Java Library Research Articles

Gene-set activity toolbox (GAT): A platform for microarray-based cancer diagnosis using an integrative gene-set analysis approach.

Cancer is a complex disease that cannot be diagnosed reliably using only single gene expression analysis. Using gene-set analysis on high throughput gene expression profiling controlled by various environmental factors is a commonly adopted technique used by the cancer research community. This work develops a comprehensive gene expression analysis tool (gene-set activity toolbox: (GAT)) that is implemented with data retriever, traditional data pre-processing, several gene-set analysis methods, network visualization and data mining tools. The gene-set analysis methods are used to identify subsets of phenotype-relevant genes that will be used to build a classification model. To evaluate GAT performance, we performed a cross-dataset validation study on three common cancers namely colorectal, breast and lung cancers. The results show that GAT can be used to build a reasonable disease diagnostic model and the predicted markers have biological relevance. GAT can be accessed from http://gat.sit.kmutt.ac.th where GAT's java library for gene-set analysis, simple classification and a database with three cancer benchmark datasets can be downloaded.

Xtraitj : Traits for the Java platform

Abstract Traits were proposed as a mechanism for fine-grained code reuse to overcome many limitations of class-based inheritance. A trait is a set of methods that is independent from any class hierarchy and can be flexibly used to build other traits or classes by means of a suite of composition operations. In this paper we present the new version of Xtraitj , a trait-based programming language that features complete compatibility and interoperability with the Java platform. Xtraitj is implemented in Xtext and Xbase , and it provides a full Eclipse IDE that supports an incremental adoption of traits in existing Java projects. The new version of Xtraitj allows traits to be accessed from any Java project or library, even if the original Xtraitj source code is not available, since traits can be accessed in their byte-code format. This allows developers to create Xtraitj libraries that can be provided in their binary only format. We detail the technique we used to achieve such an implementation; this technique can be reused in other languages implemented in Xtext for the Java platform. We formalize our traits by means of flattening semantics and we provide some performance benchmarks that show that the runtime overhead introduced by our traits is acceptable.

HELIOS: A MULTI-PURPOSE LIDAR SIMULATION FRAMEWORK FOR RESEARCH, PLANNING AND TRAINING OF LASER SCANNING OPERATIONS WITH AIRBORNE, GROUND-BASED MOBILE AND STATIONARY PLATFORMS

In many technical domains of modern society, there is a growing demand for fast, precise and automatic acquisition of digital 3D models of a wide variety of physical objects and environments. Laser scanning is a popular and widely used technology to cover this demand, but it is also expensive and complex to use to its full potential. However, there might exist scenarios where the operation of a <i>real</i> laser scanner could be replaced by a computer simulation, in order to save time and costs. This includes scenarios like teaching and training of laser scanning, development of new scanner hardware and scanning methods, or generation of artificial scan data sets to support the development of point cloud processing and analysis algorithms. To test the feasibility of this idea, we have developed a highly flexible laser scanning simulation framework named <i>Heidelberg LiDAR Operations Simulator (HELIOS)</i>. HELIOS is implemented as a Java library and split up into a core component and multiple extension modules. Extensible Markup Language (XML) is used to define scanner, platform and scene models and to configure the behaviour of modules. Modules were developed and implemented for (1) loading of simulation assets and configuration (i.e. 3D scene models, scanner definitions, survey descriptions etc.), (2) playback of XML survey descriptions, (3) TLS survey planning (i.e. automatic computation of recommended scanning positions) and (4) interactive real-time 3D visualization of simulated surveys. As a proof of concept, we show the results of two experiments: First, a survey planning test in a scene that was specifically created to evaluate the quality of the survey planning algorithm. Second, a simulated TLS scan of a crop field in a precision farming scenario. The results show that HELIOS fulfills its design goals.

