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PubMed2004

Biosphere: the interoperation of web services in microarray cluster analysis.

UNLABELLED: The growing use of DNA microarrays in biomedical research has led to the proliferation of analysis tools. These software programs address different aspects of analysis (e.g. normalisation and clustering within and across individual arrays) as well as extended analysis methods (e.g. clustering, annotation and mining of multiple datasets). Therefore, microarray data analysis typically requires the interoperability of multiple software programs involving different analysis types and methods. Such interoperation is often hampered by the heterogeneity inherent in the software tools (which may function by implementing different interfaces and using different programming languages). To address this problem, we employed the simple object access protocol (SOAP)-based web service approach that provides a uniform programmatic interface to these heterogeneous software components. To demonstrate this approach in the microarray context, we created a web server application, Biosphere, which interoperates a number of web services that are geographically widely distributed. These web services include a clustering web service, which is a suite of different clustering algorithms for analysing microarray data; XEMBL, developed at the European Bioinformatics Institute (EBI) for retrieving EMBL Nucleotide Sequence Database sequence data; and three gene annotation web services: GetGO, GetHAPI and GetUMLS. GetGO allows retrieval of Gene Ontology (GO) annotation, and the other two web services retrieve annotation from the biomedical literature that is indexed based on the Medical Subject Headings (MeSH) terms. With these web services, Biosphere allows the users to do the following: (i) cluster gene expression data using seven different algorithms; (ii) visualise the clustering results that are grouped statistically in colour; and (iii) retrieve sequence, annotation and citation data for the genes of interest. AVAILABILITY: Biosphere and its web services described in Web Service Description Language (WSDL) can be accessed at http://rook.cecid.hku.hk:8280/BiosphereServer.

Cluster Analysis↗
PubMed2006

Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot.

Oligonucleotide fingerprinting of rRNA genes (OFRG) is an array-based method that generates microbial community profiles through analysis of rRNA gene clone libraries. The original OFRG method allowed 1536 clones to be analyzed per experiment. This report describes a procedure for analyzing 9600 clones per experiment, including a new probe set for bacterial analysis, and improved data processing and statistical analysis tools. The software tools are available at the OFRG website (). Use of the 9600-clone procedure was demonstrated by examining the bacterial rRNA gene compositions of soils subjected to various temperature treatments. These treatments produced a series of soils with a range of abilities to suppress avocado root rot, enabling the identification of bacterial rRNA genes that correlate in abundance with root rot suppressiveness. OFRG analysis of these soils produced 8876 bacterial rRNA gene fingerprints grouped into 5123 clusters, or operational taxonomic units (OTUs). Eleven OTUs exhibited a positive correlation between the number of clones and the percentage of healthy roots. An in silico analysis was performed to examine the relationship between the number of rRNA genes analyzed and the number of correlates (rRNA gene-avocado root rot symptoms) identified. As the number of clones decreased, fewer correlates were identified. To further increase the throughput of the OFRG method, use of a glass slide-fluorescent probe microarray format was also explored.

DNA Fingerprinting↗
PubMed2002

ScanProsite: a reference implementation of a PROSITE scanning tool.

Many different software tools are available publicly to scan the PROSITE database of protein families. However, none of them, to our knowledge, wholly implements the PROSITE syntax, or satisfies all the rules for scanning a pattern against a sequence. We hereby propose a strict definition of how a PROSITE pattern is to be scanned against a sequence, and provide a reference implementation of a tool to scan PROSITE patterns, rules and profiles against protein sequences.

Computational Biology↗
PubMed1996

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.

Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://@www.sdsc.edu/CompSci/Biomed/ MEME.

Algorithms↗
PubMed2004

Evaluation of air pollution modelling tools as environmental engineering courseware.

