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PubMed2003

Modeling regulatory networks at Virginia Tech.

The life of a cell is governed by the physicochemical properties of a complex network of interacting macromolecules (primarily genes and proteins). Hence, a full scientific understanding of and rational engineering approach to cell physiology require accurate mathematical models of the spatial and temporal dynamics of these macromolecular assemblies, especially the networks involved in integrating signals and regulating cellular responses. The Virginia Tech Consortium is involved in three specific goals of DARPA's computational biology program (Bio-COMP): to create effective software tools for modeling gene-protein-metabolite networks, to employ these tools in creating a new generation of realistic models, and to test and refine these models by well-conceived experimental studies. The special emphasis of this group is to understand the mechanisms of cell cycle control in eukaryotes (yeast cells and frog eggs). The software tools developed at Virginia Tech are designed to meet general requirements of modeling regulatory networks and are collected in a problem-solving environment called JigCell.

Animals↗
PubMed2004

Using online analytical processing to manage emergency department operations.

The emergency department (ED) is a unique setting in which to explore and evaluate the utility of information technology to improve health care operations. A potentially useful software tool in managing this complex environment is online analytical processing (OLAP). An OLAP system has the ability to provide managers, providers, and researchers with the necessary information to make decisions quickly and effectively by allowing them to examine patterns and trends in operations and patient flow. OLAP software quickly summarizes and processes data acquired from a variety of data sources, including computerized ED tracking systems. It allows the user to form a comprehensive picture of the ED from both system-wide and patient-specific perspectives and to interactively view the data using an approach that meets his or her needs. This article describes OLAP software tools and provides examples of potential OLAP applications for care improvement projects, primarily from the perspective of the ED. While OLAP is clearly a helpful tool in the ED, it is far more useful when integrated into the larger continuum of health information systems across a hospital or health care delivery system.

Decision Support Systems, Clinical↗
PubMed2006

Visual and automatic grading of coronary artery stenoses with 64-slice CT angiography in reference to invasive angiography.

The aim of this study was to assess the performance of a software tool for quantitative coronary artery analysis of computed tomography coronary angiography (CT-QCA) in comparison with invasive coronary angiography with quantitative analysis (CAG-QCA) as standard of reference. Two radiologists reviewed the CT angiography data sets (Siemens Sensation 64) of 25 patients, grading coronary artery stenoses visually and with a software tool (Circulation, Siemens). Twenty-three data sets with sufficient image quality were included in the final analysis. CAG revealed a total of 30 wall irregularities and 28 stenoses, of which 17 were graded as moderate and nine as hemodynamically significant. CT-QCA showed a better agreement to CAG-QCA, with a systematic overestimation of the degree of stenosis of 6.1% and limits of agreement of +36.1% and -23.9; the correlation coefficient was 0.82 (p < 0.0001). Using CT-QCA, sensitivity, specificity, and positive and negative predictive value were 89%, 100%, 89%, and 100%, respectively, for significant area stenoses greater than 75%. The positive predictive value for the visual assessment amounted to 53%. Interobserver variability between CT-QCA and visual assessment showed a kappa value of 0.72. In conclusion, software-supported CT-QCA makes it possible to quantify significant coronary artery stenoses automatically, with good agreement to CAG-QCA.

Contrast Media↗
PubMed1995

Assessment of mass properties of human head using various three-dimensional imaging modalities.

Better methods are needed to analyse personal protective devices, such as helmets or facemasks, before they are used in practice. Software tools to quantify three-dimensional craniofacial mass properties are developed to improve our understanding of craniofacial impact biomechanics, supplement existing knowledge of osseous structure and provide a comprehensive description of human head morphology. The application of state-of-the-art imaging systems, solid modelling and other software tools are studied to determine the associated errors in mass property estimation by spiral computed tomography, three-dimensional magnetic resonance and optical surface scanning using phantoms and cadaver head studies. Volume, centre of gravity and principal moments of inertia are determined from solid mathematical models for each scanning modality. Landmark-based registration is used to register scans of the same object obtained from the three imaging modalities to a common reference co-ordinate system. Physically and analytically determined mass properties are used as the standard for truth. Although this comparative study does not lend itself to statistical analysis owing to the small sample size, results indicate that any of the three imaging modalities can be used to predict mass properties within the uncertainty of existing methods. Applying these techniques in vivo is practical and feasible.

