Java Library Research Articles

JOOQ-JAVA OBJECT ORIENTED QUERYING

JOOQ is a query language as derived from SQL or JOOQ is a query language in which SQL uses the objects of OOQ. As there are many issues in integration of java application with various databases via JDBC. This paper proposes a new java library known as JOOQ. The primary aim of JOOQ focuses on integration issues in java programming language. With JOOQ, programmers can write SQL queries in a simpler and faster way. JOOQ thus decreases the programming effort by 10-20% which leads to higher quality of code with low error rate. Thus the application is also significantly light and less prone to errors.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

BackgroundAdvances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered.FindingsFastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines.ConclusionsThe accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Program SummaryProgram title: JaSTA: Java Superposition T-matrix App.Catalogue identifier: AETB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 571570No. of bytes in distributed program, including test data, etc.: 120226886Distribution format: tar.gzProgramming language: Java, Fortran95.Computer: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler; Developed on 2.40 GHz Intel Core i3.Operating system: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler.RAM: Ranging from a few Mbytes to several Gbytes, depending on the input parameters.Classification: 1.3.External routines: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] (3D visualization).Nature of problem: Optical properties of cosmic dust aggregates.Solution method: Java application based on Mackowski and Mischenko’s Superposition T-Matrix code.Restrictions: The program is designed for single processor systems.Additional comments: The distribution file for this program is over 120 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent.Running time: Ranging from few minutes to several hours, depending on the input parameters.

Jannovar: A Java Library for Exome Annotation

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar.

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

FastMPJ: a scalable and efficient Java message-passing library

The performance and scalability of communications are key for high performance computing (HPC) applications in the current multi-core era. Despite the significant benefits (e.g., productivity, portability, multithreading) of Java for parallel programming, its poor communications support has hindered its adoption in the HPC community. This paper presents FastMPJ, an efficient message-passing in Java (MPJ) library, boosting Java for HPC by: (1) providing high-performance shared memory communications using Java threads; (2) taking full advantage of high-speed cluster networks (e.g., InfiniBand) to provide low-latency and high bandwidth communications; (3) including a scalable collective library with topology aware primitives, automatically selected at runtime; (4) avoiding Java data buffering overheads through zero-copy protocols; and (5) implementing the most widely extended MPI-like Java bindings for a highly productive development. The comprehensive performance evaluation on representative testbeds (InfiniBand, 10 Gigabit Ethernet, Myrinet, and shared memory systems) has shown that FastMPJ communication primitives rival native MPI implementations, significantly improving the efficiency and scalability of Java HPC parallel applications.

Efficient ring perception for the Chemistry Development Kit

BackgroundThe Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings. The rings of a structure are used areas including descriptors, stereochemistry, similarity, screening and atom typing. The CDK includes multiple algorithms for determining the rings of a structure on demand. Non-unique descriptions of rings were often used due to the slower performance of the unique alternatives.ResultsEfficient algorithms for handling chemical ring perception have been implemented and optimised in the CDK. The algorithms provide much faster computation of new and existing types of rings. Several optimisation and implementation considerations are discussed which improve real case usage. The performance is measured on several publicly available data sets and in several cases the new implementations were found to be more than an order of magnitude faster.ConclusionsAlgorithmic improvements allow handling of much larger datasets in reasonable time. Faster computation allows more appropriate rings to be utilised in procedures such as aromaticity. Several areas that require ring perception have also seen a noticeable improvement. The time taken to compute the unique rings is now comparable allowing a correct usage throughout the toolkit. All source code is open source and freely available.

MATLAB-Like Scripting of Java Scientific Libraries in ScalaLab

Although there are a lot of robust and effective scientific libraries in Java, the utilization of these libraries in pure Java is difficult and cumbersome, especially for the average scientist that does not expertise in software development. We illustrate that ScalaLab presents an easier and productive MATLAB like front end. Also, the main strengths and weaknesses of the core Java libraries of ScalaLab are elaborated. Since performance is of paramount importance for scientific computation, the article discusses extensively performance aspects of the ScalaLab environment. Also, Java bytecode performance is compared to native code.

JINDY: A java library to support invokedynamic

Java 7 has included the new invokedynamic opcode in the Java virtual machine. This new instruction allows the user to define method linkage at runtime. Once the link is established, the virtual machine performs its common optimizations, providing better runtime performance than reflection. However, this feature has not been offered at the abstraction level of the Java programming language. Since the functionality of the new opcode is not provided as a library, the existing languages in the Java platform can only use it at the assembly level. For this reason, we have developed the JINDY library that offers invokedynamic to any programming language in the Java platform. JINDY supports three modes of use, establishing a trade-off between runtime performance and flexibility. A runtime performance and memory consumption evaluation is presented. We analyze the efficiency of JINDY compared to reflection, the MethodHandle class in Java 7 and the Dynalink library. The memory and performance costs compared to the invokedynamic opcode are also measured.

