Paul Shaw
- 2011 - present: Database Developer / Computational Biologist - The James Hutton Institute
- 2009-2015 - PhD Computational Sciences - The James Hutton Institute and Edinburgh Napier University
- 2002 - 2011: Bioinformatics Database Developer, Genetics Programme, The Scottish Crop Research Institute
- 1999-2002: Bioinformatics Programmer - Roslin Institute, Edinburgh.
- 1998 - 1999 MSc Bioinformatics
- 1994-1998 BSc (Hons) Microbial Biotechnology
Current research interests
- Plant pedigree visualization.
- Development of the Germinate platform.
- Development of bespoke applications to support the storage, manipulation and visualisation of biological data and new high throughput genotyping technologies.
The increasingly diverse range of data-types that are being used in modern plant genetics and breeding is a problem, both in how data is stored and how scientists can query and visualize in scientifically meaningful ways. My primary research focus is on how we efficiently store and query large datasets and investigating how user interfaces can allow researchers access to this data in ways that allow increased scientific value to be gained. I am particularly interested in how we can increase the overall data quality of data-sets through error identification and the development of electronic data capture and reference applications (mobile based) to aid field scientists. Any problems we can reduce at the data capture stage ensures high data quality for downstream processing and analysis.
A main focus of my work is in the development of complex online databases implemented in MySQL for the dissemination of data to both internal and external (academic and industrial) audiences and the development of the supporting programming infrastructure based on Perl and Java that is required to build on these customized tools. More recently I have been examining the problems associated with visualization of large plant pedigrees and addressing some of these with the development of visualization tools such as Helium.
The above video shows an example of visualization of a large barley pedigree in the Helium pedigree visualization application.
I have been actively involved in a number of international collaborations including involvement in the Seeds of Discovery project in collaboration with CIMMYT in Mexico where the tools which my team and I develop have been used to allow the online presentation of the CIMMYT maize and wheat genebank accessions which are part of this initiative. More recently I have started managing a new 3.5 year project with the Crop Trust in which we are utilising the database and visualization toolls which I develop to support the presentation of data across a wide variety of crop wild relative (CWR) species. Germinate will be the underlying platform on to which this data will be stored and presented and gives Germinate an increasing exposure within the plant genetic resources community.
Germinate 3
Germinate is a generic plant genetic resources database and offers facilities to store both standard collection information and passport data along with more advanced data types such as phenotypic, genotypic and field trial data. Germinate was originally implemented in MySQL and Perl but is moving with version 3 to MySQL and Google Web Toolkit (GWT). Germinate is not a standalone desktop application and requires MySQL, Apache Tomcat and GWT to run. The usual use case would be installation on a Linux based server.
Currently there are Germinate installations for barley, wheat, potato, Lolium, Festuca, maize and pea although the generic nature of the system makes it suitable for storage of data from a wide variety of sources and species. We are currently developing Germinate to handle large scale trials data and data from high throughput genotpying experiments as well as supporting the Crop Trust CWR Pre-Breeding project where Germinate will be used to hold data across a wide diversity of species.
Recent advances have allowed us to further develop Germinate including the ability to restrict access to specific users or to only allow access to data based on acceptance of licence agreements. We are actively working to increase the functionality of Germinate and welcome comments and suggestions on potential collaboration, or how we can improve Germinate going forwards.
Other Databases
Germinate Pea
Pea database comprising accessions from the John Innes collection, one of the widest and most comprehensive sets of Psium germplasm worldwide. Also includes Retrotransposon-Based Insertion Polymorphism (RBIP) marker data.
Germinate Grasses
Database holding information on Lolium and Festuca accessions as well as genotypic data based on the DArT platform.
Commonwealth Potato Collection Database
This potato database contains passport and disease resistance data across the accessions contained within the Commonwealth potato collection at The James Hutton Institute. This resource is based on the Germinate 2 platform.
AtNoPDB
The Arabidopsis Nucleolar Protein database (AtNoPDB) provides information on 217 Arabidopsis proteins in comparison to human and yeast proteins.
Wheat In-Situ Database
This resource was developed and implemented at SCRI to hold the data obtained from a joint BBSRC and Syngenta project for high-throughput wheat in situ hybridisation.