Cephalometry↗
PubMed2005

A fast and effective method to assess myocardial necrosis by means of contrast magnetic resonance imaging.

PURPOSE: Contrast magnetic resonance (CMR) can identify myocardial necrosis after gadolinium administration as a hyperenhanced (HE) area. Yet there are no software tools that can effectively quantify such an area. The aim of this study is to develop a robust and effective algorithmic method for defining the extent of myocardial necrosis evidenced through CMR. METHOD: Fifteen patients with previous myocardial infarction underwent nitrate Tetrofosmin G-SPECT and CMR. A software tool was developed, allowing semiautomatic detection of endocardial and epicardial borders and the automatic detection of HE regions. The accuracy of the proposed quantitative method of analysis has been tested with G-SPECT analysis that it is less than an ideal method for assessing myocardial viability, but at present is accepted and widely used in the clinical arena. RESULTS: Segmental (SEHE) and global extension of HE were evaluated. HE was present in 161 of the 255 analyzed segments. Of the 161 HE segments, the mean SEHE was 36 +/- 30%. The operator independence (intraobserver: r = 0.97, p < 0.0001, interobserver: r = 0.95, p < 0.0001) was good and significant, with noticeable time savings with respect to manual analysis. There was strong and inverse correlation between SEHE and scintigraphic regional uptake reduction (r = -0.66, p < 0.0001), and also a positive correlation between SEHE and SPECT defect extension (r = 0.75, p < 0.0001). When assessing the global extent of necrosis, the correlation between the two techniques was strong (r = 0.79, p = 0.0004). CONCLUSIONS: The proposed method of quantifying myocardial necrosis by CMR is highly reliable, reproducible, and operator-independent for quantifying.

Algorithms↗
PubMed2003

A software tool-box for analysis of regulatory RNA elements.

We describe an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5' UTR, CDS, 3' UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3' UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops. In addition, consensus templates are used to determine whether there are any functional structures present for translational control (template: IRE), structured RNA (template: tRNA consensus) or catalytic RNA (template: trans-splicing RNA), giving indications as to how well the structures found match to these templates. The tool box has been implemented as a WWW server at http://wb2x01.biozentrum.uni-wuerzburg.de/.

Internet↗
PubMed1994

Bioinformatics.

Computer databases, networks and software tools are essential materials and methods for biomedical research and are involved in almost every aspect of disease gene mapping and positional cloning. Public databases of DNA and protein sequences and genetic and physical map information are increasing rapidly in size and complexity and are also improving in quality, comprehensiveness, interoperability and access. A new generation of software tools for navigating through the biomedical literature has become available. Programs for sequence homology searching and genetic map construction have become more sophisticated, yet easier to use. Global computer networks are bringing state-of-the-art capabilities to all.

Chromosome Mapping↗
PubMed2005

Randomized algorithms for motif detection.

MOTIVATION: Motif detection for DNA sequences has many important applications in biological studies, e.g. locating binding sites regulatory signals, designing genetic probes etc. In this paper, we propose a randomized algorithm, design an improved EM algorithm and combine them to form a software tool. RESULTS: (1) We design a randomized algorithm for consensus pattern problem. We can show that with high probability, our randomized algorithm finds a pattern in polynomial time with cost error at most x l for each string, where l is the length of the motif and can be any positive number given by the user. (2) We design an improved EM algorithm that outperforms the original EM algorithm. (3) We develop a software tool, MotifDetector, that uses our randomized algorithm to find good seeds and uses the improved EM algorithm to do local search. We compare MotifDetector with Buhler and Tompa's PROJECTION which is considered to be the best known software for motif detection. Simulations show that MotifDetector is slower than PROJECTION when the pattern length is relatively small, and outperforms PROJECTION when the pattern length becomes large. AVAILABILITY: It is available for free at http://www.cs.cityu.edu.hk/~lwang/software/motif/index.html, subject to copyright restrictions.

Algorithms↗
PubMed2006

An integrative software package for gastrointestinal biomagnetic data acquisition and analysis using SQUID magnetometers.