Understanding software artifact provenance

In a well designed software system, units of related functionality are organized into modules and classes, which are in turn arranged into inheritance trees, package hierarchies, components, libraries, frameworks, and services. The trade-offs between simplicity versus flexibility and power are carefully considered, and interfaces are designed that expose the key functional properties of a component while hiding much of the complexity of the implementation details. However, over time the design integrity of a well-engineered system tends to decay as new features are added, as new quality attributes are emphasized, and as old architectural knowledge is lost when experienced development personnel shift to new jobs. Consequently, as developers and as users we often find ourselves looking at a piece of functionality or other design artifact and wondering, “Why is this here?” That is, we would like to examine the provenance of an artifact to understand its history and why it is where it is within the current design of the system. In this brief paper, we sketch some of the dimensions of the broad problem of extracting and reasoning about the provenance of software development artifacts. As a motivating example, we also describe some recent related work that uses hashing to quickly and accurately identify version information of embedded Java libraries.

Binary social impact theory based optimization and its applications in pattern recognition

The human opinion formation can be understood as a social approach to optimization. In the real world, the opinions on different issues encode a “candidate solution”, which is evaluated by a complex and unknown fitness function. The computer models of such processes can be easily modified by introducing a fitness value, which leads to novel family of optimization techniques. This paper demonstrates how the novel algorithms can be derived from opinion formation models and empirically demonstrates their usability in the area of binary optimization. Particularly, it introduces a general SITO algorithmic framework and describes four algorithms based on this general framework. Recent applications of these algorithms to pattern recognition in electronic nose, electronic tongue, new born EEG and ICU patient mortality prediction are discussed. Finally, an open source SITO library for MATLAB and JAVA is introduced.

The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies

The semantic measures library and toolkit are robust open-source and easy to use software solutions dedicated to semantic measures. They can be used for large-scale computations and analyses of semantic similarities between terms/concepts defined in terminologies and ontologies. The comparison of entities (e.g. genes) annotated by concepts is also supported. A large collection of measures is available. Not limited to a specific application context, the library and the toolkit can be used with various controlled vocabularies and ontology specifications (e.g. Open Biomedical Ontology, Resource Description Framework). The project targets both designers and practitioners of semantic measures providing a JAVA library, as well as a command-line tool that can be used on personal computers or computer clusters. Downloads, documentation, tutorials, evaluation and support are available at http://www.semantic-measures-library.org.

Bubble fountain with wandering black hole

Programming assignments with graphics elements may be used to spark student interest and enthusiasm, especially in early courses. We have created a sequence of CS I labs, built on the ACM Java Library, which culminates in a Bubble Fountain with Wandering Black Hole, where a particle emitter spews colorful bubbles that bounce around the graphics window while a larger black circle, also bouncing around the window, consumes any particles that cross its path. This assignment requires that students extend an oval class (GOval) from the graphics library. The following is the class hierarchy: • circle: an oval that has same width and height, always • smart-circle: a circle that knows where it is relative to the edges of its graphics window (canvas) • moving-circle: a smart-circle with its own displacement that knows how to move inside its window, bouncing against the boundaries • particle: a moving-circle with a built-in lifetime. When the lifetime expires, the object is removed from the canvas.

Using Biological Pathway Data with Paxtools

A rapidly growing corpus of formal, computable pathway information can be used to answer important biological questions including finding non-trivial connections between cellular processes, identifying significantly altered portions of the cellular network in a disease state and building predictive models that can be used for precision medicine. Due to its complexity and fragmented nature, however, working with pathway data is still difficult. We present Paxtools, a Java library that contains algorithms, software components and converters for biological pathways represented in the standard BioPAX language. Paxtools allows scientists to focus on their scientific problem by removing technical barriers to access and analyse pathway information. Paxtools can run on any platform that has a Java Runtime Environment and was tested on most modern operating systems. Paxtools is open source and is available under the Lesser GNU public license (LGPL), which allows users to freely use the code in their software systems with a requirement for attribution. Source code for the current release (4.2.0) can be found in Software S1. A detailed manual for obtaining and using Paxtools can be found in Protocol S1. The latest sources and release bundles can be obtained from biopax.org/paxtools.

UML2SC: A tool for developing complex electronic systems using UML and SystemC

In this paper, we propose a transformation process in which SystemC skeleton code is extracted from UML models that describe hardware/software based systems. The tool UML2SC, which is based on Java libraries, is also introduced. This tool allows the transformation of UML class and composite structure diagrams to SystemC skeleton code. An implementation example is given to illustrate the transformation process implemented in the UML2SC tool. The example describes the model of a CPU RISC of 16 bits.

