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Poster Basel Oct 2011

SyBIT Tools for

Peter Kunszt and Ela Hunt

SyBIT has developed several tools for to manage the large volumes of data, automate processing of data, to visualize and analyze the data and also to publish and share results. We give an overview on the multitude of tools that have been developed by SyBIT until now.


ICSB 2011 Heidelberg/Mannheim
28 Aug - 2 Sept 2011

SyBIT Tools for

E Hunt and P Kunszt

SyBIT Tools for SystemsX.docx


Basel, June 23-24 2011

Wien, July 15-19 2011

FMI Annual Meeting
Saas Fee,
September 2011

QuasR : Quantify and Annotate Short Reads in R

Anita Lerch, Dimos Gaidatzis, Florian Hahne, Michael Stadler

Deep sequencing technology, due to its high throughput and low cost, has become a powerful research tool in a wide range of applications, such as RNA-seq and ChIP-seq. In the last years there have been many efforts in the bioinformatics community to provide software in R/Bioconductor to simplify the processing and the biological interpretation of such large data sets. However until now, there is no integrated start-to-end analysis solution within R that sufficiently abstracts the technical details and would be suitable for use by biologists. In particular, alignments need to be performed outside of R and genome annotation information must be manually incorporated. Here we outline the deep sequencing analysis package QuasR, a further development of the FMI deep sequencing pipeline, built to make efficient use of available hardware resources and to simplify analysis of next generation sequencing data.


BC2 Basel, June 23-24 2011

Accelerating 3D Protein Modeling Using Cloud Computing


Detailed knowledge about the protein structures in highly virulent pathogens is essential in the fight against antibiotics-resistant bacteria like new strains of streptococcus. However, to prediction a proteins structure from the amino acid sequence, researchers often do not have access to the amount of computing power they would need. In a collaboration between IBM, the ETH Zurich and the Swiss high-performance cloud computing start-up CloudBroker, we have demonstrated that this type of calculation can be done using existing Cloud Computing technology in a very reasonable amount of time. In just 10days we were able to model 249 proteins that would have otherwise taken almost a year on the computational resources available to the ETH research team. Using CloudBroker's technology to provide easy access to Rosetta on the IBM Cloud, over 30'000 work units were sent to 1000 cores in the IBM Cloud. The IBM Cloud environment is especially interesting for life science research because unlike on the Amazon EC2, access is only granted to authorized partners and customers, and data access is more strictly controlled and monitored.


XGEN 2011 San Diego

Deep Sequencing Data Management and Exploration: A Robust and Scalable Open Source Solution

Manuel Kohler, Christian Beisel, Piotr Buczek, Franz-­Josef Elmer, Kaloyan Enimanev, Ina Nissen, Tomasz Pylak, Chandrasekhar Ramakrishnan, John Ryan, Marcel Czink and Bernd Rinn



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