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LABORATORY & STATISTICAL SCIENCE


Mount Sinai reduces genomic sequencing time


Mount Sinai School of Medicine in New York has implemented an Avere Systems FXT Series to reduce job processing times of I/O intensive genomic sequencing research. Modern experimental technologies for genetic and genome sequencing projects involve massive datasets that require researchers to not only think about the biology of their projects, but the technologies needed to handle the analysis of hundreds of millions of genomic sequences generated. ‘Organisations performing data- intensive operations have, for too long, got by with a “good enough” approach to their computational needs,’ said Ron Bianchini, CEO at Avere. ‘They too often accept read/write times as fi xed, turn to over-provisioning of disk-based systems or add expensive Flash, aimlessly, to make up for this loss. By implementing automatically tiered NAS appliances, like the FXT 2300,


organisations like Mount Sinai School of Medicine can accelerate read and write workloads by dynamically moving data in real time to the most appropriate storage tier to improve the cost/ performance ratio without additional administrative overhead.’ The Avere FXT Series contains both solid state storage and traditional hard drives to optimise performance without compromises on all types of workloads. Reads, writes, and metadata are allocated to storage media via Avere’s dynamic tiering. Allocation algorithms running on the FXT appliances monitor access frequency patterns and workload type and manage data placement on multiple internal tiers. This increases performance, distributes the workload in the cluster and minimises requests to the mass storage server. Movement of data occurs automatically in real- time and at the fi le or block level.


AB Sciex and GeneBio announce joint solutions


AB Sciex and Geneva Bioinformatics (GeneBio) SA will be co-marketing joint solutions to improve the ability of scientists to conduct rapid screening of large sets of molecules. GeneBio’s SmileMS software provides advanced library searching capabilities that can be used with AB Sciex’s mass spectrometers and software applications.


SmileMS can be used with the broad range of AB Sciex systems, including triple quadrupole and QTRAP systems, as well as the new TripleTOF 5600 System; a high-resolution mass spectrometer for high-performance qualitative


4 SCIENTIFIC COMPUTING WORLD


and quantitative analysis. SmileMS has the capability to process a wide range of data, including high mass accuracy MS and MS/MS data. This GeneBio software


complements AB Sciex’s Analyst and Cliquid software as well as being fully compatible with AB SCIEX’s LC/MS/MS libraries for forensic, pesticide, veterinary and antibiotics analysis. Adapted to fast routine analysis, SmileMS also allows in-depth evaluation of results for use in food testing, pharmaceutical research, environmental testing and biomedical research.


PROGRAMS PREDICT PROTEIN COMPLEXES


The fi rst extensive study demonstrating the ability to use computational docking programs to predict protein- protein interactions has been done through the use of facilities at the Barcelona Supercomputing Center. The research presented in the article Towards the prediction of protein interaction partners using physical docking, and published in the journal Molecular Systems Biology, was carried out by Mark Wass and Gloria Fuentes, from the Spanish National Cancer Research Centre (CNIO); Carles Pons from the Barcelona Supercomputer Center (BSC); and Florencio Pazos, from the Spanish National Centre for Biotechnology (CNB- CSIC), under the direction of Alfonso Valencia, head of the CNIO’s Structural Biology and Biocomputing programme. ‘In this study we showed,


for the fi rst time, that a docking method can be used to differentiate between interacting and non-interacting proteins.


We observed that the score distribution of interacting proteins can be distinguished from that of non-interacting proteins. This fi nding was possible after running more than 100,000 docking experiments using the MareNostrum supercomputer,’ commented Carles Pons, from the BSC.


The authors used protein docking programs, which are normally used to model the details of the structure of complexes between proteins already known to interact, to detect the components of protein complexes scanning large collections of protein structures. Protein complexes are central to all the processes occurring in our cells, but to date only a small fraction of the composition and molecular details of their interaction have been characterised. This knowledge is essential for the understanding of the consequences of mutations and for the development of potential inhibitors.


David Sexton joins Sapio Sciences


Sapio Sciences has announced that David Sexton has joined the company as director of consulting. Sexton was previously the director of the computational genomics core at Vanderbilt University where he managed a 24-person research resource in the Centre for Human Genetics Research. In this capacity he was responsible for architecting solutions for information technology infrastructure, bioinformatics, software development and data analysis. Sexton’s group worked


on supporting CLIA-compliant initiatives as well as research oriented projects. At Sapio, he will engage with Exemplar LIMS customers to provide project management, LIMS workfl ow design and implementation services. Sexton will also oversee Sapio’s services for next-gen sequencing (NGS) data management and analysis pipelines, as well as other high- volume data management needs such as for chemical compounds and cell imaging data.


www.scientific-computing.com


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