Plant snoRNA Database
This resource brings together information from three independant computer-assisted searches of the Arabidopsis genome for box C/D snoRNA genes and from studies of ncRNAs.
Areas of Expertise
- Database design and implementation.
- Web application and interface development.
- Biological data visualization.
- Large scale biological data handling and error checking.
Bibliography
- 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, Article No. btz190.
- Looseley, M.E.; Griffe, L.L.; Büttner, B.; Wright, K.M.; Middlefell-Williams, J.; Bull, H.; Shaw, P.D.; Macaulay, M.; Booth, A.; Schweizer, G.; Russell, J.R.; Waugh, R.; Thomas, W.T.B.; Avrova, A. (2018) Resistance to Rhynchosporium commune in a collection of European spring barley germplasm., Theoretical and Applied Genetics, 131, 2513-2528.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- 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.
- 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.
- Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O'Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Kearsey, M.J.; Luo, Z.; Wang, M.; Tapsell, C.; Harrap, D.; Werner, P.; Klose, S.; Bury, P.; Wroth, J.; Argilllier, O.; Habgood, R.; Glew, M.; Bochard, A-M.; Gymer, P.; Vequaud, D.; Christerson, T.; Allvin, B,; Davies, N.; Broadbent, R.; Brosnan, J.; Bringhurst, T.; Booer, C.; Waugh, R. (2014) Association genetics of UK elite barley (AGOUEB)., Final Project Report to HGCA, No 528, 125pp.
- 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.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
- Streitner, C.; Köster, T.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2012) An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana., Nucleic Acids Research, 40, 11240-11255.
- Comadran, J.; Kilian, B.; Russell, J.R.; Ramsay, L.; Stein, N.; Ganal, M.; Shaw, P.; Bayer, M.; Thomas, W.T.B.; Marshall, D.F.; Hedley, P.E.; Tondelli, A.; Pecchioni, N.; Francia, E.; Korzun, V.; Walther, A.; Waugh, R. (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley., Nature Genetics, 44, 1388-1392.
- Forster, B.P.; Franckowiak, J.D.; Lundqvist, U.; Thomas, W.T.B.; Leader, D.; Shaw, P.; Lyon, J.; Waugh, R. (2012) Mutant phenotyping and pre-breeding in barley., In: Shu, Q.Y., Forster, B.P. & Nakagawa, H. (eds.). Plant Mutation Breeding and Biotechnology. CAB International, Wallingford. Chapter 25, pp327-346.
- 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.
- Ramsay, L.; Thomas, W.T.B.; Comadran, J.; Marshall, D.F.; Shaw, P.; Waugh, R. (2011) Genetic diversity in modern barley varieties., Annual Report of the Scottish Crop Research Institute for 2010, pp23-24.
- 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.
- Jing, R.C.; Vershinin, A.V.; Grzebyta, J.; Shaw, P.; Smykal, P.; Marshall, D.F.; Ambrose, M.J.; Ellis, T.H.N.; Flavell, A.J. (2010) The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis., BMC Evolutionary Biology, 10(44).
- 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.
- Kopecky, D.; Bartos, J.; Lukaszewski, A.J.; Baird, J.H.; Cernoch, V.; Kolliker, R.; Rognli, O.A.; Blois, H.; Caig, V.; Lubberstedt, T.; Studer, B.; Shaw, P.; Dolexel, J.; Kilian, A. (2009) Development and mapping of DArT markers within the Festuca - Lolium complex., BMC Genomics, 10(473).
- Brown, J.W.S.; Shaw, P.J.; Shaw, P.; Marshall, D.F. (2005) Arabidopsis nucleolar protein database (AtNoPDB)., Nucleic Acids Research, 33, D633-D636.
- Caldwell, D.G.; McCallum, N.; Shaw, P.; Muehlbauer, G.J.; Marshall, D.F.; Waugh, R. (2004) A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.)., Plant Journal, 40, 143-150.