HELIOS: A MULTI-PURPOSE LIDAR SIMULATION FRAMEWORK FOR RESEARCH, PLANNING AND TRAINING OF LASER SCANNING OPERATIONS WITH AIRBORNE, GROUND-BASED MOBILE AND STATIONARY PLATFORMS

Abstract. In many technical domains of modern society, there is a growing demand for fast, precise and automatic acquisition of digital 3D models of a wide variety of physical objects and environments. Laser scanning is a popular and widely used technology to cover this demand, but it is also expensive and complex to use to its full potential. However, there might exist scenarios where the operation of a real laser scanner could be replaced by a computer simulation, in order to save time and costs. This includes scenarios like teaching and training of laser scanning, development of new scanner hardware and scanning methods, or generation of artificial scan data sets to support the development of point cloud processing and analysis algorithms. To test the feasibility of this idea, we have developed a highly flexible laser scanning simulation framework named Heidelberg LiDAR Operations Simulator (HELIOS). HELIOS is implemented as a Java library and split up into a core component and multiple extension modules. Extensible Markup Language (XML) is used to define scanner, platform and scene models and to configure the behaviour of modules. Modules were developed and implemented for (1) loading of simulation assets and configuration (i.e. 3D scene models, scanner definitions, survey descriptions etc.), (2) playback of XML survey descriptions, (3) TLS survey planning (i.e. automatic computation of recommended scanning positions) and (4) interactive real-time 3D visualization of simulated surveys. As a proof of concept, we show the results of two experiments: First, a survey planning test in a scene that was specifically created to evaluate the quality of the survey planning algorithm. Second, a simulated TLS scan of a crop field in a precision farming scenario. The results show that HELIOS fulfills its design goals.

Leveraging annotation-based modeling with Jump

The capability of UML profiles to serve as annotation mechanism has been recognized in both research and industry. Today’s modeling tools offer profiles specific to platforms, such as Java, as they facilitate model-based engineering approaches. However, considering the large number of possible annotations in Java, manually developing the corresponding profiles would only be achievable by huge development and maintenance efforts. Thus, leveraging annotation-based modeling requires an automated approach capable of generating platform-specific profiles from Java libraries. To address this challenge, we present the fully automated transformation chain realized by Jump, thereby continuing existing mapping efforts between Java and UML by emphasizing on annotations and profiles. The evaluation of Jump shows that it scales for large Java libraries and generates profiles of equal or even improved quality compared to profiles currently used in practice. Furthermore, we demonstrate the practical value of Jump by contributing profiles that facilitate reverse engineering and forward engineering processes for the Java platform by applying it to a modernization scenario.

Over-exposed classes in Java: An empirical study

Java access modifiers regulate interactions among software components. In particular, class modifiers specify which classes from a component are publicly exposed and therefore belong to the component public interface. Restricting the accessibility as specified by a programmer is key to ensure a proper software modularity. It has been said that failing to do so is likely to produce maintenance problems, poor system quality, and architecture decay. However, how developers uses class access modifiers or how inadequate access modifiers affect software systems has not been investigated yet in the literature.In this work, we empirically analyze the use of class access modifiers across a collection of 15 Java libraries and 15 applications, totaling over 3.6M lines of code. We have found that an average of 25% of classes are over-exposed, i.e., classes defined with an accessibility that is broader than necessary. A number of code patterns involving over-exposed classes have been formalized, characterizing programmers׳ habits. Furthermore, we propose an Eclipse plugin to make component public interfaces match with the programmer׳s intent.

MiToBo - A Toolbox for Image Processing and Analysis

MiToBo is a toolbox and Java library for solving basic as well as advanced image processing and analysis tasks. It features a rich collection of fundamental, intermediate and high-level image processing operators and algorithms as well as a couple of sophisticated tools for specific biological and biomedical applications. These tools include operators for elucidating cellular morphology and locomotion as well as operators for the characterization of certain intracellular particles and structures.MiToBo builds upon and integrates into the widely-used image analysis software packages ImageJ and Fiji [11, 10], and all of its operators can easily be run in ImageJ and Fiji via a generic operator runner plugin. Alternatively MiToBo operators can directly be run from command line, and using its functionality as a library for developing own applications is also supported. Thanks to the Alida library [8] forming the base of MiToBo all operators share unified APIs fostering reusability, and graphical as well as command line user interfaces for operators are automatically generated. MiToBo is available from its website http://www.informatik.uni-halle.de/mitobo, on Github, via an Apache Archiva Maven repository server, and it can easily be activated in Fiji via its own update site.

