Proteomics

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The Netherlands Bioinformatics for Proteomics Platform or NBPP is one of the task forces of NBIC's BioAssist programme. Its main goal is to build a software platform that will make it possible for non-experts to run a typical proteomics analysis, and for experts to experiment with different variations of the analysis.

Introduction

New technological developments in proteomics research have lead to an explosive expansion of generated data. Data sets are getting larger and more complex as the number of samples increases, and individual spectra are growing dramatically in size as resolution improves and tandem mass spectrometry options are more fully used. This leads to urgent needs for further developments of proteomics-related bioinformatics for better management and interpretation of the generated data.

The task force will be built on strong collaboration between participants. This will make it possible to integrate the different expertise of the contributing scientists. Existing tools will be collected and will be made to interoperate. New algorithms will be developed to fill the current technological gaps. All software that is developed will be distributed to the proteomics community by NBPP and NBIC in such a way that it is possible for non-experts to use it. NBPP will serve as a core analysis platform for users with little bioinformatics expertise.

Please join, you're welcome!

NBPP was set up as a collaboration between several groups in The Netherlands, but it is not limited to this original group. The NBPP is open to all other researchers, in The Netherlands as well as elsewhere. NBPP therefore is an integrative project trying to give a common platform for proteomics-related bioinformatics developments, which is unique at international level. The goal of NBPP is to become a competitive global player in technological development of proteomics-related bioinformatics.

How can you contribute?

If you work with proteomics and you want to collaborate in NBPP, please do so.

There are several ways in which you can contribute:

  • Join our Meetings of the Proteomics Task Force or subscribe to our mailing list
  • Publish your workflow. We are interested in what is happening in your group and how you use common approaches in your research. Please, add them to proteomics pipelines.
  • Make the tools you use available. If you have in-house developed scripts, filters, converters, ..., which can be used by the community, follow proteomics platform tools.
  • You can improve these Wiki pages, add more information and make existing information more complete and accurate.
  • You can test/re-use the approaches of other groups and comment on those.

Project embedding and structure

The role in NBPP among other institutes / initiative groups

The Netherlands have numerous excellent proteomics, bioinformatics and systems biology laboratories, and several groups are performing high-quality research in proteomics-related bioinformatics. However, this research field is still considered to be in its early stages compared to other research domains like genomics and transcriptomics. New analytical technologies are still emerging, and the bioinformatics research effort has to keep up with these rapid developments. Technology centres like the Netherlands Proteomics Centre aim at developing novel tools and methods to obtain faster and more reliable proteomics data. The present initiative "Bioinformatics for Proteomics" intends to supplement this initiative by creating a central forum to join and coordinate all national efforts for proteomics-related bioinformatics. To this end, the Netherlands Proteomics Centre (NPC) and the Netherlands Bioinformatics Centre (NBIC) have brought together a broad national consortium of bioinformatics groups (project leader Dr. Ir. Bas van Breukelen) and intend to finance 6 scientific positions, to address the observed major bottleneck of the NPC program as highlighted in the evaluation of NPC by the QANU-coordinated international science assessment in March 2007. To organize the research program, a committee of experts (see next chapter) in the field was formed, which outlined the aim of establishing a core group of bioinformatics research laboratories in the Netherlands with sufficient critical mass and expertise to create a Netherlands Bioinformatics for Proteomics Platform (NBPP). This platform will be closely integrated with proteomics-related bioinformatics projects of the NBIC BioRange and BioAssist, and NPC projects that are currently in progress. The main aim is the rapid and standardized deployment of powerful cutting-edge tools and functionality to the wider proteomics community. For maximal computational capacity, the platform will use the Dutch Life Science GRID (DLSG) as basic hardware infrastructure, which consists of one large GRID at SARA and several small GRID points located at several national universities interconnected via fast SURFnet research network. The DLSG points that are not yet established (e.g., at Groningen University) will be designed in collaboration with NBIC to satisfy special needs for proteomics. DLSG will provide the required computational power and large amounts of storage capacity within the BIG GRID program. The NBIC BioAssist program will provide a generic e-science infrastructure (Virtual laboratory for e-science), within their proof-of-concept environment using the most recent developments in grid-computing data management and storage systems (e.g. SDSC Storage Resource Broker), Taverna workflow management software and visualization techniques, which also enable to share tools and data.

Committee of Experts

  1. Bas van Breukelen (UU)
  2. Péter Horvatovich (RUG)
  3. Twan America (WUR)
  4. Roeland van Ham (WUR)
  5. Perry Moerland (AMC)
  6. Jeroen Krijgsveld (UU)

Research structure

The committee invited several bioinformatics groups and experts to write initial research proposals based on their activities and expertise in bioinformatics for proteomics. The research program was defined based on the submitted proposals in order to increase synergy between the bioinformatics developments, to enhance collaborations between research groups, enable higher specialization of individual researchers in defined subjects, filling gaps in expertise and development needs, and to provide and develop generic tools enhancing data management. Based on these goals the committee defined 3 work packages (WPs), plus one lead scientist and several contributing scientists for each work package. All WPs include the work of the programmer positions assigned to the participating laboratories within the BioAssist program and 2 new additional positions per work package (3 years postdoctoral or scientific programmer positions) financed by NGI via NPC and NBIC within the present initiative.

Knowledge Base

Other pages about the organization

External links

Survey on bioinformatics bottlenecks and expertise of NPC members!

Please click the following link or on the section header to see the bioinformatics bottlenecks and expertise of NPC members.

Dynamic Lightpath for high-throughput proteomics data processing

The Proteomics Platform won in 2009. 5 dynamics lightpaths for DLSG in "Enlighten your research" competition from Surfnet. Please click on the following link to get update on the current status of the connected sites and use cases.