Nottingham University



|THE UNIVERSITY OF NOTTINGHAM |

|Role Profile Form |

Job Title: Research Associate Bioinformatics/Image Analysis – Two Posts

School/Department: School of Computer Science

Salary: £28,695 - £37,394 per annum, depending on skills and experience. Salary progression beyond this scale is subject to performance.

Job Family and Level: Research and Teaching Level 4 (Appointment will be Level 4 Career training grade where an appointment is made before PhD has been completed)

Contract Status: Fixed-term ends 30 June 2016

Hours of Work: Full Time, 36.25h per week

Location: Jubilee Campus

Reporting to: Professor Tony Pridmore

Purpose of the Role:

The iPlant Collaborative is a major initiative aimed at creating a software platform that enables a large community of plant biologists to make use of advanced computational tools for research purposes. The University’s School of Computer Science and Centre for Plant Integrative Biology have developed a set of image analysis methods and software tools that have proven effective in extracting quantitative descriptions of plant organs from confocal laser microscope, colour and X-ray Computed Tomography images The purpose of this post is to integrate these tools into the iPlant environment to substantially widened user base and a step-change in the impact that bioimage analysis research and tool development at Nottingham has on plant science both nationally and internationally.

| |Main Responsibilities |

|1. |Provide image analysis expertise and implementation skills to maximise the potential of existing bioimage analysis tools, making them |

| |both valuable to and easily usable by a large set of users via iPlant. |

|2. |Re-implement existing code in C or C++ to make best use of the iPlant framework and increase computational efficiency. |

|3. |Interact with iPlant staff to define interfaces between their software framework and Nottingham’s contributions. |

|4. |Support the parallelisation of tools inside the iPlant framework as required. |

|5. |Perform rigorous tests and evaluations of computational tools. |

|6. |Contribute to user interfaces and software documentation. |

|7. |Maintain close contacts with colleagues and with relevant managers, sharing expertise and information to ensure that developments are |

| |co-ordinated, and that a coherent development and service environment is maintained. |

|8. |Organise and contribute to internal and external workshops on the use of the iPlant tools for researchers and graduate students |

|9. |Write up research work for publication and/or contribute to the dissemination at national/international conferences, resulting in |

| |successful research outputs. |

Knowledge, Skills, Qualifications & Experience

| |Essential |Desirable |

|Qualifications/ Education |PhD in Computer Science, Bioinformatics, or a related area | |

| | | |

|Skills/Training |Ability to develop software in C/C++ |Experience of image processing, analysis and/or |

| | |computer vision research |

| |Ability to develop software in at least one of Perl, MATLAB,|Experience of parallel computing and/or interface |

| |and Python |design |

| | | |

| |Basic knowledge of image processing and analysis | |

| | | |

| |Ability to work independently and as part of an | |

| |interdisciplinary team | |

| | | |

| |Effective communication (oral and written) skills | |

|Experience |Some practical experience of applying the specialist skills,| |

| |approaches and techniques required for the role. | |

| | | |

|Statutory/Legal | | |

Decision Making

i) Taken independently by the role holder;

• Software design/structure

• Design of any interfaces and parallelisation strategies required

ii) Taken in collaboration with others;

|Choice of software tools and methods used |

|Addition of new and extension of existing bioimage analysis methods and tools |

iii) Referred to the appropriate line manager by the role holder

|Wider strategy of our research and development work |

|Purchasing decisions |

Additional Information

|The Centre for Plant Integrative Biology (cpib.ac.uk) is an interdisciplinary unit bringing together biologists, computer scientists, |

|mathematicians and engineers to address fundamental problems in plant and crop science. The School of Computer Science, and particularly the |

|Computer Vision Laboratory, has been closely involved since CPIB’s inception, addressing a range of image analysis and computer vision problems |

|associated with the recovery of quantitative two and three-dimensional data from various microscope, colour and X-ray computed tomography images |

|of plants. This work has resulted in the production of a range of computational methods and associated software tools, which have been made |

|available to and well-received by the plant and crop science communities. These tools and methods underpin a range of research projects and are |

|central to the operation of the University’s recently opened Hounsfield Facility, a unique resource built around a set of X-ray micro-Computed |

|Tomography scanners and associated automation. |

|These posts provide opportunities to develop our bioimage analysis capability further, significantly increasing its power and uptake by |

|integrating it into the US-developed iPlant environment. The iPlant Collaborative is a major initiative aimed at creating a software platform that|

|enables a wide community of plant biologists to make use of advanced computational tools in order to generate and analyse large data sets. The |

|role holders will join an established and highly regarded interdisciplinary team to help build the first iPlant node outside the US, populating it|

|with appropriately implemented and modified versions of Nottingham’s bioimage analysis tools. |

|Depending on the tool this may involve adapting the core methods used, re-coding in a faster language (C or C++), parallelising computations using|

|iPlant’s framework, adapting the tool to iPlant interfaces, as well as testing and following up on user feedback. The outcome of this project will|

|be a substantially widened user base and a step-change in the impact that bioimage analysis research and tool development at Nottingham has on |

|plant science both nationally and internationally. |

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Recruitment

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