14 papers · ranked by Valyu relevance
Andrey Tovchigrechko, Pratap Venepally, Samuel H. Payne
Summary: We present the first public release of our proteogenomic annotation pipeline. We have previously used our original unreleased implementation to improve the annotation of 46 diverse prokaryotic genomes by discovering novel genes, post-translational modifications and correcting the erroneous annotations by…
Daniele Dall’Olio, Nico Curti, Eugenio Fonzi, Claudia Sala + 3 more
'Daniel Remondini' 'Gastone Castellani' 'Enrico Giampieri'] Background Current high-throughput technologies-i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.-generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several…
Marco Aldinucci, Cristina Calcagno, Mario Coppo, Ferruccio Damiani + 5 more
'Maurizio Drocco' 'Eva Sciacca' 'Salvatore Spinella' 'Massimo Torquati' 'Angelo Troina'] The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the…
Xiaonan Wu, Hongfang Lu, Shijuan Wu
Geological conditions along long distance pipelines are complex. In consideration of differences in elevation and terrain obstacles, long distance pipelines are commonly laid through tunnels. Oil and gas pipelines are often laid side by side to reduce construction costs and minimize geological impact. The layout and…
Marcin Cieślik, Cameron Mura
Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In…
Federica Marone, Alain Studer, Heiner Billich, Leonardo Sala + 1 more
'Marco Stampanoni'] Sub-second full-field tomographic microscopy at third-generation synchrotron sources is a reality, opening up new possibilities for the study of dynamic systems in different fields. Sustained elevated data rates of multiple GB/s in tomographic experiments will become even more common at…
Marek Sztuka, Krzysztof Kotlarz, Magda Mielczarek, Piotr Hajduk + 2 more
'Jakub Liu' 'Joanna Szyda'] Title: Abstract This study compared computational approaches to parallelization of an SNP calling workflow. The data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome…
Michael Grauer, Patrick Reynolds, Marion Hoogstoel, Francois Budin + 2 more
'Martin A. Styner' 'Ipek Oguz'] Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that…
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki + 3 more
'Hikaru Inoue' 'Rui Yamaguchi' 'Satoru Miyano'] Background Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics…
Onur Yukselen, Osman Turkyilmaz, Ahmet Rasit Ozturk, Manuel Garber + 1 more
'Alper Kucukural'] Background The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and…
Patrizio Dazzi
Embarrassingly parallel problems are characterised by a very small amount of information to be exchanged among the parts they are split in, during their parallel execution. As a consequence they do not require sophisticated, low-latency, high-bandwidth interconnection networks but can be efficiently computed in…
Yuxing Zhang, Caigang Ge, Ziru Chang, Yanxia Du + 3 more
'Zitao Jiang' 'Thomas Fiedler'] By monitoring the alternating interference voltage at the intersections and parallels of gas pipelines with high-speed railways, the alternating voltage between the high-speed railway track supports and the ground, the alternating ground voltage gradient along parallel and perpendicular…
Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
Background R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example…
Paul Cardosi, Bérenger Bramas, Bilal Alatas
Parallelization is needed everywhere, from laptops and mobile phones to supercomputers. Among parallel programming models, task-based programming has demonstrated a powerful potential and is widely used in high-performance scientific computing. Not only does it allow efficient parallelization across distributed…