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Job: Principal / Senior Software Developer - Malaria

August 17, 2018 - 09:54 -- MalariaWorld Jobs

Organisation: Sanger Institute, UK
Salary in the region of £47,812 - £57,853 (Principal Software Developer) or £40,850 - £49,428 ( Senior Software Developer) plus excellent benefits
Fixed term for 2 years with possibility of extension (dependent on external funding)
Job Reference: 83174
Deadline for applications: 15th September 2018

The role purpose is to support the architecture design and the creation of an informatics system for genomic surveillance of malaria in endemic countries. The post-holder will work with the leads of a newly funded project - Global Health Research Group on genomic surveillance of malaria in West Africa funded by NIHR - to develop software products that support the translation of genomic data into actionable knowledge for malaria control and elimination.

Malaria is a major cause of childhood mortality and socio-economic disruption; control efforts have been ramped up significantly in the last 15 years and this has made a significant impact. However, there is a serious risk that these gains could be reversed in the foreseeable future, because Plasmodium parasites (that cause malaria) and Anopheles mosquitoes (that transmit the parasites from one person to another) are becoming increasingly resistant to malaria control interventions. The overall goal of this project is to establish local capacity in several malaria endemic countries for monitoring drug and insecticide resistance and to develop analytical outputs that will be of practical value to National Malaria Control Programmes (NMCPs) in planning effective interventions. This is an exciting time to join our team as we start a new paradigm where genomic surveillance is integrated into malaria control and elimination decision making.

Genomic surveillance is one of the most rapidly growing and exciting areas of 'Big Data', where the data generated by a local sequencing machine are amplified in information content and practical value if it is part of a global data sharing network. This raises crucial questions such as: how do we develop informatics systems that can work both in resource limited settings and on cloud platforms? How locally-generated data can be integrated with, and augmented by, central resources? What informatics technology can we use to communicate analytical results in an impactful way?

In this context, you will be pivotal in the design, implementation, and deployment of software solutions that:

  • provides a scalable data environment for the collection, storage, and integration of data from local and remote resources;
  • orchestrates the execution of bioinformatics analysis pipelines, both on local systems as well as on cloud-based environments;
  • allows users to interactively visualise the key findings through creative user interface technologies.

Together with the MRC Centre for Genomics and Global Health at Oxford University, the Kwiatkowski group serves as the resource centre for MalariaGEN, a data-sharing network of malaria researchers in more than 40 malaria-endemic countries (www.malariagen.net). Over the past 12 years, MalariaGEN has established an international reputation for generating large open access datasets. These data have become the benchmark for Plasmodium and Anopheles population genomics; for promoting equitable data sharing between researchers in rich and poor countries; and for research capacity building in malaria endemic countries. Providing equal opportunities and valuing diversity are intrinsically part of our core values. You will also be member of a software team that is well-known for having top-level expertise in scientific computing and long-standing dedication to open source projects, and participate in high quality and high impact projects themselves.

**please note: discussions will take place during the interview process as to which role profile you are being considered for.


Essential Skills

For the Principle Software Developer

  • A degree (BSc/MSc) in Computer Science/Bioinformatics or equivalent and significant experience
  • Extensive and documented experience as a Python software engineer and ability to employ additional languages when required
  • Experience providing lead technical design skills to complex or large scale projects, and creating novel solutions and concepts
  • Experience with all stages of application development life-cycle
  • Experience managing and coordinating all operational aspects of large and complex projects, including troubleshooting, development, optimisation, and delivery
  • Experience co-ordinating and overseeing teams’ activities
  • Ability to communicate technical knowledge and experience within both the team and the Institute to influence best practice; and externally through presentations and publications nationally and internationally
  • System administration and scripting
  • To be able to elicit complex requirements from, and convey complex requirements to, groups with differing technical backgrounds

For the Senior Software Developer

  • A degree (BSc/MSc) in Computer Science/Bioinformatics or equivalent and significant experience
  • Extensive and documented experience as a Python software engineer
  • Experience with deploying production-quality, scalable solutions
  • Experience with all stages of application development life-cycle
  • System administration and scripting
  • To be able to elicit complex requirements from, and convey complex requirements to, groups with differing technical backgrounds
     

Ideal Skills

For the Principle Software Developer

  • Experience of programming in C, C++ or Cython
  • Experience of scientific computing, including data processing workflows (e.g., Cromwell, Nextflow, Snakemake)
  • Experience of design and use of relational databases, e.g., MySQL, SQL server or Oracle
  • Experience with front-end web application development using modern web-based technologies and frameworks (e.g., JavaScript, React)
  • Experience in data parsing, cleansing, data modelling, analysis, and database design and implementation
  • Knowledge (or experience) of cloud-based environments and environments (OpenStack, AWS, GCP, Azure)
  • Knowledge of bioinformatics pipelines
  • Knowledge of leading NGS processing techniques for the identification of SNPs, INDELs and structural variants; direct experience processing NGS data is a plus
  • Providing advice, training, mentoring, and support to other researchers in the areas of bioinformatics and data analysis

For the Senior Software Developer

  • Experience of programming in C, C++ or Cython
  • Experience of scientific computing, including data processing workflows (e.g., Cromwell, Nextflow, Snakemake)
  • Experience of design and use of relational databases, e.g., MySQL, SQL server or Oracle
  • Experience with front-end web application development using modern web-based technologies and frameworks (e.g., JavaScript, React)
  • Experience in data parsing, cleansing, data modelling, analysis, and database design and implementation
  • Knowledge (or experience) of cloud-based environments and environments (OpenStack, AWS, GCP, Azure)
  • Knowledge of bioinformatics pipelines
  • Knowledge of leading NGS processing techniques for the identification of SNPs, INDELs and structural variants; direct experience processing NGS data is a plus
  • Providing advice, training, mentoring, and support to other researchers in the areas of bioinformatics and data analysis


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:

  • Group 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, cricket pitch and sports hall plus a range of dining facilities
  • Active Campus Sports and Social Club
  • Free Campus Bus Service

Genome Research Limited is an Equal Opportunity employer. As part of our commitment to equality, diversity and inclusion and promoting equality in careers in science, we hold an Athena SWAN Bronze Award and have an active Equality, Diversity and Inclusion programme of activity. We will consider all applicants without discrimination on grounds of disability, sexual orientation, pregnancy or maternity leave status, race or national or ethnic origin, age, religion or belief, gender identity or re-assignment, marital or civil partnership status, protected veteran status (if applicable) or any other characteristic protected by law. We are open to a range of UK-based flexible working options including part-time or full-time employment as well as flexible hours due to caring or other commitments.

Click here to apply for this position

Please include a covering letter and CV with your application. Closing date: 15th September 2018 


Don't forget to mention MalariaWorld when applying for this position!