TY  - CONF
T1  - RapidBrain: Developing a Portal for Brain Research Imaging
T2  - All Hands Meeting 2011, York
Y1  - 2011
A1  - Kenton D'Mellow
A1  - Rodríguez, David
A1  - Carpenter, Trevor
A1  - Jos Koetsier
A1  - Dominic Job
A1  - van Hemert, Jano
A1  - Wardlaw, Joanna
A1  - Fan Zhu
AB  - Brain imaging researchers execute complex multistep workflows in their computational analysis. Those workflows often include applications that have very different user interfaces and sometimes use different data formats. A good example is the brain perfusion quantification workflow used at the BRIC (Brain Research Imaging Centre) in Edinburgh.  Rapid provides an easy method for creating portlets for computational jobs, and at the same it is extensible.  We have exploited this extensibility with additions that stretch the functionality beyond the original limits. These changes can be used by other projects to create their own portals, but it should be noted that the development of such portals involve a greater effort than the required in the regular use of Rapid for creating portlets. In our case it has been used to provide a user-friendly interface for perfusion analysis that covers from volume
JF  - All Hands Meeting 2011, York
CY  - York
ER  - 

TY  - CONF
T1  - TOPP goes Rapid
T2  - Cluster Computing and the Grid, IEEE International Symposium on
Y1  - 2010
A1  - Gesing, Sandra
A1  - van Hemert, Jano
A1  - Jos Koetsier
A1  - Bertsch, Andreas
A1  - Kohlbacher, Oliver
AB  - Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for analysis. TOPP and OpenMS are open-source packages for proteomics data analysis; however, they do not provide support for Grid computing. In this work we present a portal interface for high-throughput data analysis with TOPP. The portal is based on Rapid, a tool for efficiently generating standardized portlets for a wide range of applications. The web-based interface allows the creation and editing of user-defined pipelines and their execution and monitoring on a Grid infrastructure. The portal also supports several file transfer protocols for data staging. It thus provides a simple and complete solution to high-throughput proteomics data analysis for inexperienced users through a convenient portal interface.
JF  - Cluster Computing and the Grid, IEEE International Symposium on
PB  - IEEE Computer Society
CY  - Los Alamitos, CA, USA
SN  - 978-0-7695-4039-9
ER  - 

TY  - CONF
T1  - Grid Infrastructures for Secure Access to and Use of Bioinformatics Data: Experiences from the BRIDGES Project
T2  - Proceedings of the First International Conference on Availability, Reliability and Security, ARES
Y1  - 2006
A1  - Richard O. Sinnott
A1  - Micha Bayer
A1  - A. J. Stell
A1  - Jos Koetsier
JF  - Proceedings of the First International Conference on Availability, Reliability and Security, ARES
T3  - Proceedings of the The First International Conference on Availability, Reliability and Security
CY  - Vienna, Austria
ER  - 

TY  - CONF
T1  - A Shibboleth-Protected Privilege Management Infrastructure for e-Science Education
T2  - Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006
Y1  - 2006
A1  - J. Watt
A1  - Oluwafemi Ajayi
A1  - J. Jiang
A1  - Jos Koetsier
A1  - Richard O. Sinnott
KW  - security
JF  - Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2006
PB  - IEEE Computer Society
CY  - Singapore
ER  -