The study of phenomena related to the dispersion of pollutants usually takes advantage of the use of mathematical models based on the description of the different processes involved. This educational approach is especially important in air pollution dispersion, when the processes follow a non-linear behaviour so it is difficult to understand the relationships between inputs and outputs, and in a 3D context where it becomes hard to analyze alphanumeric results. In this work, three different software tools, as computer solvers for typical air pollution dispersion phenomena, are presented. Each software tool developed to be implemented on PCs, follows approaches that represent three generations of programming languages (Fortran 77, VisualBasic and Java), applied over three different environments: MS-DOS, MS-Windows and the world wide web. The software tools were tested by students of environmental engineering (undergraduate) and chemical engineering (postgraduate), in order to evaluate the ability of these software tools to improve both theoretical and practical knowledge of the air pollution dispersion problem, and the impact of the different environment in the learning process in terms of content, ease of use and visualization of results.

Air Pollution↗
PubMed2000

Visualization of multiple influences on ocellar flight control in giant honeybees with the data-mining tool Viscovery SOMine.

Viscovery SOMine is a software tool for advanced analysis and monitoring of numerical data sets. It was developed for professional use in business, industry, and science and to support dependency analysis, deviation detection, unsupervised clustering, nonlinear regression, data association, pattern recognition, and animated monitoring. Based on the concept of self-organizing maps (SOMs), it employs a robust variant of unsupervised neural networks--namely, Kohonen's Batch-SOM, which is further enhanced with a new scaling technique for speeding up the learning process. This tool provides a powerful means by which to analyze complex data sets without prior statistical knowledge. The data representation contained in the trained SOM is systematically converted to be used in a spectrum of visualization techniques, such as evaluating dependencies between components, investigating geometric properties of the data distribution, searching for clusters, or monitoring new data. We have used this software tool to analyze and visualize multiple influences of the ocellar system on free-flight behavior in giant honeybees. Occlusion of ocelli will affect orienting reactivities in relation to flight target, level of disturbance, and position of the bee in the flight chamber; it will induce phototaxis and make orienting imprecise and dependent on motivational settings. Ocelli permit the adjustment of orienting strategies to environmental demands by enforcing abilities such as centering or flight kinetics and by providing independent control of posture and flight course.

Animals↗
PubMed2003

Volumetric measurements of pulmonary nodules at multi-row detector CT: in vivo reproducibility.

The aim of this study was to assess the in vivo measurement precision of a software tool for volumetric analysis of pulmonary nodules from two consecutive low-dose multi-row detector CT scans. A total of 151 pulmonary nodules (diameter 2.2-20.5 mm, mean diameter 7.4+/-4.5 mm) in ten subjects with pulmonary metastases were examined with low-dose four-detector-row CT (120 kVp, 20 mAs (effective), collimation 4x1 mm, normalized pitch 1.75, slice thickness 1.25 mm, reconstruction increment 0.8 mm; Somatom VolumeZoom, Siemens). Two consecutive low-dose scans covering the whole lung were performed within 10 min. Nodule volume was determined for all pulmonary nodules visually detected in both scans using the volumetry tool included in the Siemens LungCare software. The 95% limits of agreement between nodule volume measurements on different scans were calculated using the Bland and Altman method for assessing measurement agreement. Intra- and interobserver agreement of volume measurement were determined using repetitive measurements of 50 randomly selected nodules at the same scan by the same and different observers. Taking into account all 151 nodules, 95% limits of agreement were -20.4 to 21.9% (standard error 1.5%); they were -19.3 to 20.4% (standard error 1.7%) for 105 nodules <10 mm. Limits of agreement were -3.9 to 5.7% for intraobserver and -5.5 to 6.6% for interobserver agreement. Precision of in vivo volumetric analysis of nodules with an automatic volumetry software tool was sufficiently high to allow for detection of clinically relevant growth in small pulmonary nodules.

Adult↗
PubMed1994

Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package.