RELIABILITY ASSESSMENT OF STRINGERS SPACINGS IN BRIDGES AS FUNCTION OF TIMBER PROPERTIES

This presentation accounts for established functions of stringer spacing of major Nigerian woods when used as bridge decks. It entails stochastic evaluation of bridge wood decks with absolute regards to the spacing of supporting stringers. A timber bridge deck is modelled on timber stringers in accordance with current specifications as outline in AASHTO LRFD (2010), to represent real life experiment in order to depict the structural behaviour of Nigerian timbers when used for bridge decks. This model is then subjected to some degree of entropy using Advance Second Moment Reliability Assessment (ASMRA) method, which is subsequently analysed using JAVA library with the help of Flanagan polynomial. The concept of ASMRA with Flanagan polynomial returns optimum output values for any input array of data along the input normal distribution curve. Taking Lophira alata (EKKI), Afzelia bipindensis (APA),Chlorophora exceisa (IROKO) and Mitragyna ciliate (ABURA) to represent N 1 , N 2 , N 3 , and N 4 classes of Nigerian timber suitable for bridge decks, convincingly, it was established that, stringer spacing, strength classes, timber thicknesses and width are some of the major factors among others influencing the structural behaviour of Nigerian timber species used for bridge decks. These data are treated as random variables to generate relative optimum values which, are used to predict the relationship between stringer spacing as a dependent variable on other variables using Analysis of Variance (ANOVA) and multiple Regression line analysis. For the considered timber species, it was observed that large percentages, (R 2 ≌ 1 that is 100% for EKKI, APA, IROKO and ABURA of the variation in the dependent variable (stringer spacing) is explained by the independent variables (strength classes, timber thicknesses, timber width, plank deck unit weight, unit weight of surfacing material, lane load, thickness of surfacing material and reliability indices) which are all good fit. Also all the predicted regression lines are reliable and statistically significant as the significance F, (3.59709E-05 for EKKI, 5.58768E-05 for APA, 3.59709E-05 for IROKO and 8.55563E-05 for ABURA) are all less than 0.05. Thus, these established relationships will help in future forecast of stringer spacing for bridge deck design and analysis within acceptable structural reliability indices which are statistically significant (and are all within acceptable values ≤0.05) http://dx.doi.org/10.4314/njt.v35i2.10

Rapid Android Parser for Investigating DEX files (RAPID)

Android malware is a well-known challenging problem and many researchers/vendors/practitioners have tried to address this issue through application analysis techniques. In order to analyze Android applications, tools decompress APK files and extract relevant data from the Dalvik EXecutable (DEX) files. To acquire the data, investigators either use decompiled intermediate code generated by existing tools, e.g., Baksmali or Dex2jar or write their own parsers/dissemblers. Thus, they either need additional time because of decompiling the application into an intermediate representation and then parsing text files, or they reinvent the wheel by implementing their own parsers. In this article, we present Rapid Android Parser for Investigating DEX files (RAPID) which is an open source and easy-to-use JAVA library for parsing DEX files. RAPID comes with well-documented APIs which allow users to query data directly from the DEX binary files. Our experiments reveal that RAPID outperforms existing approaches in terms of runtime efficiency, provides better reliability (does not crash) and can support dynamic analysis by finding critical offsets. Notably, the processing time for our sample set of 22.35 GB was only 1.5 h with RAPID while the traditional approaches needed about 23 h (parsing and querying).

