10 papers · ranked by Valyu relevance
Guangjie Feng, Nick Burton, Bill Hill, Duncan Davidson + 4 more
'Janet Kerwin' 'Mark Scott' 'Susan Lindsay' 'Richard Baldock'] Background Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging…
Tobias Pietzsch, Stephan Preibisch, Pavel Tomančák, Stephan Saalfeld
Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and…
K. P. Pernstich
It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat…
Costanza Pascal, Herzeel Charlotte, Verachtert Wilfried
elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other…
Stijn de Gouw, Frank S. de Boer, Richard Bubel, Reiner Hähnle + 2 more
'Jurriaan Rot' 'Dominic Steinhöfel'] TimSort is the main sorting algorithm provided by the Java standard library and many other programming frameworks. Our original goal was functional verification of TimSort with mechanical proofs. However, during our verification attempt we discovered a bug which causes the…
Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert
Background elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory.…
Rafael Bravo, Mark Robertson-Tessi, Alexander R. A. Anderson
The Hybrid Automata Library (HAL) is a Java Library made of simple, efficient, generic components that can be used to model complex spatial systems. HAL’s components can broadly be classified into: on- and off-lattice agent containers, finite difference diffusion fields, a Gui building system, and additional tools and…
Yukun Huang, Rong Chen, Jingbo Wei, Xilong Pei + 3 more
'Prem Prakash Jayaraman' 'Rajiv Ranjan'] JNI in the Android platform is often observed with low efficiency and high coding complexity. Although many researchers have investigated the JNI mechanism, few of them solve the efficiency and the complexity problems of JNI in the Android platform simultaneously. In this paper…
Gianni D'Angelo, Salvatore Rampone
Background The huge quantity of data produced in Biomedical research needs sophisticated algorithmic methodologies for its storage, analysis, and processing. High Performance Computing (HPC) appears as a magic bullet in this challenge. However, several hard to solve parallelization and load balancing problems arise in…
Joséphine Abi-Ghanem, Djomangan Adama Ouattara
The need of digital tools for integrative analysis is today important in most scientific areas. It leads to several community-driven initiatives to standardize the sharing of data and computational workflows. However, there exists no open agnostic framework to model and implement computation workflows, in particular in…