The peptide sequential assignment algorithm presented here was implemented as a macro within the CONnectivity TRacing ASsignment Tools (CONTRAST) computer software package. The algorithm provides a semi- or fully automated global means of sequentially assigning the NMR backbone resonances of proteins. The program's performance is demonstrated here by its analysis of realistic computer-generated data for IIIGlc, a 168-residue signal-transducing protein of Escherichia coli [Pelton et al. (1991) Biochemistry, 30, 10043-10057]. Missing experimental data (19 resonances) were generated so that a complete assignment set could be tested. The algorithm produces sequential assignments from appropriate peak lists of nD NMR data. It quantifies the ambiguity of each assignment and provides ranked alternatives. A 'best first' approach, in which high-scoring local assignments are made before and in preference to lower scoring assignments, is shown to be superior (in terms of the current set of CONTRAST scoring routines) to approaches such as simulated annealing that seek to maximize the combined scores of the individual assignments. The robustness of the algorithm was tested by evaluating the effects of imposed frequency imprecision (scatter), added false signals (noise), missing peaks (incomplete data), and variation in user-defined tolerances on the performance of the algorithm.

Algorithms↗
PubMed2007

[Electronic documentation of injuries of the hand with a semantic network: effective and efficient methods for the documentation of clinical and administrative processes].

BACKGROUND: An efficient medical documentation is mandatory for a trauma-oriented department in the DRG environment. Besides the continuously increasing clinical/administrative demands, the additional documentation for quality assurance, clinical studies, and research requires additional efforts. Standard solutions are only partially effective. Especially in hand surgery there is a high demand for sophisticated clinical documentation, represented by a wide variety of classifications in diagnosis and therapy. The standard documentation tools lack accuracy. The development of a software tool that defines administrative/business processes and simultaneously generates clinical and administrative information was the goal of this project. METHODS AND RESULTS: With a standard medical terminology, an innovative semantic network, and a completely new graphical user interface, it was possible to develop and introduce a software program specifically adjusted for hand surgery. This program facilitated for the first time a single-stage acquisition of clinically relevant scientific data and the simultaneous generation of DRG, quality assurance, and administrative data relevant for the hospital's revenues. CONCLUSIONS: The newly developed software tool is a step forward into a new dimension of medical software, obviating the need for multi/documentation and significantly improving the quality of clinically relevant medical data.

Computer Graphics↗
PubMed2006

Data standards for flow cytometry.

Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture the full scope of FCM experiments and there is a demand for software tools that can assist in the exploration and analysis of large FCM datasets. We are implementing a standardized approach to capturing, analyzing, and disseminating FCM data that will facilitate both more complex analyses and analysis of datasets that could not previously be efficiently studied. Initial work has focused on developing a community-based guideline for recording and reporting the details of FCM experiments. Open source software tools that implement this standard are being created, with an emphasis on facilitating reproducible and extensible data analyses. As well, tools for electronic collaboration will assist the integrated access and comprehension of experiments to empower users to collaborate on FCM analyses. This coordinated, joint development of bioinformatics standards and software tools for FCM data analysis has the potential to greatly facilitate both basic and clinical research--impacting a notably diverse range of medical and environmental research areas.

Cell Separation↗
PubMed1999

The SPORT-NMR software: a tool for determining relaxation times in unresolved NMR spectra.

A software package which allows the correct determination of individual relaxation times for all the nonequivalent nuclei in poorly resolved NMR spectra is described. The procedure used, based on the fitting of each spectrum in the series recorded in the relaxation experiment, should improve the analysis of relaxation data in terms of quantitative dynamic information, especially in anisotropic phases. Tests on simulated data and experimental examples concerning 1H and 13C T1rho measurement in a solid copolymer and 2H T1Z and T1Q measurement in a liquid crystal are shown and discussed.

Anisotropy↗
PubMed2006

Improvements in the analysis strategy make single nucleotide polymorphism analysis a powerful tool in the detection and characterization of amplified chromosomal regions in human tumors.

