BioQuery: an object framework for building queries to biomedical databases

SUMMARY: BioQuery is an application that helps scientists automate database searches. Users can build and store queries to public biomedical databases, and receive periodic updates on the results of those queries when new data is available. The application is implemented on a portable object framework that can provide database-searching capability to other applications. This framework is easily extensible, allowing users to develop plug-ins that provide access to new databases. BioQuery thus provides end-users with a complete database searching interface and updating service, and gives developers a toolkit to provide database-searching capability to their applications. AVAILABILITY: Free to all users: http://www.bioquery.org.     

A suite of Perl modules for handling microarray data

We describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. AVAILABILITY: Software is available at http://sourceforge.net/projects/perlmat     

HotSwap for bioinformatics: A STRAP tutorial

Background

Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique.

Results

Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the Java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at http://strapjava.de and http://www.charite.de/bioinf/strap.

Conclusion

HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory.     

Genview and Gencode : a pair of programs to test theories of genetic code evolution

GENVIEW: and GENCODE: are tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. GENVIEW: provides a user friendly, point-and-click interface by which a user may reproduce and extend analysis of the adaptive properties of the standard genetic code or any of its secondary derivatives. GENVIEW: is a graphical user interface (GUI) program which runs on Linux, Unix and Microsoft Windows platforms and is based on the GTKf + toolkit. GENVIEW: outputs ASCII configuration files which are interpreted by GENCODE: to perform an analysis. GENCODE: is available for the same platforms as GENVIEW.     

Adapting EcoCyc for use on the World Wide Web

The World Wide Web (WWW) offers the potential to deliver specialized information to an audience of unprecedented size. Along with this exciting new opportunity comes a challenge for software developers: instead of rewriting our software applications to operate over the WWW, how can we maximize software reuse by retrofitting existing applications? We have developed a Web server tool. written in Common Lisp, that allows existing graphical user interface applications written using the Common Lisp Interface Manager (CLIM) to hook easily into the WWW. This tool — CWEST (CLIM-WEb Server Tool, pronounced “quest”) — was developed to operate with EcoCyc, an electronic encylopedia of the genes and metabolism of the bacterium E. coli. EcoCyc consists of a database of objects relevant to E. coli biochemistry and a user interface, implemented in CLIM, that runs on the X-window system and generates graphical displays appropriate to biological objects. Each query to the EcoCyc WWW server is treated as a command to the EcoCyc program, which dynamically generates an appropriate CLIM drawing. CWEST translates that drawing, which can be a mixture of text and graphics, into the HyperText Markup Language (HTML) and/or the Graphics Interchange Format (GIF), which are returned to the client. Sensitive regions embedded in the CLIM drawing are converted to hyperlinks with Universal Resource Locators (URLs) that generate further EcoCyc queries. This tight coupling of CLIM output with Web output makes CLIM a powerful high-level programming tool for Web applications. The flexibility of Common Lisp and CLIM made implementation of the server tool surprisingly easy, requiring few changes to the existing EcoCyc program. The results can be seen at URL http://www.ai.sri.com/ecocyc/browser.html. We have made CWEST available to the CLIM community at large, with the hope that it will spur other software developers to make their CLIM applications available over the WWW.     

The TOPAS tool for particle simulation,a Monte Carlo simulation tool for physics,biology and clinical research

PurposeThis paper covers recent developments and applications of the TOPAS TOol for PArticle Simulation and presents the approaches used to disseminate TOPAS.Materials and methodsFundamental understanding of radiotherapy and imaging is greatly facilitated through accurate and detailed simulation of the passage of ionizing radiation through apparatus and into a patient using Monte Carlo (MC). TOPAS brings Geant4, a reliable, experimentally validated MC tool mainly developed for high energy physics, within easy reach of medical physicists, radiobiologists and clinicians. Requiring no programming knowledge, TOPAS provides all of the flexibility of Geant4.ResultsAfter 5 years of development followed by its initial release, TOPAS was subsequently expanded from its focus on proton therapy physics to incorporate radiobiology modeling. Next, in 2018, the developers expanded their user support and code maintenance as well as the scope of TOPAS towards supporting X-ray and electron therapy and medical imaging. Improvements have been achieved in user enhancement through software engineering and a graphical user interface, calculational efficiency, validation through experimental benchmarks and QA measurements, and either newly available or recently published applications. A large and rapidly increasing user base demonstrates success in our approach to dissemination of this uniquely accessible and flexible MC research tool.ConclusionsThe TOPAS developers continue to make strides in addressing the needs of the medical community in applications of ionizing radiation to medicine, creating the only fully integrated platform for four-dimensional simulation of all forms of radiotherapy and imaging with ionizing radiation, with a design that promotes inter-institutional collaboration.     

MollDE: a homology modeling framework you can click with

SUMMARY: Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. AVAILABILITY: http://dunbrack.fccc.edu/molide/molide.php CONTACT: rl_dunbrack@fccc.edu.     