Taking Arduino to the Internet of Things: The ASIP programming model

Micro-controllers such as Arduino are widely used by all kinds of makers worldwide. Popularity has been driven by Arduino’s simplicity of use and the large number of sensors and libraries available to extend the basic capabilities of these controllers. The last decade has witnessed a surge of software engineering solutions for “the Internet of Things”, but in several cases these solutions require computational resources that are more advanced than simple, resource-limited micro-controllers.Surprisingly, in spite of being the basic ingredients of complex hardware–software systems, there does not seem to be a simple and flexible way to (1) extend the basic capabilities of micro-controllers, and (2) to coordinate inter-connected micro-controllers in “the Internet of Things”. Indeed, new capabilities are added on a per-application basis and interactions are mainly limited to bespoke, point-to-point protocols that target the hardware I/O rather than the services provided by this hardware.In this paper we present the Arduino Service Interface Programming (ASIP) model, a new model that addresses the issues above by (1) providing a “Service” abstraction to easily add new capabilities to micro-controllers, and (2) providing support for networked boards using a range of strategies, including socket connections, bridging devices, MQTT-based publish–subscribe messaging, discovery services, etc. We provide an open-source implementation of the code running on Arduino boards and client libraries in Java, Python, Racket and Erlang. We show how ASIP enables the rapid development of non-trivial applications (coordination of input/output on distributed boards and implementation of a line-following algorithm for a remote robot) and we assess the performance of ASIP in several ways, both quantitative and qualitative.

Attack’s Feature Selection-Based Network Intrusion Detection System Using Fuzzy Control Language

Network intrusion detection system has wide range of disputes due to lack of security over the networks. The network intrusion detection system must be reliable to detect the emerging threats over the networks and perform effectively, efficiently to manage large amount of traffic. This paper proposes entropy-based feature selection to select the important features, layered fuzzy control language to generate fuzzy rules, and layered classifier to detect various network attacks namely neptune, smurf, back, and mailbomb. Layered classifier has improved the performances and reduces the computational time. KDD Dataset which consists of three components, namely “Corrected Dataset,” “10 % Dataset,” and “Full Dataset,” are employed to evaluate the performances of the proposed system. The experiments are carried out using an open source java library called jFuzzyLogic and the results show considerable improvement in the detection rate, reduce the false positive rate, significant improvement in recall value and reduces the computational time.

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.

BackgroundDifferential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time.ResultsIn this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator.AvailabilityDiffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0863-y) contains supplementary material, which is available to authorized users.

LibSBOLj 2.0: A Java Library to Support SBOL 2.0

libSBOLj 2.0: A Java Library to Support SBOL 2.0

Real-time analysis of video by means of the Actor Prolog language

Object-oriented logical means for a real-time analysis of video were developed. The software includes a translator of the Actor Prolog object-oriented logic language to Java, an open source Java library that contains built-in classes of Actor Prolog, and a programming environment of the Actor Prolog language. An example of using the software for intelligent video monitoring of abnormal behavior in people is considered. Object-oriented means of the Actor Prolog language make it possible to divide a logic program into several parallel processes corresponding to various stages of the video processing. The translation of logic programs to Java provides reliability, portability, and openness of the intelligent video surveillance programs.

Design patterns for multi-agent programming

Various agent-based programming languages and frameworks have been proposed to support the development of autonomous agents and multi-agent systems. They have provided a valuable contribution to the identification and operationalisation of agent concepts and abstractions by proposing specific programming constructs. Unfortunately, these contributions have not yet been widely adopted by industry. In this paper, we follow the argument that multi-agent programming technology can find its way to industry by providing a methodology that guides the development of autonomous agents and multi-agent systems in standard programming technology. The proposed methodology explains how some characteristic concepts and abstractions related to autonomous agents and multi-agent systems can be implemented in object-oriented technology. This is done by initiating a Java library of object-oriented design patterns for some characteristic but established programming constructs that have been developed in some agent-based programming languages.