OBJECTIVE: Single nucleotide polymorphism analysis (SNP) has recently been proposed as an alternative technique to comparative genomic hybridization (CGH) for defining loss of heterozygosity and gene copy number changes in a single experimental setup. In order to assess the potential of SNP analysis to complement or, ultimately, substitute CGH results, we applied both techniques to five primary tumor samples and two tumor cell lines. This was complemented by dilution experiments based on normal lymphocyte DNA to decipher the lower detection limit for genetic alterations. METHODS/RESULTS: Using an in-house software tool, we demonstrated that SNP analysis permits the generation of chromosomal alteration patterns that largely resemble conventional CGH ratio profiles of a given tumor/cell line. Moreover, compared to CGH, our SNP software tool allows a much more detailed definition of amplicon sizes and involved candidate genes. This advantage even persisted when the technique was applied to DNA with more than 60% of nontumor content. However, the detection of chromosomal losses is severely hampered by the presence of nontumor DNA so that the use of the SNP technique should be limited to tumor samples with more than 80% tumor DNA. CONCLUSION: SNP analysis is a very valuable tool for the detection and characterization of high-level chromosomal amplifications in the vast majority of primary tumor samples. Our software tool improves the analysis of SNP data and the presentation of the results, bridging the gap to existing CGH knowledge (http://bioinformatics.uni-muenster.de, 'Publications and Supplements').

Algorithms↗
PubMed2005

Scripting-customized microscopy tools for Digital Micrograph.

Software is an integral part of all electron microscopy systems, encompassing hardware control, data acquisition and processing. It is unlikely that any one software system will meet all the requirements of experienced users. However, if the software supports custom scripting, then users are well placed to address any shortcomings by writing their own software. In this paper, we highlight the scripting capability within Gatan Inc.'s Digital Micrograph (DM) software, a widely used program for TEM imaging and EELS spectroscopy. We show how scripting can greatly extend the capabilities of the DM software, in tasks ranging in complexity from simple image manipulation through to full-blown microscope/imaging filter control and data acquisition. Scripting enables customized software tools to be developed to meet individual experimental needs, something which no software manufacturer could ever hope to do on a commercial basis. In essence, scripting allows the microscopist to drive the software rather than the software drive the microscopist. To foster an increased awareness and interest in DM scripting we have developed a web-based archive for DM scripts, which is freely accessible via the internet.

Journal Article↗
PubMed2004

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases.

MOTIVATION: The prediction of transcription units (TUs, which are similar to operons) is an important problem that has been tackled using many different approaches. The availability of complete microbial genomes has made genome-wide TU predictions possible. Pathway-genome databases (PGDBs) add metabolic and other organizational (i.e. protein complexes) information to the annotated genome, and are able to capture TU organization information. These characteristics of PGDBs make them a suitable framework for the development and implementation of TU predictors. RESULTS: We implemented a TU predictor that uses only intergenic distance and functional classification of genes to predict TU boundaries, and applied it to EcoCyc, our PGDB of Escherichia coli. To this original predictor, we added information on metabolic pathways, protein complexes and transporters, all readily available in EcoCyc, in order to generate an enhanced predictor. The enhanced predictor correctly predicted 80% of the known E.coli TUs (69% of the known operons), a moderate improvement over the original predictor's performance (75% of TUs and 65% of operons correctly predicted), demonstrating that the extra information available in the PGDB does indeed improve prediction performance. Performance of this E.coli-based predictor on a genome other than that of E.coli was tested on BsubCyc, our computationally generated PGDB for Bacillus subtilis, for which a set of 100 known operons is available. Prediction accuracy decreased substantially (46% of the known operons correctly predicted). This was due in part to missing information in BsubCyc, which prevented full use of the predictor's features. The augmented predictor has been implemented as part of our Pathway Tools software suite, and can be used to populate a PGDB with predicted TUs. AVAILABILITY: The TU predictor is included in version 7.0 of the Pathway Tools software suite. Pathway Tools 7.0 is available free of charge to academic institutions and for a fee to commercial enterprises. It runs on Sun Solaris 8, Linux and Windows. TUs predicted on the Caulobacter crescentus and Mycobacterium tuberculosis (H37Rv) genomes are available in our CauloCyc and MtbrvCyc databases, available at the BioCyc web site (http://biocyc.org). To obtain version 7.0 of Pathway Tools, follow the directions in our web site, http://biocyc.org/download.shtml.

