23 papers · ranked by Valyu relevance
Mark P Waller, Thomas Dresselhaus, Jack Yang
Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code.…
Andreas Holzinger, Mario Zupan
Background Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there…
В. А. Захаров, Yegor Bugayenko
Open Source Java Frameworks Authors: ['В. А. Захаров' 'Yegor Bugayenko'] In today's software development landscape, the extent to which Java applications utilize object-oriented programming paradigm remains a subject of interest. Although some researches point to the considerable overhead associated with object…
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of…
Pedro Martins, Rohan Achar, Cristina Videira Lopes
Large repositories of source code for research tend to limit their utility to static analysis of the code, as they give no guarantees on whether the projects are compilable, much less runnable in any way. The immediate consequence of the lack of large compilable and runnable datasets is that research that requires such…
Diego Alonso, Francisco Sánchez-Ledesma, Pedro Sánchez, Juan A. Pastor + 1 more
'Juan A. Pastor' 'Bárbara Álvarez'] The use of frameworks and components has been shown to be effective in improving software productivity and quality. However, the results in terms of reuse and standardization show a dearth of portability either of designs or of component-based implementations. This paper, which is…
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…
Md Jubair Basha N
The deployment of a software product requires considerable amount of time and effort. In order to increase the productivity of the software products, reusability strategies were proposed in the literature. However effective reuse is still a challenging issue. This paper presents a framework studio for effective…
Andrei Olaru, Monica Pricope, Roberto Teti
Current multi-agent frameworks usually use centralized, fixed communication infrastructures for the entities that are deployed using them. This decreases the robustness of the system but is less challenging when having to deal with mobile agents that can migrate between nodes. We introduce, in the context of the…
Henning Puttnies, Peter Danielis, Christian Koch, Dirk Timmermann
—On the one side, network simulation frameworks are important tools for research and development activities to evaluate novel approaches in a time- and cost-efficient way. On the other side, Java as a highly platform-independent programming language is ideally suited for rapid prototyping in heterogeneous scenarios.…
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…
Safeeullah Soomro, Mohammad Riyaz Belgaum, Zainab Alansari, Mahdi H. Miraz
'Mahdi H. Miraz'] Abstract— In the domain of Software Engineering, program analysis and understanding has been considered to be a very challenging task since decade, as it demands dedicated time and efforts. The analysis of source code may occasionally be comparatively easier due to its static nature, however, the…
Olivia W Lang, Benjamin Beer, Dean Zhang, Courtney LeSon + 3 more
The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability…
Dipesh Walia, Pankaj Pant, Mahendra Neela, Naveen Kumar + 1 more
'Ram Babu Kunchala'] The main significance of this document is two source systems namely GIPSY and DMARF. Intensional languages are required like GIPSY for absoluteness and forward practical investigations on the subject.DMARF mainly focuses on software arechetictual design and implementation on Distributed Audio…
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…
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…
Guillaume Bouffard, Vincent Giraud, Léo Gaspard
The Java Card Virtual Machine (JCVM) platform is widely deployed on security-oriented components. JCVM implementations are mainly evaluated under security schemes. However, existing implementation are close-source without detail. We believe studying how to design JCVM will improve them and it can be reused by 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…
Jamie Alnasir, Hugh P. Shanahan
The paper reviews the use of the Hadoop platform in Structural Bioinformatics applications. Specifically, we review a number of implementations using Hadoop of high-throughput analyses, e.g. ligand-protein docking and structural alignment, and their scalability in comparison with other batch schedulers and MPI. We find…
Shichen Qiao, Chen Shen
In this study, a web database application with the Flask framework was developed to implement three types of queries and visualize the results over a bioinformatical dataset from Alfalfa (Medicago sativa). A backend SQLite database was constructed from genome FASTA, population variations, transcriptome, and annotation…
Antonio Prestes García, Alfonso Rodríguez-Patón
In order to produce dependable results, the output of models must be carefully evaluated and compared to the experimental data. One of the main goals of analyzing a model is the understanding the effect of input factors on the model output. This task is carried out using a methodology known as sensitivity analysis. The…
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…
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…