Java Software Tool Research Articles

An Open-Source Cross-Section Tool for Hydrodynamic Model Geometric Input Development

Hydrodynamic models are widely used in simulating water dynamics in riverine and estuarine systems. A reasonably realistic representation of the geometry (e.g., channel length, junctions, cross-sections, etc.) of the study area is imperative for any successful hydrodynamic modeling application. Typically, hydrodynamic models do not digest these data directly but rely on pre-processing tools to convert the data to a readable format. This study presents a parsimonious open-source and user-friendly Java software tool, the Cross-Section Development Program (CSDP), that is developed by the authors to prepare geometric inputs for hydrodynamic models. The CSDP allows the user to select bathymetry data collected in different years by different agencies and create cross-sections and computational points in a channel automatically. This study further illustrates the application of this tool to the Delta Simulation Model II, which is the operational forecasting and planning hydrodynamic and water quality model developed for the Sacramento–San Joaquin Delta in California, United States. Model simulations on water levels and flow rates at key stations are evaluated against corresponding observations. The simulations mimic the patterns of the corresponding observations very well. The square of the correlation coefficient is generally over 0.95 during the calibration period and over 0.80 during the validation period. The absolute bias is generally less than 5% and 10% during the calibration and validation periods, respectively. The Kling–Gupta efficiency index is generally over 0.70 during both calibration and validation periods. The results illustrate that CSDP can be efficiently applied to generate geometric inputs for hydrodynamic models.

An Open Source Software Suite for Multi-Dimensional Meteorological Data Computation and Visualisation

MeteoInfo Java software tools were developed for multi-dimensional meteorological data analysis and visualisation by integrating a Geographic Information System (GIS) and Scientific Computation Environment (SCE). Included are a Java class library for software developing, a GIS desktop application for spatial data operation and interactive multi-dimensional geoscientific data exploration, and a scientific computation and visualisation environment with Jython scripting. The popular geoscience data formats, such as NetCDF, HDF and GRIB, are supported based on a Unidata NetCDF Java library; also, its multi-dimensional array data model is used for scientific computation. In this paper, the software design framework and its implementation are presented. Furthermore, the software application capabilities are illustrated using several examples.

FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c \u2192u RNA editing

BackgroundRNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and the corresponding coding DNA sequences. Software tools successful for the search of genes in other organisms not always are able to correctly perform this task in plants organellar genomes. Moreover, the available software tools predicting RNA editing events utilise algorithms that do not account for events which may generate a novel start codon.ResultsWe present Fedro, a Java software tool implementing a novel strategy to generate candidate Open Reading Frames (ORFs) resulting from Cytidine to Uridine (c→u) editing substitutions which occur in the mitochondrial genome (mtDNA) of a given input plant. The goal is to predict putative proteins of plants mitochondria that have not been yet annotated. In order to validate the generated ORFs, a screening is performed by checking for sequence similarity or presence in active transcripts of the same or similar organisms. We illustrate the functionalities of our framework on a model organism.ConclusionsThe proposed tool may be used also on other organisms and genomes. Fedro is publicly available at http://math.unipa.it/rombo/FEDRO.

On domain driven design using annotation-based domain specific language

The aim of object-oriented domain-driven design (DDD) is to iteratively develop software around a realistic domain model. Recent work in DDD use an annotation-based extension of object-oriented programming language to build the domain model. This model becomes the basis for a ubiquitous language and is used as input to generate software. However, the annotation-based extensions of these work do not adequately address the primitive and essential structural and behavioural modelling requirements of practical software. Further, they do not precisely characterise the software that is generated from the domain model. In this paper, we propose a DSL-based DDD method to address these limitations. We make four contributions: (1) an annotation-based domain-specific language (DSL) named DCSL, whose annotation extension expresses a set of essential structural constraints and the essential behaviour of a domain class. (2) A structural mapping between the state and behaviour spaces of a domain class. This mapping enables a technique for generating the behavioural specification. (3) A technique that uses DCSL to support behavioural modelling with UML activity diagram. (4) A 4-property characterisation of the software generated from the domain model. We demonstrate our method with a Java software tool and evaluate DCSL in the context of DDD.