Algorithms↗
PubMed1998

SAAM II: Simulation, Analysis, and Modeling Software for tracer and pharmacokinetic studies.

Kinetic analysis and integrated systems modeling have contributed substantially to our understanding of the physiology and pathophysiology of metabolic systems and the distribution and clearance of drugs in humans and animals. In recent years, many researchers have become aware of the usefulness of these techniques in the experimental design. With this has come the recognition that the discipline of kinetic analysis requires its own expertise. The expertise can impact experimental design in many ways, from the collaborative and service activities in which individuals interact in formal ways to the development of software tools to aid in kinetic analysis. The purpose of this report is to describe one such software tool, Simulation, Analysis, and Modeling Software II (SAAM II). In the first part, we describe in general how the user can take advantage of the capabilities of the software system, and in the second part, we give three specific examples using multicompartmental models found in lipoprotein (apolipoprotein B [apoB] kinetics) and diabetes (glucose minimal model) research.

Algorithms↗
PubMed2004

Comparative evaluation of microarray analysis software.

A wide variety of software tools are available to analyze microarray data. To identify the optimum software for any project, it is essential to define specific and essential criteria on which to evaluate the advantages of the key features. In this review we describe the results of our comparison of several software tools. We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the "ideal microarray analysis software suite."

Data Interpretation, Statistical↗
PubMedDate not supplied

Comparative life-cycle assessments for biomass-to-ethanol production from different regional feedstocks.

This study compares life-cycle (cradle-to-gate) energy consumption and environmental impacts for producing ethanol via fermentation-based processes starting with two lignocellulosic feedstocks: virgin timber resources or recycled newsprint from an urban area. The life-cycle assessment in this study employed a novel combination of computer-aided tools. These tools include fermentation process simulation coupled with an impact assessment software tool for the manufacturing process life-cycle stage impacts. The process simulation file was provided by the National Renewable Energy Laboratory (NREL) and was modified slightly to accommodate these different feedstocks. For the premanufacturing process life-cycle stage impacts, such as the fuels and process chemicals used, transportation, and some preparatory steps (wood chipping, etc.), a life-cycle inventory database (the Boustead Model) coupled with an impact assessment software tool were used (the Environmental Fate and Risk Assessment Tool). The Newsprint process has a slightly lower overall composite environmental index (created from eight impact categories) compared to the Timber process. However, the Timber process consumes less electricity, produces fewer emissions in total, and has less of a human health impact. The amount of life-cycle fossil energy required to produce ethanol is 14% of the energy content of the product, making the overall efficiency 86%. Process improvement strategies were evaluated for both feedstock processes, including recycle of reactor vent air and heat integration. Heat integration has the greatest potential to reduce fossil-derived energy consumption, to an extent that fossil-derived energy over the life cycle is actually saved per unit of ethanol produced. These energy efficiency values are superior to those observed in conventional fossil-based transportation fuels.

Biotechnology↗
PubMed2004

The "Sym'Previus" software, a tool to support decisions to the foodstuff safety.

Describing the Sym'Previus project, the software and its deliverable facilities is the aim of this present paper. This software concerns all the partners of the food industry who are involved in the management of food safety and allows food-borne pathogen behaviour in food to be predicted, as function of the environment (nature of the food, manufacturing process, conditions of conservation). This analysis of microbial behaviour has been possible thanks to the progress made in predictive microbiology since the 1980s. Sym'Previus offers to food industry professionals and their partners the possibility of applying this progress, by giving access to a database, to simulation systems and expertise.

Computer Simulation↗