In this era of explosive high throughput (HT) data in molecular biology, there is a growing need for accessible software solutions that can help unlock biological/clinical characteristics from such data. With the biomedical researcher (with limited or no bioinformatics skills) in mind, we developed a comprehensive open access web-based platform called R2 (r2.amc.nl). R2 aids in the analysis and visualization of public as well as private/shielded high throughput data and their associated annotated features. Because the R2 bioinformatics team is embedded in a molecular biology research group, development of the platform was guided by requirements of molecular biologists, thereby contributing to its user friendliness.

Over the years the R2 platform has expanded greatly, offering analyses and visualizations for many types of omics data. The platform has been cited in PubMed >730 times and been used in publications including Nature and Cell. We are currently refactoring many parts of the platform, to prepare for the future.

You will be helping the team with implementations in the R2 platform making use of Perl / R / JavaScript / Python programming / scripting languages.

You can also participate in our user support and data processing activities (building / maintaining / executing pipe lines for the diverse data types and formats) for the R2 platform.

Finally you can participate in data-mining tasks that we are performing for a number of internal and (inter)-national collaborations.

As such our ideal candidate is a well-organized and analytical thinker, who additionally has:

• A BSc in (Bio)informatics or equivalent (required);

• Proficiency in English (required);

• Excellent programming skills in Perl, Javascript or equivalent languages (required);

• Experience with database and software design (MySQL, UML);

• Experience with version control systems, github, svn;

• Experience with open source software;

• Affinity with molecular biology data;

• Familiarity with Linux operating systems;

• Ample opportunities for education and broadening of your scope. A place to grow. Being employed in the • a temporary, full time  employment as scientific programmer (Datamanager) by AMC Medical Research BV;

• a range of added fringe benefits, such as an annual bonus of 8.3 %, holiday allowance, collective discounted rates for a number of insurances, an attractive bicycle scheme and/or public transport allowance, and free parking.

• a salary in line with the Collective Labor Agreement for University Medical Centers in the Netherlands (CAO UMC). The gross monthly salary ranges from EUR 2.212 to EUR 3.202, depending on your skills and experience;

AMC Medical Research

The AMC is more than just a hospital. It is a world in which patient care, research and education are integrated, and in which people are always central. It is an academic world full of possibilities for talented individuals that are looking for a place where they can excel. Thinking big, daring to dream, cooperating internationally. And never letting yourself be put off by ‘It’s not possible’ or ’It won’t work anyway’. That is the AMC mentality.

http://www.amc.nl/

You will work within the group of Dr. Jan Koster, who has conceived the R2 platform and is leading a small team of bioinformaticians within the department of Oncogenomics (AMC, Amsterdam). The group has been involved in many (inter-)national projects relating to many aspects of genomics (WGS, RNAseq, gene expression profiling, methylation profiling, etc). Much of our work is in the field of pediatric cancer, with emphasis to neuroblastoma. However, we also collaborate with groups in other fields of oncology.