MulticoreBSP for C: A High-Performance Library for Shared-Memory Parallel Programming

The bulk synchronous parallel (BSP) model, as well as parallel programming interfaces based on BSP, classically target distributed-memory parallel architectures. In earlier work, Yzelman and Bisseling designed a MulticoreBSP for Java library specifically for shared-memory architectures. In the present article, we further investigate this concept and introduce the new high-performance MulticoreBSP for C library. Among other features, this library supports nested BSP runs. We show that existing BSP software performs well regardless whether it runs on distributed-memory or shared-memory architectures, and show that applications in MulticoreBSP can attain high-performance results. The paper details implementing the Fast Fourier Transform and the sparse matrix---vector multiplication in BSP, both of which outperform state-of-the-art implementations written in other shared-memory parallel programming interfaces. We furthermore study the applicability of BSP when working on highly non-uniform memory access architectures.

The BioPAX Validator

Summary: BioPAX is a community-developed standard language for biological pathway data. A key functionality required for efficient BioPAX data exchange is validation—detecting errors and inconsistencies in BioPAX documents. The BioPAX Validator is a command-line tool, Java library and online web service for BioPAX that performs >100 classes of consistency checks.Availability and implementation: The validator recognizes common syntactic errors and semantic inconsistencies and reports them in a customizable human readable format. It can also automatically fix some errors and normalize BioPAX data. Since its release, the validator has become a critical tool for the pathway informatics community, detecting thousands of errors and helping substantially increase the conformity and uniformity of BioPAX-formatted data. The BioPAX Validator is open source and released under LGPL v3 license. All sources, binaries and documentation can be found at sf.net/p/biopax, and the latest stable version of the web application is available at biopax.org/validator.Contact: igor.rodchenkov@utoronto.ca or gary.bader@utoronto.ca

Scalable transactions across heterogeneous NoSQL key-value data stores

Many cloud systems provide data stores with limited features, especially they may not provide transactions, or else restrict transactions to a single item. We propose a approach that gives multi-item transactions across heterogeneous data stores, using only a minimal set of features from each store such as single item consistency, conditional update, and the ability to include extra metadata within a value. We offer a client-coordinated transaction protocol that does not need a central coordinating infrastructure. A prototype implementation has been built as a Java library and measured with an extension of YCSB benchmark to exercise multi-item transactions.

ENZPRED-Enzymatic Protein Class Predicting by Machine Learning

Recent times have seen flooding of biological data into the scientific community. Due to increase in large amounts of data from genome and other sequencing projects become available, being diverted on to Insilco approach for data collection and prediction has become a priority also progresses in sequencing technologies have found an exponential function rise in the number of newly found enzymes. Commonly, function of such enzymes is determined by experiments that can be time consuming and costly. As new approaches are needed to determine the functions of the proteins these genes encode. The protein parameters that can be used for an enzyme/ non-enzyme classification includes features of sequences like amino acid composition, dipeptide composition, grand Average of hydropathicity (GRAVY), probability of being in alpha helix, probability of being in beta sheet Probability of being in a turn. We show how large-scale computational analysis can help to address this challenge by help of java and support vector machine library. In this paper, a recently developed machine learning algorithm referred to as the svm library Learning Machine is used to classify protein sequences with six main classes of enzyme data downloaded from a public domain database. Comparative studies on different type of kernel methods like 1.radial basis function, 2.polynomial available in SVM library. Results show that RBF method take less time in training and give more accurate result then other kernel methods to also less training time compared to other kernel methods. The classification accuracy of RBF is also higher than various methods in respect of available sequences data.

Concurrent libraries with foresight

Linearizable libraries provide operations that appear to execute atomically. Clients, however, may need to execute a sequence of operations (a composite operation) atomically. We consider the problem of extending a linearizable library to support arbitrary atomic composite operations by clients. We introduce a novel approach in which the concurrent library ensures atomicity of composite operations by exploiting information (foresight) provided by its clients. We use a correctness condition, based on a notion of dynamic right-movers, that guarantees that composite operations execute atomically without deadlocks, and without using rollbacks. We present a static analysis to infer the foresight information required by our approach, allowing a compiler to automatically insert the foresight information into the client. This relieves the client programmer of this burden and simplifies writing client code. We present a generic technique for extending the library implementation to realize foresight-based synchronization. This technique is used to implement a general-purpose Java library for Map data structures -- the library permits composite operations to simultaneously work with multiple instances of Map data structures. We use the Maps library and the static analysis to enforce atomicity of a wide selection of real-life Java composite operations. Our experiments indicate that our approach enables realizing efficient and scalable synchronization for real-life composite operations.