticeae Mapping Initiative - 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August - 4 September 2009 (Talk).
  • Marshall, D.F.; Close, T.; Ramsay, L.; Druka, A.; Thomas, W.T.B.; Flavell, A.J.; Shaw, P.; Milne, I.; Waugh, R. (2008) Barley genomics and genetic analysis - new trends in barley genomics., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
  • Hackett, C.A.; Milne, I.; Bradshaw, J.E.; Luo, Z.W. (2007) TetraploidMap for Windows: Linkage map construction and QTL mapping in autotetraploid species., Journal of Heredity, 98, 727-729.
  • Husmeier, D.; Wright, F.; Milne, I. (2005) Detecting interspecific recombination with a pruned probabilistic divergence measure., Bioinformatics, 21, 1797-1806.
  • Milne, I.; Rowe, G. (2004) OGRE: Three-dimensional program visualization for novice programmers., Education and Information Technologies, 9, 219-237.
  • Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D.; McGuire, G. (2004) TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments., Bioinformatics, 20, 1806-1807.
  • Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D. (2004) TOPALi - Software for detecting recombinants in DNA multiple alignments., Plant and Animal Genome Conference (PAG) XII Proceedings, San Diego, California, 10-12 January 2004.
  • Milne, I.; Rowe, G. (2002) Difficulties in learning and teaching programme - views of students and tutors., Education and Information Technologies, 7, 55-66.
  • Parkes, S.M.; Martin, I.; Milne, I. (1999) Lunar surface simulation-modelling for vision-guided lunar landers., DASI '99. Lisbon, 369-374.

  • Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F. (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.

  • Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Thomas, W.T.B.; Ramsay, L.; Comadran, J.; Stephen G.; Bayer, M.; Graham, M.; Kennedy J.; Oakey, H.; Marshall, D.F. (2012) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XX, San Diego, California, 14-18 January 2012.
  • Bayer, M.; Liu, H.; Marshall, D.F.; Russell, J.; Hedley, P.E.; Milne, I.; Stephen G.; Waugh, R.; (2011) A GBS data processing pipeline for barley., StatSeq Meeting on Genotyping by Sequencing. Wageningen, Netherlands, 3-4 November 2011 (Talk).
  • Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
  • Russell, J.R.; Moragues, M.; Dawson, I.K.; Waugh, R.; Marshall, D.F.; Milne, I.; Grando, S.; Tondelli, A.; Cattivelli, L.; Hubner, S.; Fridman, E.; Flavell, A.J. (2009) Genetic diversity analysis of wild and landrace barleys using the BODA1 Illumina genotyping platform., 19th International Triticeae Mapping Initiative - 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August - 4 September 2009 (Talk).
  • Marshall, D.F.; Close, T.; Ramsay, L.; Druka, A.; Thomas, W.T.B.; Flavell, A.J.; Shaw, P.; Milne, I.; Waugh, R. (2008) Barley genomics and genetic analysis - new trends in barley genomics., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
  • Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D. (2004) TOPALi - Software for detecting recombinants in DNA multiple alignments., Plant and Animal Genome Conference (PAG) XII Proceedings, San Diego, California, 10-12 January 2004.
  • Parkes, S.M.; Martin, I.; Milne, I. (1999) Lunar surface simulation-modelling for vision-guided lunar landers., DASI '99. Lisbon, 369-374.

Printed from /staff/iain-milne on 04/12/22 05:07:21 AM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.