A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS

Abstract Numerous software packages exist to provide support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many support only a subset of experimental methods or instrument types, meaning that laboratories often have to use multiple software packages. The Progenesis LC-MS software package from Nonlinear Dynamics is a software solution for label-free quantitation. However, many laboratories using Progenesis also wish to employ stable isotope-based methods that are not natively supported in Progenesis. We have developed a Java programming interface that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods. We have developed post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labeling data and top3 pseudo-absolute quantitation. We have also created export ability to the new data standard, mzQuantML, produced by the Proteomics Standards Initiative to facilitate the development and standardization process. The software is provided to users with a simple graphical user interface for accessing the different features. The underlying programming interface may also be used by Java developers to develop other routines for analyzing data produced by Progenesis.     

Recording information on protein complexes in an information management system

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein-protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described.     

The ImageJ ecosystem: Open‐source software for image visualization,processing, and analysis

For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open‐source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user‐centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.     

The protein fluorescence and structural toolkit: Database and programs for the analysis of protein fluorescence and structural data

Protein fluorescence is a powerful tool for studying protein structure and dynamics if we have a means to interpret the spectral data in terms of protein structural properties. Our previous research successfully provided this support through the development of individual software modules implementing the algorithms for fluorescence and structural analyses. Now we have integrated the developed software modules, introduced a new program for the assignment of tryptophan residues to spectral-structural classes, and created a web-based toolkit PFAST: protein fluorescence and structural toolkit: http://pfast.phys.uri.edu/. PFAST contains three modules: (1) FCAT is a fluorescence-correlation analysis tool, which decomposes protein fluorescence spectra to reveal the spectral components of individual tryptophan residues or groups of tryptophan residues located close to each other, and assigns spectral components to one of five previously established spectral-structural classes. (2) SCAT is a structural-correlation analysis tool for the calculation of the structural parameters of the environment of tryptophan residues from the atomic structures of the proteins from the Protein Data Bank (PDB), and for the assignment of tryptophan residues to one of five spectral-structural classes. (3) The last module is a PFAST database that contains protein fluorescence and structural data obtained from results of the FCAT and SCAT analyses.     

REST: a toolkit for resting-state functional magnetic resonance imaging data processing

Resting-state fMRI (RS-fMRI) has been drawing more and more attention in recent years. However, a publicly available, systematically integrated and easy-to-use tool for RS-fMRI data processing is still lacking. We developed a toolkit for the analysis of RS-fMRI data, namely the RESting-state fMRI data analysis Toolkit (REST). REST was developed in MATLAB with graphical user interface (GUI). After data preprocessing with SPM or AFNI, a few analytic methods can be performed in REST, including functional connectivity analysis based on linear correlation, regional homogeneity, amplitude of low frequency fluctuation (ALFF), and fractional ALFF. A few additional functions were implemented in REST, including a DICOM sorter, linear trend removal, bandpass filtering, time course extraction, regression of covariates, image calculator, statistical analysis, and slice viewer (for result visualization, multiple comparison correction, etc.). REST is an open-source package and is freely available at http://www.restfmri.net.     

IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform

IlluminaGUI is a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform. All key components of a microarray experiment, including quality control, normalization, inference and classification methods are provided in a 'point and click' approach. IlluminaGUI is implemented as a R package based on the R-Tcl/Tk interface and is available for platforms on which R runs including Windows, Mac and Unix-type machines. AVAILABILITY: http://IlluminaGUI.dnsalias.org     

A collection of open source applications for mass spectrometry data mining

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front‐end graphical user interface that combines several Thermo RAW formats to MASCOT? Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode.     

A fault detection service for wide area distributed computations

The potential for faults in distributed computing systems is a significant complicating factor for application developers. While a variety of techniques exist for detecting and correcting faults, the implementation of these techniques in a particular context can be difficult. Hence, we propose a fault detection service designed to be incorporated, in a modular fashion, into distributed computing systems, tools, or applications. This service uses well-known techniques based on unreliable fault detectors to detect and report component failure, while allowing the user to trade off timeliness of reporting against false positive rates. We describe the architecture of this service, report on experimental results that quantify its cost and accuracy, and describe its use in two applications, monitoring the status of system components of the GUSTO computational grid testbed and as part of the NetSolve network-enabled numerical solver. This revised version was published online in July 2006 with corrections to the Cover Date.     

A visual environment for the manipulation and integration of JAVA beans

MOTIVATION: Visual programming has the potential to allow non- programmers to redesign and rebuild applications to suit their individual needs. We have built such a visual programming environment, which allows non-programmers to interrogate and combine software components graphically to form new applications. As the needs of the biological community grow, so too will the need for more powerful and easy to use software tools. Intelligent visual programming environments will allow users to design and develop applications easily, so that they can concentrate on the application they wish to build rather than how it is to be done. RESULTS: The environment can read in JAVA Beans, and present relevant information about the beans to the user. The user can then graphically specify how they would like information to flow between the beans by performing simple docking operations. Unnecessary complexities associated with such visual design have been removed by providing intelligent docking of components and visual feedback. With such mechanisms, the complexities of building new applications are reduced. When the biologist has finished the visual construction, the design system is able to generate the new application automatically. The system has been designed specifically to meet the needs of the biological community, and a range of 'BioBeans' are being developed. These include beans for visualization (sequence displays and data visualizers), analysis (feature recognition, error detection) and communication (database access, URL retrieval, DDE communication). AVAILABILITY: Freely available. CONTACT: boyle@synomics.com