JDotter: a Java interface to multiple dotplots generated by dotter

Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. AVAILABILITY: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.     

CoPE: a collaborative pedigree drawing environment.

SUMMARY: We developed a collaborative pedigree environment called CoPE. This environment includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. AVAILABILITY: At http://www.infobiogen.fr/services/CoPE     

GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences

Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs plays a significant role in biomedical research since such align genomic regions usually contain important features, such as pathogenic genes. We have developed a use friendly graphic user interface, Genomic Island Suite of Tools (GIST), which is a platform for scientific users to predict GIs. This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction. The tools in GIST can be used either separately or sequentially. GIST also includes a downloadable feature that facilitates collecting the input genomes automatically from the FTP server of the National Center for Biotechnology Information (NCBI). GIST was implemented in Java, and was compiled and executed on Linux/Unix operating systems. AVAILABILITY: The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST.     

VisRD--visual recombination detection

SUMMARY: VisRD, a program for visual recombination detection in a sequence alignment is presented. VisRD is written in Java and is designed to complement the multi-purpose phylogenetic software package SplitsTree4. AVAILABILITY: The software is freely available from http://www.lcb.uu.se/~vmoulton/software/visrd/     

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols ) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open‐source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog .     

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between population genetics programs, we introduce PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats. The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines. AVAILABILITY: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/.     

VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer

VarSifter is a graphical software tool for desktop computers that allows investigators of varying computational skills to easily and quickly sort, filter, and sift through sequence variation data. A variety of filters and a custom query framework allow filtering based on any combination of sample and annotation information. By simplifying visualization and analyses of exome-scale sequence variation data, this program will help bring the power and promise of massively-parallel DNA sequencing to a broader group of researchers. Availability and Implementation: VarSifter is written in Java, and is freely available in source and binary versions, along with a User Guide, at http://research.nhgri.nih.gov/software/VarSifter/.     

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.     

StrBioLib: a Java library for development of custom computational structural biology applications

SUMMARY: StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. AVAILABILITY: StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/     

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing

SUMMARY: Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for this process. In an easy-to-use manner, the tool helps the user to import the sequence files from the sequencer, to align them, to exclude or correct critical sequences, to document the experiment, to perform basic statistics and to produce publication-quality diagrams.Emphasis is put on quality control: The program automatically assesses data quality and provides warnings and suggestions for dealing with critical sequences. The BiQ Analyzer program is implemented in the Java programming language and runs on any platform for which a recent Java virtual machine is available. AVAILABILITY: The program is available without charge for non-commercial users and can be downloaded from http://biq-analyzer.bioinf.mpi-inf.mpg.de/     

BicAT: a biclustering analysis toolbox

SUMMARY: Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments. AVAILABILITY: The BicAT toolbox is freely available at http://www.tik.ee.ethz.ch/sop/bicat and runs on all operating systems. The Java source code of the program and a developer's guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions.     

FLOSS: flexible ordered subset analysis for linkage mapping of complex traits

The FLOSS software package is a flexible framework for ordered subset analysis. FLOSS is specifically designed for use with the Merlin linkage analysis package, but FLOSS can be used with any linkage analysis software package that reports NPL Z-scores for each locus and family. When FLOSS is used with the Merlin linkage analysis package, one can use either non-parametric Z-scores or Kong and Cox linear allele sharing model LOD scores. Monte Carlo P-values are calculated using a permutation test with an efficient Besag-Clifford sequential stopping rule. FLOSS also has a flexible tool for assigning family covariate scores from Merlin input files. FLOSS includes user documentation and is written in Java for easy portability. The FLOSS source code is documented and designed to be extensible.     

