Sergio Maffioletti

SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid

The identification and characterization of peptides from MS/MS data represents a critical aspect of proteomics. It has been the subject of extensive research in bioinformatics resulting in the generation of a fair number of identification software tools. Most often, only one program with a specific and unvarying set of parameters is selected for identifying proteins. Hence, a significant proportion of the experimental spectra do not match the peptide sequences in the screened database due to inappropriate parameters or scoring schemes. The Swiss protein identification toolbox (swissPIT) project provides the scientific community with an expandable multitool platform for automated in‐depth analysis of MS data also able to handle data from high‐throughput experiments. With swissPIT many problems have been solved: The missing standards for input and output formats (A), creation of analysis workflows (B), unified result visualization (C), and simplicity of the user interface (D). Currently, swissPIT supports four different programs implementing two different search strategies to identify MS/MS spectra. Conceived to handle the calculation‐intensive needs of each of the programs, swissPIT uses the distributed resources of a Swiss‐wide computer Grid (http://www.swing‐grid.ch).

The SwissBioGrid Project : objectives, preliminary results and lessons learned

Modern biology has become a science of information, analysis and prediction, coalescing into computational biology - a single discipline at the crossroads of life sciences, informatics, and mathematics. New developments in information and communications technology as well as high-performance computing enable researchers to address new demanding scientific problems which seemed far out of reach only a few years ago. The computational requirements of most applications in computational biology differ significantly from the requirements of other users of highthroughput computing such as high energy physics. To address these needs, the SwissBioGrid initiative, a collaboration among several partner institutions with a broad spectrum of expertise, was started over a year ago. In this paper, we report on its current status and achievements as well as the lessons learned which are of interest to the wider e-Science and Grid communities.

swissPIT: A novel approach for pipelined analysis of mass spectrometry data

The identification and characterization of peptides from tandem mass spectrometry (MS/MS) data represents a critical aspect of proteomics. Today, tandem MS analysis is often performed by only using a single identification program achieving identification rates between 10-50% (Elias and Gygi, 2007). Beside the development of new analysis tools, recent publications describe also the pipelining of different search programs to increase the identification rate (Hartler et al., 2007; Keller et al., 2005). The Swiss Protein Identification Toolbox (swissPIT) follows this approach, but goes a step further by providing the user an expandable multi-tool platform capable of executing workflows to analyze tandem MS-based data. One of the major problems in proteomics is the absent of standardized workflows to analyze the produced data. This includes the pre-processing part as well as the final identification of peptides and proteins. The main idea of swissPIT is not only the usage of different identification tool in parallel, but also the meaningful concatenation of different identification strategies at the same time. The swissPIT is open source software but we also provide a user-friendly web platform, which demonstrates the capabilities of our software and which is available at http://swisspit.cscs.ch upon request for account.

The SwissBioGrid Project: Objectivse, Preliminary Results and Lessons Learned

Modern biology has become a science of information, analysis and prediction, coalescing into computational biology -- a single discipline at the crossroads of life sciences, informatics, and mathematics. New developments in information and communications technology as well as high-performance computing enable researchers to address new demanding scientific problems which seemed far out of reach only a few years ago. The computational requirements of most applications in computational biology differ significantly from the requirements of other users of highthroughput computing such as high energy physics. To address these needs, the SwissBioGrid initiative, a collaboration among several partner institutions with a broad spectrum of expertise, was started over a year ago. In this paper, we report on its current status and achievements as well as the lessons learned which are of interest to the wider e-Science and Grid communities.

The Swiss ATLAS Grid

In this paper the technical solutions, the usage and the future development of the Swiss ATLAS Grid are presented. In 2009 the Swiss ATLAS Grid consists of four clusters with about 2000 shared computing cores and about 250 TB of disk space. It is based on middlewares provided by the NorduGrid Collaboration and the EGEE project. It supports multiple virtual organisations and uses additional middleware, developed by the ATLAS collaboration, for data management. The Swiss ATLAS grid is interconnected with both NorduGrid and the Worldwide LHC Grid. This infrastructure primarly serves Swiss research institutions working within the ATLAS experiment at LHC, but is open for about two thousand users on lower priority. The last three years about 80 000 wall clock time days have been processed by ATLAS jobs on the Swiss ATLAS Grid.

Initializing a National Grid Infrastructure Lessons Learned from the Swiss National Grid Association Seed Project

In addition to multi-national Grid infrastructures, several countries operate their own national Grid infrastructures to support science and industry within national borders. These infrastructures have the benefit of better satisfying the needs of local, regional and national user communities. Although Switzerland has strong research groups in several fields of distributed computing, only recently a national Grid effort was kick-started to integrate a truly heterogeneous set of resource providers, middleware pools, and users. In the following article we discuss our efforts to start Grid activities at a national scale to combine several scientific communities and geographical domains. We make a strong case for the need of standards that have to be built on top of existing software systems in order to provide support for a heterogeneous Grid infrastructure.

Grid Activities of the Swiss National Supercomputing Centre CSCS

ABSTRACT Grid Computing is addressing the new paradigm of collaborative science, where discoveries are being sought in large national and international collaborations. Grids provide a means to share resources between different scientific communities. The aim is not only to enable collaborations through resource sharing, but also to make optimal use of each participating resource, trying to maximize the overall resource capacity to the benefit of science. Researchers throughout Switzerland have already engaged in several Grid-related projects of national and international scope. The Swiss National Supercomputing Centre CSCS is involved in many of these projects. This article describes some of the projects and their aims, and gives a brief overview on the next steps that may be taken to prepare Switzerland for the future in Grid technology.