- Brown, J.W.S.; Echeverria, M.; Qu, L.; Lowe, T.M.; Bachellerie, J.; Huttenhofer, A.; Kastenmayer, J.P.; Green, P.J.; Shaw, P.; Marshall, D.F. (2003) Plant snoRNA database., Nucleic Acids Research, 31, 432-435.
- 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, Article No. btz190.
- Looseley, M.E.; Griffe, L.L.; Büttner, B.; Wright, K.M.; Middlefell-Williams, J.; Bull, H.; Shaw, P.D.; Macaulay, M.; Booth, A.; Schweizer, G.; Russell, J.R.; Waugh, R.; Thomas, W.T.B.; Avrova, A. (2018) Resistance to Rhynchosporium commune in a collection of European spring barley germplasm., Theoretical and Applied Genetics, 131, 2513-2528.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- 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.
- 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.
- 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.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
- Streitner, C.; Köster, T.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2012) An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana., Nucleic Acids Research, 40, 11240-11255.
- Comadran, J.; Kilian, B.; Russell, J.R.; Ramsay, L.; Stein, N.; Ganal, M.; Shaw, P.; Bayer, M.; Thomas, W.T.B.; Marshall, D.F.; Hedley, P.E.; Tondelli, A.; Pecchioni, N.; Francia, E.; Korzun, V.; Walther, A.; Waugh, R. (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley., Nature Genetics, 44, 1388-1392.
- 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.
- 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.
- Jing, R.C.; Vershinin, A.V.; Grzebyta, J.; Shaw, P.; Smykal, P.; Marshall, D.F.; Ambrose, M.J.; Ellis, T.H.N.; Flavell, A.J. (2010) The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis., BMC Evolutionary Biology, 10(44).
- Kopecky, D.; Bartos, J.; Lukaszewski, A.J.; Baird, J.H.; Cernoch, V.; Kolliker, R.; Rognli, O.A.; Blois, H.; Caig, V.; Lubberstedt, T.; Studer, B.; Shaw, P.; Dolexel, J.; Kilian, A. (2009) Development and mapping of DArT markers within the Festuca - Lolium complex., BMC Genomics, 10(473).
- Brown, J.W.S.; Shaw, P.J.; Shaw, P.; Marshall, D.F. (2005) Arabidopsis nucleolar protein database (AtNoPDB)., Nucleic Acids Research, 33, D633-D636.
- Caldwell, D.G.; McCallum, N.; Shaw, P.; Muehlbauer, G.J.; Marshall, D.F.; Waugh, R. (2004) A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.)., Plant Journal, 40, 143-150.
- Brown, J.W.S.; Echeverria, M.; Qu, L.; Lowe, T.M.; Bachellerie, J.; Huttenhofer, A.; Kastenmayer, J.P.; Green, P.J.; Shaw, P.; Marshall, D.F. (2003) Plant snoRNA database., Nucleic Acids Research, 31, 432-435.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
- Forster, B.P.; Franckowiak, J.D.; Lundqvist, U.; Thomas, W.T.B.; Leader, D.; Shaw, P.; Lyon, J.; Waugh, R. (2012) Mutant phenotyping and pre-breeding in barley., In: Shu, Q.Y., Forster, B.P. & Nakagawa, H. (eds.). Plant Mutation Breeding and Biotechnology. CAB International, Wallingford. Chapter 25, pp327-346.
- Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O'Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Kearsey, M.J.; Luo, Z.; Wang, M.; Tapsell, C.; Harrap, D.; Werner, P.; Klose, S.; Bury, P.; Wroth, J.; Argilllier, O.; Habgood, R.; Glew, M.; Bochard, A-M.; Gymer, P.; Vequaud, D.; Christerson, T.; Allvin, B,; Davies, N.; Broadbent, R.; Brosnan, J.; Bringhurst, T.; Booer, C.; Waugh, R. (2014) Association genetics of UK elite barley (AGOUEB)., Final Project Report to HGCA, No 528, 125pp.
- Ramsay, L.; Thomas, W.T.B.; Comadran, J.; Marshall, D.F.; Shaw, P.; Waugh, R. (2011) Genetic diversity in modern barley varieties., Annual Report of the Scottish Crop Research Institute for 2010, pp23-24.
- 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.
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