The study of bioelectric and biomagnetic activity in the human gastrointestinal (GI) tract is of great interest in clinical research due to the proven possibility to detect pathological conditions thereof from electric and magnetic field recordings. The magnetogastrogram (MGG) and magnetoenterogram (MENG) can be recorded using superconducting quantum interference device (SQUID) magnetometers, which are the most sensitive magnetic flux-to-voltage converters currently available. To address the urgent need for powerful acquisition and analysis software tools faced by many researchers and clinicians in this important area of investigation, an integrative and modular computer program was developed for the acquisition, processing and analysis of GI SQUID signals. In addition to a robust hardware implementation for efficient data acquisition, a number of signal processing and analysis modules were developed to serve in a variety of both clinical procedures and scientific investigations. Implemented software features include data processing and visualization, waterfall plots of signal frequency spectra as well as spatial maps of GI signal frequencies. Moreover, a software tool providing powerful 3D visualizations of GI signals was created using realistic models of the human torso and internal organs.

Gastrointestinal Diseases↗
PubMed2004

Interleaved echo-planar imaging for fast multiplanar magnetic resonance temperature imaging of ultrasound thermal ablation therapy.

PURPOSE: To develop a multiplanar magnetic resonance temperature imaging (MRTI) technique based on interleaved gradient-echo echo-planar imaging (EPI), verify in phantom, develop software tools to process and display data on a clinical scanner in near real-time, and demonstrate feasibility to monitor ultrasound thermal ablation therapy in vivo. MATERIALS AND METHODS: Temperature estimation used complex phase-difference subtraction of the EPI MRTI data to indirectly measure the temperature-dependent water proton-resonance-frequency shift. Software tools were developed to run on a clinical 1.5-T MR scanner that processed and displayed relevant temperature and thermal dosimetry data during the course of thermal ablation treatments in canine brain and prostate in vivo. RESULTS: EPI MRTI provided multi-planar acquisitions and increased temperature sensitivity and lipid suppression. Relative to a single-plane fast gradient-echo MRTI sequence at comparable spatial and temporal resolutions in phantom, EPI MRTI demonstrated a three-fold increase in sensitivity and slice coverage per TR. In vivo monitoring of ultrasound thermal ablation therapy in canine brain and prostate demonstrated the usefulness of the temperature and thermal dose information. CONCLUSION: Multi-planar MRTI allowed progression of thermal damage to be monitored and treatment parameters adjusted in near real-time (less than five second delay). EPI MRTI is an effective multi-planar monitoring method during ultrasound thermal ablation procedures.

Animals↗
PubMed2006

An automated method for rapid identification of putative gene family members in plants.

BACKGROUND: Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We have simplified the process and significantly shortened the time required by condensing many steps into a few scripts or programs to rapidly identify putative gene family members beginning with a single query sequence. RESULTS: In this report we 1) describe the software tools (SimESTs, PCAT, and SCAT) developed to automate the gene family identification, 2) demonstrate the validity of the method by correctly identifying 3 of 4 PAL gene family members from Arabidopsis using EST data alone, 3) identify 2 to 6 CAD gene family members from Glycine max (previously unidentified), and 4) identify 2 members of a putative Glycine max gene family previously unidentified in any plant species. CONCLUSION: Gene families in plants, particularly that subset where purifying selection has occurred in the coding region, can be identified quickly and easily by integrating our software tools and commonly available contig assembly and ORF identification programs.

Arabidopsis↗
PubMed2005

Advanced multimodal visualisation of clinical gait and fluoroscopy analyses in the assessment of total knee replacement.

Traditional gait and fluoroscopy analysis of human movement are largely utilised but are still limited in registration, integration, synchronisation and visualisation capabilities. The present work exploits the features of a recently developed software tool based on multimodal display (Data Manager developed within the EU-funded project 'Multimod') in an exemplary clinical case. Standard lower limb gait analysis, comprising segment position, ground reaction force and EMG data collection, and three-dimensional fluoroscopy analysis at the replaced joint were performed in a total knee replacement patient while ascending stairs. Clinical information such as X-rays and standard scores were also available. Data Manager was able to import all this variety of data and to structure these in an original hierarchical tree. Bone and prosthesis component models were registered to corresponding marker position data for effective three-dimensional animations. These were also synchronised with corresponding standard video sequences. Animations, video, time-histories of collected and also processed data were shown in various combinations, according to specific interests of the bioengineering and medical professionals expected to observe and to interpret this large amount of data. This software tool demonstrated to be a valuable means to enhance representation and interpretation of measurements coming from human motion analysis. In a single software, a thorough and effective clinical and biomechanical analysis of human motion was performed.