Polymorphic bytecode instrumentation

SummaryBytecode instrumentation is a widely used technique to implement aspect weaving and dynamic analyses in virtual machines such as the Java virtual machine. Aspect weavers and other instrumentations are usually developed independently and combining them often requires significant engineering effort, if at all possible. In this article, we present polymorphic bytecode instrumentation(PBI), a simple but effective technique that allows dynamic dispatch amongst several, possibly independent instrumentations. PBI enables complete bytecode coverage, that is, any method with a bytecode representation can be instrumented. We illustrate further benefits of PBI with three case studies. First, we describe how PBI can be used to implement a comprehensive profiler of inter‐procedural and intra‐procedural control flow. Second, we provide an implementation of execution levels for AspectJ, which avoids infinite regression and unwanted interference between aspects. Third, we present a framework for adaptive dynamic analysis, where the analysis to be performed can be changed at runtime by the user. We assess the overhead introduced by PBI and provide thorough performance evaluations of PBI in all three case studies. We show that pure Java profilers like JP2 can, thanks to PBI, produce accurate execution profiles by covering all code, including the core Java libraries. We then demonstrate that PBI‐based execution levels are much faster than control flow pointcuts to avoid interference between aspects and that their efficient integration in a practical aspect language is possible. Finally, we report that PBI enables adaptive dynamic analysis tools that are more reactive to user inputs than existing tools that rely on dynamic aspect‐oriented programming with runtime weaving. These experiments position PBI as a widely applicable and practical approach for combining bytecode instrumentations. © 2015 The Authors. Software: Practice and Experience Published by John Wiley & Sons Ltd.

LibSBOLj 2.0: A Java Library to Support SBOL 2.0

The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic design automation tools. The latest version of the standard, SBOL 2.0, enables the annotation of a large variety of biological components (e.g., DNA, RNA, proteins, complexes, small molecules, etc.) and their interactions. SBOL 2.0 also allows researchers to organize components into hierarchical modules, to specify their intended functions, and to link modules to models that describe their behavior mathematically. To support the use of SBOL 2.0, we have developed the <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">libSBOLj 2.0</monospace> Java library, which provides an easy to use Application Programming Interface (API) for developers, including manipulation of SBOL constructs, serialization to and from an RDF/XML file format, and migration support in the form of conversion from the prior SBOL 1.1 standard to SBOL 2.0. This letter describes the <monospace xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">libSBOLj 2.0</monospace> library and key engineering decisions involved in its design.

Synthesizing Java expressions from free-form queries

We present a new code assistance tool for integrated development environments. Our system accepts as input free-form queries containing a mixture of English and Java, and produces Java code expressions that take the query into account and respect syntax, types, and scoping rules of Java, as well as statistical usage patterns. In contrast to solutions based on code search, the results returned by our tool need not directly correspond to any previously seen code fragment. As part of our system we have constructed a probabilistic context free grammar for Java constructs and library invocations, as well as an algorithm that uses a customized natural language processing tool chain to extract information from free-form text queries. We present the results on a number of examples showing that our technique (1) often produces the expected code fragments, (2) tolerates much of the flexibility of natural language, and (3) can repair incorrect Java expressions that use, for example, the wrong syntax or missing arguments.

Metadata management for high content screening in OMERO

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org.

Nondeterministic Programming in Java with JSetL

JSetL is a Java library that endows Java with a number of facilities that are intended to support declarative and constraint (logic) programming. In this paper we show how JSetL can be used to support general forms of nondeterministic programming in an object-oriented framework. This is obtained by combining different but related facilities such as logical variables, set data structures, unification, along with a constraint solver that allows the user to solve nondeterministic constraints, as well as to define new constraints using the nondeterminism handling facilities provided by the solver itself. Thus, the user can define her/his own general nondeterministic procedures as new constraints, letting the constraint solver handle them. The proposed solutions are illustrated by showing a number of concrete Java implementations using JSetL, including the implementation of simple Definite Clause Grammars.