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Research IT


The Research IT facility has the mission to develop solid and sustainable Information Technology (IT) infrastructure to provide state-of-the-art IT services to NKI-AvL researchers.

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Services we offer:

  • High Performance Computing (HPC) and Storage on local HPC servers
  • A source code repository for researchers and projects
  • Access to the national Life Science Grid of SURFsara
  • Hosting of research group and publication websites
  • Archiving of research data sets
  • Data integration and project management consultancy (focusing on clinical and molecular data)

In development are:

  • A patient centric data warehouse aggregating (and integrating) clinical and research data sources
  • Front end for researchers to inspect the data catalogue and make data requests
  • A data stewardship platform for securing and sharing research data
  • Front end for Principle Investigators, researchers and data managers to manage data for projects, research groups and core facilities

We achieve our goals by participating in local, national, and international projects. Projects we take part in include the Datawarehouse project (NKI-AvL), the Next Generation Sequencing project (NKI-AvL), the CombatCancer project (ERC Synergy grant, a collaboration between Sanger and NKI) and the Center for Translational Molecular Medicine Translational Research IT project (CTMM-TraIT, national level).

We collaborate with the Center for Personalised Cancer Treatment (CPCT, national level), the Mouse Clinic for Cancer and Ageing (MCCA, national), the Core Facility for Molecular Pathology and Biobanking (CF-MPB, NKI-AvL), the Molecular Diagnostics unit at the Pathology department (AvL), the Computational Cancer Biology laboratory (NKI) and the central IT department, including the Library (I&A, NKI-AvL).

As a team we have adopted SCRUM methodology.

This is our team:
- Jelle ten Hoeve (bioinformatician, head)
- Robbert Hardenberg (data manager and scrum master)
- Jan Hudeček (scientific programmer, TraIT liason)
- Rubayte Rahman (bioinformatician, CombatCancer/NGS project liason)
- Henk van de Pol (data integration specialist)
- Bisheng Liu (software architect, MCCA liason)
- Wouter Kievit (student/software developer, CF-MPB liason)
- Ruben Moritz (Bioinformatician for projects for Pathology and AKL)

The Team of Research IT

Ten Hoeve, Jelle

Jelle ten Hoeve

Bioinformatician, Head of Research IT Facility

Experience

As a bioinformatician I

  1. participate in many research projects for which I perform computational analyses;
  2. support researchers that perform computational analyses themselves;
  3. set up the NKI-wide IT infrastructure for computational analysis;
  4. develop tools and software ranging from simple  scripts for basic computational analyses to full end-user applications and
  5. am involved in national en international consortia representing the NKI as a computational biologist.
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Hardenberg, Robbert

Robbert Hardenberg

Data Manager

Experience

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Hudecek, Jan

Jan Hudeček

Scientific Programmer

Personal details

Experience

I'm a web developer and bioinformatician. I've received an MSc in Distributed Computing from VU.

I maintain the datawarehousing applications  we use - tranSMART and cBioPortal as a part of CTMM TraIT. I'm also developing an application for managing data flows in the datawarehouse codenamed Skyfall. I'm responsible for inventing crazy codenames, too. I work mostly in Java, Groovy, .NET and Javascript. I have about 10 years of experience in programming professionally.

NKI is a great place to work - freedom to pursue projects, young and smart coworkers to learn from and have fun with and helping to cure cancer!

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Liu, Bisheng (web).jpg

Bisheng Liu

Bioinformatician

Personal details

Experience

I am interested in biology and computer science. I did my PhD in viral hepatitis infection in Erasmus MC.

My main project is to develop a website  for the mouse database for the mouse clinic - transgenic core facility (http://www.mccanet.nl/)



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Moritz, Ruben

Ruben Moritz

Bioinformatician

Personal details

Experience

Researcher within the Research IT team of the NKI-AVL.

Currently working in projects for Pathology and the clinical chemistry
department (AKL). These projects include: data management, data research, data
analytics, pipeline control and management and software development in multiple
programming languages(front-end and back-end).

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Pol, van der Henk

Henk van der Pol

Data Integration Specialist

Experience

Datamanager DataWareHouse facility.

Combining of Datasources  for analysis and reporting.

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Rahman, Rubayte

Rubayte Rahman

Bioinformatician

Experience

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van Geffen, Simone

Simone van Geffen

Student

Experience

During my Bachelor's degree in Medical Informatics (AMC/UvA) I worked as an intern with Jelle ten Hoeve and Hugo Horlings, in a Pathology/Research IT project on data sharing in translational research.

Now, I work on creating resources for NKI researchers to help them manage their data in adherence to internal and Dutch guidelines. 

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