Research Software Engineer

Posted on by Charlie Johnson
Job ID:
Job date: 2014-10-12
End Date:

Company : TGAC 

Country :

Role : Research Scientist 


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Job Description:

Post Number 1002719
Job Title Research Software Engineer
Closing Date 20 Oct 2014
Grade SC5
Starting Salary £36,400 - £40,750
Hours per week 37
Project Title Collaborative Open Plant Omics (COPO): a Collaborative Bioinformatics Plant Science Platform
Expected/Ideal Start Date 03 Nov 2014
Months Duration 36
Flexible Options
Flexi Time This post has a set of core hours which must be worked - outside this, and by agreement with your Line Manager, there is flexibility in start and end times.
Main purpose of the job Initiate, develop and maintain the Collaborative Open Plant Omics (COPO) platform to become a single point-of-access for a range of web services, via their APIs, that enable plant scientists to attribute metadata, deposit data and ascribe accessions to these first-class research objects, and link these rich bundles with their publications.Manage the strategic development and delivery of high-performance middleware that provides essential tracking and interrogation of data managed by the COPO platform. Devise novel approaches, customised to different platforms, sources and applications, to improve large-scale data description, public deposition and access across the national plant research community. Contribute to and promote gold standards for data-driven informatics in the plant biosciences. Develop an expert working group for plant data management comprising other bioinformatics groups in the UK and beyond, by engaging with plant researchers, attending national and international meetings to promote data management and related infrastructure, and by providing training on the COPO platform.
Department Bioinformatics
Group Details The Sequencing Informatics group at TGAC, led by Dr. Robert Davey, is part of the Science Faculty, undertaking research into: investigating data generated by new sequencing technologies such as Oxford Nanopore, with a view to better understand data QC and downstream data-driven informatics challenges; algorithms and tools for metagenomics assembly; genomics big data infrastructure and visualisation; software engineering and best practices for the life sciences.We are a friendly, dynamic team with a wide range of research interests and backgrounds. We very much believe in the open source and open science ethos, and this is carried throughout all of our research outcomes.
Advert Text The post will initiate the project and implement the soft infrastructure components of the recently awarded BBSRC-funded project, “Collaborative Open Plant Omics (COPO): a community-driven platform for plant science” (BB/L024055/1) in collaboration with researchers from Oxford University, Warwick University, and the European Bioinformatics Institute (EBI).The work on COPO plant data management will drive the research into providing platform- and software-as-a-service (PaaS, SaaS) infrastructure to help expand TGAC’s growing strengths in bioinformatics research into data and analysis. This is an exciting role that will develop potentially ground-breaking advances to improve the access and understanding of data deposition and dissemination services to enable the plant research community to manage and publicise their data effectively. The plant research community demands a flexible approach to the dissemination of data, metadata and publication attribution. A push for open data in this community will benefit internal researchers, external collaborators and the global plant genomics and bioinformatics community. As such, TGAC will be a UK hub for innovative bioinformatics and genomics and their applications in a broad spectrum of plant bioscience. Through interactions with the TGAC 361 Division, the post will develop suitable training programmes around COPO and promote the benefits of accurate and timely data management through user experience research, workshops and other training events. The Genome Analysis Centre is an institute supported by the BBSRC to ensure that biological science in the UK has access to a skill base in genomics technologies and bioinformatics to deliver programmes leading to improved food security, advances in industrial biotechnology and improved human health and wellbeing.
Key relationships Internal: Reporting to the Sequencing Informatics group leader with a key role to play in the development and delivery of the COPO infrastructure. Working with the 361 Division to develop materials and deliver training on the COPO platform.Managing: No immediate management responsibilities. Interacting with: All TGAC staff. External: Developers of the ISA Tools suite at Univ. Oxford; data repositories at the European Bioinformatics Institute (EBI); representatives of the UK plant bioscience community at Univ. Warwick; UK and international data management scientists; API and service providers for data and analysis management services such as figshare, iPlant, Galaxy, Research Objects, Scientific Data, Data Dryad, etc
Main Activities & Responsibilities Percentage
To work with the Sequencing Informatics group leader to develop the Collaborative Open Plant Omics platform, TGAC’s strategy and tools for plant data and metadata management, driven by the analytical demands, technological advances and programme needs of the UK plant research community 35
Reduce the burden of data management for plant researchers, enabling them to share their data and results more effectively by establishing interoperability middleware between a range of existing data services 25
To establish associated best practice guidelines for plant bioscience data management, flow, exposure and publication strategies 15
To provide an efficient and cost-effective plant data management platform to exploit TGAC’s hardware and software expertise, promoting the Centre as a National Capability for UK bioscience 15
To communicate the work of TGAC in oral and written presentations and to publish novel technological developments in scientific journals 5
To network widely with academic and industrial groups on the NRP, throughout the UK and internationally, including the GARNET plant community, the European Bioinformatics Institute, other genomics facilities nationally and internationally, and with bioinformaticians globally, such as the iPlant Collaborative and Galaxy efforts 5
Education & Qualifications Requirement Importance
Significant experience in enterprise software development, with a focus on API development and frameworks for data handling Essential
MSc and/or PhD in a relevant discipline, e.g. computer science, bioinformatics Desirable
Track record in data management, preferably in the field of bioinformatics or another “big data” discipline Desirable
Specialist Knowledge & Skills Requirement Importance
Proficient in the Java and Javascript programming languages and web application frameworks, and associated libraries (Spring, JSP, HTML, jQuery, d3.js Essential
Experience in platform- and software-as-a-service (PaaS, SaaS) architectures, i.e. the “Cloud” Essential
Experience with database management systems and SQL Essential
Experience in “big data” tools and techniques Desirable
Experience in usage of high-performance computing infrastructures Desirable
Knowledge of ontologies Desirable
Experience in the C programming language Desirable
Relevant Experience Requirement Importance
Strong experience in open source software engineering and associated tools, i.e. version control (git/GitHub) agile practices, code review, etc Essential
Experience of working in a rapidly changing technological environment Essential
Experience of working in a high throughput genomics environment Desirable
Experience in bioinformatics related to high throughput DNA sequencing and metadata attribution Desirable
Knowledge of research and funding within the UK science base Desirable
Interpersonal & Communication Skills Requirement Importance
Excellent communication skills Essential
To be able to communicate clearly with TGAC staff at all levels Essential
Interest in and understanding of research into user experience (UX)

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