Senior Software Developer - Tree of Life Genomics

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Salary in the region of £41,259 - £49,922 (dependent on experience) plus excellent benefits

Fixed term for 2 years - with potential to extend for 3 years

The Sanger Institute with other partners has launched the Darwin Tree of Life project to provide high-quality genome assemblies for all eukaryotic species in the British Isles. This project will significantly contribute to the global Earth Biogenome Project, fundamentally changing scientific knowledge of evolution and interactions among millions of the planet's organisms.

We are seeking a senior software developer to contribute to building and optimising the computational infrastructure required to scale genome assembly within this project, streamlining the processing of terabytes of raw data. This will build on Sanger's world-class computational resources, including an OpenStack private cloud environment, a 15000+ core computational cluster and many petabytes of high-speed distributed file systems and object stores.

The primary responsibilities of the successful applicants will be:

To write high quality, documented code, in coordination with other team members, in order to facilitate the rapid production and analysis of genome assemblies. Develop systems to perform essential quality checks of the data prior to release, to identify errors and ensure a high level of accuracy is maintained.

Work with team members to build, maintain and run robust pipelines for building these assemblies. Pipelines must scale as more species are sequenced and be adaptable to rapid developments in sequencing technologies and software.

To work with core IT on systems configuration, packaging and monitoring to support these processes.

To participate in the agreement of achievable timelines for programming and development projects and to subsequently meet those goals.

Initiate and contribute to problem-solving discussions with the team to generate novel ideas and help the project move forward.

Contribute directly to the delivery of the Darwin Project by working with various internal and external groups to discuss and understand their analysis needs to enable them to work more quickly and more accurately.

Study existing solutions and make recommendations to team leader and faculty groups for improvements.

Team members will be expected to work independently at a technical level, while collaborating closely with colleagues on systems development, and to be comfortable communicating directly with scientific researchers regarding analysis requirements. Recent graduates are also encouraged to apply, although it is strongly desirable that any candidate has substantial development experience outside of coursework (e.g. work experience, participation in open source projects). Bioinformatic/biological knowledge is not essential for this role, but an interest in the science on campus and desire to learn bioinformatic concepts is important.

For further information or questions about this post please contact Shane McCarthy ()

Essential Skills

Demonstrable experience in software development, preferably in a scientific environment

Knowledge of core computer science concepts and practices

Capable of quickly learning and using the most suitable programming language for the job, including both interpreted and compiled languages

Excellent critical and problem-solving skills

Experience with git and GitHub

Expert knowledge of unix based operating systems, libraries, and tools

Excellent communication and presentation skills, motivation and attention to detail

Ideal Skills

Experience in bioinformatics analysis and tools

Knowledge of virtualization/containerisation technologies (Docker, Singularity)

Knowledge (or experience) of Cloud environments (OpenStack, GCP, AWS) and workflow languages (CWL, NextFlow, Snakemake)

Familiarity with Cloud technologies (e.g. Terraform, Ansible, Kubernetes, GitHub CI)

Experience with relational and non-relational databases

Experience with high performance computing environments (e.g. LSF or Slurm)

Other information

The Wellcome Sanger Institute is a charitably funded research centre and committed to training the next generation of genome scientists. Focused on understanding the role of genetics in health and disease and a world leader in the genomic revolution, our mission is to use genome sequences to advance understanding of human and pathogen biology in order to improve human health. We aim to provide results that can be translated into diagnostics, treatments or therapies that reduce global health burdens. Our science is large-scale and organised into Programmes, led by our Faculty who conceive and deliver our science, and supported by our Scientific Operations teams responsible for all data production pipelines at the Institute.

Our Campus: Set over 125 acres, the stunning and dynamic Wellcome Genome Campus is the biggest aggregate concentration of people in the world working on the common theme of Genomes and BioData. It brings together a diverse and exceptional scientific community, committed to delivering life-changing science with the reach, scale and imagination to pursue some of humanity's greatest challenges.

Our Benefits: Our employees have access to a comprehensive range of benefits and facilities including:

Defined Contribution Pension Scheme and Life Assurance

Group Income Protection

Private Health Insurance

25 days annual leave, increasing by one day a year to a maximum of 30

Family friendly environment including options for flexible and part-time working, a childcare voucher scheme, Campus Nursery and Summer holiday club

Two days paid Employee Volunteering Leave a year

Employee Discount Scheme

Campus Gym, tennis courts and sports hall plus a range of dining facilities

Active Campus Sports and Social Club

Free Campus Bus Service

Genome Research Limited hold an Athena SWAN Bronze Award and will consider all individuals without discrimination and are committed to creating an inclusive environment for all employees, where everyone can thrive.

Please include a covering letter and CV with your application. Closing date for applications: 21st July 2019