MyETL: A Java Software Tool to Extract, Transform, and Load Your Business

Abstract The project follows the development of a Java Software Tool that extracts data from Flat File (Fixed Length Record Type), CSV (Comma Separated Values), and XLS (Microsoft Excel 97-2003 Worksheet file), apply transformation to those sources, and finally load the data into the end target RDBMS. The software refers to a process known as ETL (Extract Transform and Load). Those kinds of systems are called ETL systems. The analysis involved research on the theory behind the ETL process as well as the theory behind the various phases of the applied methodology. Also an in-depth look at the design and architecture of the software has been made. To create a complete design needed to be used for the implementation, different techniques and diagrams where used to visualise and refine ideas: UML class diagrams, System Architecture Diagrams, Physical Data Model, and Project Timeline. The implementation of the project involved the translation of the system architecture into working software using the Extreme Programming Methodology and the Java programming language. A mapping algorithm module and design patterns have been used in the implementation phase. A transformation syntax has been defined to achieve data transformation. The testing of the software was done in the form of a unit test. A formal test plan was prepared to ensure that the main features of the system worked as defined. An error handling code implementation has been developed to avoid an unexpected crash of the system and to communicate to the user problems or errors.

Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

Small-angle X-ray scattering has established itself as a common technique in structural biology research. Here, two novel Java applications to aid modelling of three-dimensional macromolecular structures based on small-angle scattering data are described.MolScatis an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data.SAFIRis a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version ofMolScatis used to enable quick evaluation of the fit between the model and experimental scattering data.SAFIRalso provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte Carlo approach.

The jmzQuantML programming interface and validator for the mzQuantML data standard

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard.

J0110205 DAKOTAとJAGUARによる最適化([J011-02]解析・設計の高度化・最適化(2))

DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit is developed by Sandia National Laboratories, and available under a GNU Lesser General Public License (LGPL). DAKOTA provides the following 4 capabilities; (1) optimization with gradient and nongradient-based methods, (2) uncertainty quantification with sampling, reliability, stochastic expansion and epistemic methods, (3) parameter estimation with nonlinear least squares methods, and (4) sensitivity/variance analysis with design of experiments and parameter study methods. JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface to manipulate DAKOTA input specifications. In this paper, we report the results of the capabilities of DAKOTA, especially optimization. DAKOTA is applied to some famous optimization examples and is verified that outputs are correct. DAKOTA is applied to the gradient-based local methods with constraints, the derivative-free global method, and multi-objective problem, to confirmative its optimal capabilities. Additionally, DAKOTA is compared with other optimal system.

WGAViewer: Software for genomic annotation of whole genome association studies: Figure 1.

To meet the immediate need for a framework of post-whole genome association (WGA) annotation, we have developed WGAViewer, a suite of JAVA software tools that provides a user-friendly interface to automatically annotate, visualize, and interpret the set of P-values emerging from a WGA study. Most valuably, it can be used to highlight possible functional mechanisms in an automatic manner, for example, by directly or indirectly implicating a polymorphism with an apparent link to gene expression, and help to generate hypotheses concerning the possible biological bases of observed associations. The easily interpretable diagrams can then be used to identify the associations that seem most likely to be biologically relevant, and to select genomic regions that may need to be resequenced in a search for candidate causal variants. In this report, we used our recently completed study on host control of HIV-1 viral load during the asymptomatic set point period as an illustration for the heuristic annotation of this software and its contributive role in a successful WGA project.

Developing a Java software tool for oriented matroids

As part of a summer internship, we worked on developing a Java software that would facilitate the visualization of dualities for educational and research purposes. The design of this software tool was inspired by the Model View Control paradigm for project design, where the same set of objects can be viewed in different frameworks. This programming approach is strongly object oriented and requires the programmer to separate the application, user input, and display logics. The Model is an interface independent application. We have a linked list called "SetOfPoints" as our model. The View is responsible for maintaining an updated view of the model and must be notified of changes to the model. We can view our model in three different views, namely a Point Frame (primal view), a Line Frame (dual view), and an Information Window. The Control, which is implemented as Menu Bar options in our project, initiates changes to the model, which can be viewed in the frames.