Arthroplasty, Replacement, Knee↗
PubMed2003

[MGAP-A microbe genome annotation platform].

A Microbe Genome Annotation Platform (MGAP) was developed and applied to the cynobacterium PCC7002 genome annotation. Various bioinformatics software tools from sequence analysis to gene identification and function prediction were implemented in MGAP. Protein sequence databases SWISSPROT and PDBseq, protein information resource InterPro and COG were also integrated in the platform. The web interface of MGAP has the functionality to display a circular map of gene distribution and GC contents throughout the genome. Detailed information such as the DNA and protein sequence, the location of genes on chromosomes can be viewed by clicking the corresponding object within the map. MGAP is based on a PC/Linux system affordable for small biological laboratories and has the advantage of using free software tools including MySQL, Apache and Perl.

Cyanobacteria↗
PubMed2002

Combining fuzzy querying of imprecise data and predictive microbiology using category-based reasoning for prediction of the possible microbial spoilage in foods: application to Listeria monocytogenes.

Various predictive models of microbial behavior have been created and extensive data collection has been done by numerous private or public laboratories. However, significant differences between predicted and observed values in foods have been observed and need to be stressed, understood and explained as much as possible. In this paper, we present a software tool (currently at the level of a prototype) able: (i) to store in a database all relevant information expressed on one hand as qualitative or quantitative data and on the other hand as precise or imprecise data; (ii) to retrieve the more relevant information from the database using queries where criteria may be expressed as fuzzy values in order to enhance the flexibility of the search: (iii) to compute, in addition to the nearest data, an estimation of searched values using statistical models. The architecture of this software tool is structured as a category-based reasoning system. Example queries about Listeria monocytogenes (L. monocytogenes) illustrate the functionalities of this tool.

Computer Simulation↗
PubMed2006

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

BACKGROUND: We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable. RESULTS: We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the Project Manager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping. CONCLUSION: The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.

Animals↗
PubMed2025

Generating multiple alignments on a pangenomic scale.

MOTIVATION: Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data. RESULTS: We show that the combination of a well-known anchor-based method with the technique of prefix-free parsing yields an approach that is able to generate multiple alignments on a pangenomic scale, provided that large-scale structural variants are rare. Furthermore, experiments with real world data show that our software tool PANgenomic Anchor-based Multiple Alignment significantly outperforms current state-of-the art programs. AVAILABILITY AND IMPLEMENTATION: Source code is available at: https://gitlab.com/qwerzuiop/panama, archived at swh:1:dir:e90c9f664995acca9063245cabdd97549cf39694.

Software↗
PubMed2006

The plasminogen-like molecule apically secreted by epithelial thyroid cells is sulfated.

Plasminogen (Pl), a circulating protease synthesized in the liver, is also present in several tissues. In the thyroid gland a Pl-like protease was found in the apical lumen where it is involved, through its proteolytic activity, in luminal degradation of thyroglobulin (Tg). Here, we showed for the first time that the Pl-like protease apically secreted by epithelial thyroid cells is sulfated, both on tyrosine residue(s) and on oligosaccharide side chains. The Pl molecule is composed of a large N-terminal moiety made of five distinct Kringle domains (K1-K5) separated by small peptidic fragments, and of a C-terminal domain with serine protease activity. Using a software tool able to predict tyrosine sulfation sites in protein sequences we localized the potential tyrosine sulfation sites of Pl. Then, we became aware that, whatever the species considered, at least three of the four potential tyrosine sulfation sites of Pl were located on Kringle sites, and more precisely, for K1, on the highly conserved binding domain of K1. We determined with the same software tool which potential sulfation sites were the most likely to be really sulfated. We hypothesize that the sulfation of these sites modulates the binding properties of Pl.

Amino Acid Sequence↗