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Sebastian Raubach

Staff picture: Sebastian Raubach
Information and Computational Sciences
Information and Computational Sciences
Bioinformatics Software Developer
sebastian.raubach@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

I am a Research Software Engineer (RSE) working as part of the Information & Computational Sciences (ICS) Department. I am responsible for the conceptualisation, management and development of cutting-edge mobile applications, databases and web applications for funders (BBSRC, EU, CGIAR, Crop Trust, Norwegian Government) as well as commercial breeding companies through James Hutton Limited (JHL). My role is to drive the development of software solutions for plant genetic resources collections, phenotypic data collection and visualization tools.

Current research interests

  • Modern manual phenotypic data collection.
  • Design and development of software solutions for plant genetic resources.
  • Conceptualization, maintenance and development of state-of-the-art web, mobile and database applications to support crop researchers and breeders.

Current Software Applications

Germinate

Germinate is an open source plant database infrastructure and application programming platform on which complex data from genetic resource collections can be stored, queried and visualized using common, reusable, programming components. Germinate utilises modern web and database standards to provide a common architecture and high performance web-based user interface and analytics functionality across a wide variety of data types including: passport, phenotypic, field trial, pedigree, genetic, climatic, geographic location data as well as user-submitted annotations. In addition, it provides links to an expanding variety of external visualization and analysis tools such as Helium for pedigree visualization, Flapjack for graphical genotyping and CurlyWhirly for 3D coordinate data.

GridScore

GridScore is a field trial phenotyping app for trait data. It lets you keep track of what's happening in the field on a plot-level basis. This could be anything from plant emergence, flowering date, plant height, flower colour, etc. You can define the layout of your field trial and the traits you want to score. GridScore then presents your data in a table format representing your field layout. Data is recorded by clicking on a specific plot in a field and then entering your data.

Germinate Scan

Germinate Scan is designed to make scanning and storing barcodes easy! Just connect an external barcode scanner to your Android device and start scanning or use your device's inbuilt camera. Germinate Scan will scan barcodes as a row of a key and multiple values, i.e. the first code represents the key while the following codes in the row are the values. All scanned codes are tagged with the time and date of the scan event as well as the geographic location of the device if GPS is enabled. As long as the attached barcode scanner is connected as an input device, Germinate Scan can handle all types of bar codes the scanner is able to read. All scanned bar codes are saved in an internal database to make sure that you can continue exactly where you left off. The database can be exported to a text file at any time.

Buntata

Buntata is an Android based mobile application which aids in the identification of plant disease and pathogens and offers information to farmers where they can go to get more details about any pests. It provides downloadable datasets allowing users to use the application in the field without the need of a mobile signal.

Bibliography

  • 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.
  • 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.

  • 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.
  • 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.

Printed from /staff/sebastian-raubach on 26/05/22 03:08:41 PM

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.