天花粉蛋白基因的克隆及序列分析

本文应用ＤＮＡ多聚酶链式反应（ＰＣＲ）技术,从括楼基因组ＤＮＡ中扩增并克隆了天花粉蛋白（ＴＣＳ）基因。核酸序列分析结果表明,克隆片段包括ＴＣＳ的前原蛋白的编码序列和５＇一侧翼区段。其编码序列与已发表的不同来源的３种ＴＣＳ基因的核苷酸序列的同源性分别为９９．２０％,９８．７４％和９８．６４％。推导出的氨基酸序列与已发表的４种ＴＣＳ的氨基酸序列的同源性分别为９８．６２％、９８．６２％、９７．４１％和９     

ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text

ABNER (A Biomedical Named Entity Recognizer) is an open source software tool for molecular biology text mining. At its core is a machine learning system using conditional random fields with a variety of orthographic and contextual features. The latest version is 1.5, which has an intuitive graphical interface and includes two modules for tagging entities (e.g. protein and cell line) trained on standard corpora, for which performance is roughly state of the art. It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora.     

JSBML: a flexible Java library for working with SBML

SUMMARY: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. AVAILABILITY: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.     

SDAR: a practical tool for graphical analysis of two-dimensional data

ABSTRACT: BACKGROUND: Two-dimensional data needs to be processed and analysed in almost any experimental laboratory. Some tasks in this context may be performed with generic software such as spreadsheet programs which are available ubiquitously, others may require more specialised software that requires paid licences. Additionally, more complex software packages typically require more time by the individual user to understand and operate. Practical and convenient graphical data analysis software in Java with a user-friendly interface are rare. RESULTS: We have developed SDAR, a Java application to analyse two-dimensional data with an intuitive graphical user interface. A smart ASCII parser allows import of data into SDAR without particular format requirements. The centre piece of SDAR is the Java class GraphPanel which provides methods for generic tasks of data visualisation. Data can be manipulated and analysed with respect to the most common operations experienced in an experimental biochemical laboratory. Images of the data plots can be generated in SVG-, TIFF- or PNG-format. Data exported by SDAR is annotated with commands compatible with the Grace software. CONCLUSION: Since SDAR is implemented in Java, it is truly cross-platform compatible. The software is easy to install, and very convenient to use judging by experience in our own laboratories. It is freely available to academic users at http://www.structuralchemistry.org/pcsb/. To download SDAR, users will be asked for their name, institution and email address. A manual, as well as the source code of the GraphPanel class can also be downloaded from this site.     

TableView: portable genomic data visualization

TableView is a generalized scientific visualization program for exploration of various biological data, including EST, SAGE, microarray and annotation data. Written in Java, TableView is portable, is easily used together with other software including DBMSs and is versatile enough to be applied to any tabular data AVAILABILITY: TableView is freely available at: http://ccgb.umn.edu/software/java/apps/TableView/.     

Pedro: a configurable data entry tool for XML

Pedro is a Java application that dynamically generates data entry forms for data models expressed in XML Schema, producing XML data files that validate against this schema. The software uses an intuitive tree-based navigation system, can supply context-sensitive help to users and features a sophisticated interface for populating data fields with terms from controlled vocabularies. The software also has the ability to import records from tab delimited text files and features various validation routines. AVAILABILITY: The application, source code, example models from several domains and tutorials can be downloaded from http://pedro.man.ac.uk/.     

The design of Jemboss: a graphical user interface to EMBOSS

DESIGN: Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. RESULTS: This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. AVAILABILITY: The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/     

MorphoJ: an integrated software package for geometric morphometrics

Increasingly, data on shape are analysed in combination with molecular genetic or ecological information, so that tools for geometric morphometric analysis are required. Morphometric studies most often use the arrangements of morphological landmarks as the data source and extract shape information from them by Procrustes superimposition. The MorphoJ software combines this approach with a wide range of methods for shape analysis in different biological contexts. The program offers an integrated and user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. MorphoJ is written in Java and versions for the Windows, Macintosh and Unix/Linux platforms are freely available from http://www.flywings.org.uk/MorphoJ_page.htm.