Archive for March, 2012

Jobs – Bioinformatics

Posted: 23 March 2012 by Alistair Miles in Jobs
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We’re advertising bioinformatics jobs at both Oxford and Sanger (near Cambridge), see the following links for job descriptions and information on how to apply:

Here’s an excerpt from the job description:

Overview of role

All MalariaGEN projects working on parasite and vector biology depend on next-generation sequencing. Over 2,000 samples of parasite DNA have been sequenced, and at least 10,000 samples will have been sequenced by 2015. Genome sequencing has been carried out on approximately 200 Anopheles samples to date, and the aim is to sequence approximately 2,500 individuals over the next 4 years. Most parasite samples have been extracted directly from infected blood samples, and so present additional complexities such as small quantities of DNA and mixed infection.

Raw next-generation sequence data is the beginning of a complex and intellectual demanding analysis process. The primary goal is to discover robust evidence for genetic variation. However, building from raw sequence data to robust variation data is and will continue to be one of the most significant challenges facing the malaria research community over coming years. Working to iteratively improve the quality of our genetic variation data and reach deeper into the Plasmodium and Anopheles genomes is the main focus of the MalariaGEN Bioinformatician roles.

This is an extremely fast-paced area of current research and development, and new methods and tools are emerging from many leading research groups and projects, many of whom we have close contacts with. However, we have to strike a balance between looking to the future, and delivering data to MalariaGEN partners that might not be perfect or complete but which nevertheless provides a highly valuable research tool for a range of studies, such as genotype-phenotype association studies, and studies of parasite and vector population structure and dynamics.

To achieve this balance between methods development on the one hand, and production of data on the other, our bioinformatics programme is organised around two working groups. The methods development group is focused on the development, exploration and thorough evaluation of new methods, including methods for sequence alignment, variation calling and genotyping, working closely with statisticians. The production group is focused on establishing tightly specified data analysis pipelines and using them to produce high quality variation data in a reproducible way. Both working groups work to a quarterly data release cycle, where the methods development looks ahead to the next release and determines the best available methods, which are then adopted and implemented by production.

While this role may focus more on methods development or production at different times, we encourage participation in both working groups, as there are important insights that can only be gained by working across both.

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Jobs – Scientific Software Engineering

Posted: 23 March 2012 by Alistair Miles in Jobs
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We’re advertising for software engineers, the job title says “scientific” but no previous experience of scientific programming is required, applications are very welcome from anyone with a strong software engineering background and an interest in the life sciences and/or public health.

We’re advertising at both Sanger (near Cambridge) and Oxford, see the following links for job descriptions and information on how to apply:

Here’s a snippet from the job ad:

MalariaGEN aims to produce global data on natural genetic variation in parasite, mosquito and human populations, and to deliver these data via the MalariaGEN website, alongside web tools which add value by enabling people to explore, understand and analyse the data. Some of these web and data products are intended for unrestricted use by the malaria research and public health community, to inform future research directions and malaria control policy. Other web and data products are being developed for private use by researchers contributing to MalariaGEN community projects, and provide a key incentive to participation in MalariaGEN, e.g., secure web tools providing access to fine-grained genetic data on individual samples.

We have a unique opportunity for Software Engineers to take a key role in the development and implementation of software projects relating to MalariaGEN web and data products.

The job description has a bit more background:

MalariaGEN continues to present many challenges that require development of new software applications. These include:

  • Web applications to present and visualise complex data

  • Software for data analysis and analysis pipelines, typically compute-intensive involving terabytes of data

  • Laboratory information management systems (LIMS) to keep track of samples, data and high-throughput experiments

  • Business and collaboration systems to administrate and coordinate a complex global research network, and to enable partners from different institutions to share information and effectively work together

The Web continues to be our primary platform for delivering software applications, and we have specialist expertise in Web application development and Web standards within the team. However we also develop other types of application as the problem requires.

Members of the software engineering team are equally capable of working across all stages of the software project life cycle, from requirements analysis and design through to implementation and testing, and we support the development of skills and experience across these different areas.

All software we develop is or will be released under an open source license. We also make use of existing open source software where possible and actively contribute to a number of open source projects. An interest in open source software and previous experience of participation in open source projects is an advantage.

We are working in a fast-moving area of scientific research, and we are constantly having to innovate. However, we also have a strong focus on the scientific robustness of the products delivered by MalariaGEN, and value a dedication to quality and sound engineering practices.

 

Job – Clinical Data Curator

Posted: 12 March 2012 by Alistair Miles in Jobs, Uncategorized
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We’re advertising for a clinical data curator, here’s a snippet from the job ad:

Applications are invited for a MalariaGEN Clinical Data Curator to work in a data-sharing community developing new tools to control malaria by integrating epidemiology with genome science.

You will be a member of the MalariaGEN resource centre and will focus on MalariaGEN consortial data. This data relates to three of our human consortial projects; Genetic determinants of resistance to malaria; Genetic determinants of the immune response to malaria and Human genome variation in malaria-endemic regions.

…the actual work involves curating large amounts of clinical data relating to cases of severe malaria from Africa. The data originate from different countries, studies, research groups, … basically the data can be quite heterogeneous, and needs to be carefully managed, standardised and quality controlled to enable the data to be aggregated then analysed.

Dealing with clinical research data on this scale has been an ongoing challenge for our team for many years, and remains a critical part of realising MalariaGEN‘s studies of human resistance to malaria. If you enjoy dealing with real-world data management problems, have an interest in the life sciences and/or public health, and enjoy working with a diverse community of people from different parts of the world, your application would be very welcome.

Further details are available at the link below:

Job – Scientific Product Manager

Posted: 12 March 2012 by Alistair Miles in Jobs
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Just a brief post to say that we’re advertising for a Scientific Product Manager. This may not be obvious at a glance, but this job is primarily about management of web and data products – previous experience in science is desirable but not necessary, applications are very welcome from anyone with a passion for developing and delivering high quality web and data products. Here’s a snippet from the job ad:

MalariaGEN aims to produce global data on natural genetic variation in parasite, mosquito and human populations, and to deliver these data via the www.malariagen.net website, alongside web tools which add value by enabling people to explore, understand and analyse the data. Some of these web and data products are intended for unrestricted use by the malaria research and public health community, to inform future research directions and malaria control policy. Other web and data products are being developed for private use by researchers contributing to MalariaGEN community projects, and provide a key incentive to participation in MalariaGEN, e.g., secure web tools providing access to fine-grained genetic data on individual samples.

We have a unique opportunity for a Product Manager to take responsibility for the development and delivery of MalariaGEN web and data products relating to genome sequencing, genotyping and population genetic data from Plasmodium, Anopheles and human populations.

The job is being advertised both at Sanger and Oxford because you could be based at either location. Here are the job ads in full: