21 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…
Tony Clark
The Java programming language oers a number of features including: portability; graphics; networking. Java implements the ob ject-oriented execution model in terms of classes, ob jects with state, message passing and inclusion polymorphism. This work aims to provide a mixed paradigm environment which oers the…
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…
Mateusz Ujma, Nastaran Shafiei
—One of the main challenges when verifying multithreaded Java applications is the state space explosion problem. Due to thread interleavings, the number of states that the model checker has to verify can grow rapidly and impede the feasibility of verification. In the Java language, the source of thread interleavings…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
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…
George Fourtounis, Yannis Smaragdakis
Java 7 introduced programmable dynamic linking in the form of the invokedynamic framework. Static analysis of code containing programmable dynamic linking has often been cited as a significant source of unsoundness in the analysis of Java programs. For example, Java lambdas, introduced in Java 8, are a very popular…
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.…
Davide Pizzolotto, Mariano Ceccato
—Code obfuscation is a popular approach to turn program comprehension and analysis harder, with the aim of mitigating threats related to malicious reverse engineering and code tampering. However, programming languages that compile to high level bytecode (e.g., Java) can be obfuscated only to a limited extent. In fact…
Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck
The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of…
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…
Julien Ponge, Frédéric Le Mouël
Modifier les portions fonctionnelles et non-fonctionnelles des applications au cours de leur exécution est utile et parfois critique tant lors des phases de développement que de suivi en production. JooFlux est un agent JVM qui permet à la fois de remplacer dynamiquement des implémentations de méthodes que d'appliquer…
Łukasz Szeremeta
The use of computers to store and process different types of data is growing every day. The same applies to chemical data. SDF and Open Babel are recognized solutions in this field. However, each solution has its drawbacks, which are revealed in specific applications. It is important to be able to easily convert the…
Efim Grinkrug
This paper presents an approach to dynamic component composition that facilitates creating new composed components using existing ones at runtime and without any code generation. The dynamic abilities are supported by extended type notion and implementation based on additional superstructure provided with its Java API…
Felix Bänsch, Jonas Schaub, Betül Sevindik, Samuel Behr + 3 more
Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the…
Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck
The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of…
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…