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At least 613 records · Page 34Linked to original sources
PubMed1999

TargetFinder: searching annotated sequence databases for target genes of transcription factors.

UNLABELLED: TargetFinder is a new software tool to search a database of annotated sequences for transcription factor binding sites located in context with other important transcription regulatory signals and regions, like the TATA element, the promoter, and so on, thereby greatly reducing the background usually associated with this kind of search. AVAILABILITY: The TargetFinder Web service is available at http://hercules.tigem.it/TargetFinder.html CONTACT: giovanni.lavorgna@hsr.it

Binding Sites↗
PubMed2001

Towards NeuroML: model description methods for collaborative modelling in neuroscience.

Biological nervous systems and the mechanisms underlying their operation exhibit astonishing complexity. Computational models of these systems have been correspondingly complex. As these models become ever more sophisticated, they become increasingly difficult to define, comprehend, manage and communicate. Consequently, for scientific understanding of biological nervous systems to progress, it is crucial for modellers to have software tools that support discussion, development and exchange of computational models. We describe methodologies that focus on these tasks, improving the ability of neuroscientists to engage in the modelling process. We report our findings on the requirements for these tools and discuss the use of declarative forms of model description--equivalent to object-oriented classes and database schema--which we call templates. We introduce NeuroML, a mark-up language for the neurosciences which is defined syntactically using templates, and its specific component intended as a common format for communication between modelling-related tools. Finally, we propose a template hierarchy for this modelling component of NeuroML, sufficient for describing models ranging in structural levels from neuron cell membranes to neural networks. These templates support both a framework for user-level interaction with models, and a high-performance framework for efficient simulation of the models.

Animals↗
PubMed2001

A clustering method for repeat analysis in DNA sequences.

BACKGROUND: A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats. RESULTS: The resulting software tool collects all repeat classes and outputs summary statistics as well as a file containing multiple sequences (multi fasta), that can be used as the target of searches. Its use is demonstrated here on several complete microbial genomes, the entire Arabidopsis thaliana genome, and a large collection of rice bacterial artificial chromosome end sequences. CONCLUSIONS: We propose a new clustering method for analysis of the repeat data captured in suffix trees. This method has been incorporated into a system that can find repeats in individual genome sequences or sets of sequences, and that can organize those repeats into classes. It quickly and accurately creates repeat databases from small and large genomes. The associated software (RepeatFinder), should prove helpful in the analysis of repeat structure for both complete and partial genome sequences.

Algorithms↗
PubMed2004

3D-catFISH: a system for automated quantitative three-dimensional compartmental analysis of temporal gene transcription activity imaged by fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) of neural activity-regulated, immediate-early gene (IEG) expression provides a method of functional brain imaging with cellular resolution. This enables the identification, in one brain, of which specific principal neurons were active during each of two distinct behavioral epochs. The unprecedented potential of this differential method for large-scale analysis of functional neural circuits is limited, however, by the time-intensive nature of manual image analysis. A comprehensive software tool for processing three-dimensional, multi-spectral confocal image stacks is described which supports the automation of this analysis. Nuclei counterstained with conventional DNA dyes and FISH signals indicating the sub-cellular distribution of specific, IEG RNA species are imaged using different spectral channels. The DNA channel data are segmented into individual nuclei by a three-dimensional multi-step algorithm that corrects for depth-dependent attenuation, non-isotropic voxels, and imaging noise. Intra-nuclear and cytoplasmic FISH signals are associated spatially with the nuclear segmentation results to generate a detailed tabular/database and graphic representation. Here we present a comprehensive validation of data generated by the automated software against manual quantification by human experts on hippocampal and parietal cortical regions (96.5% concordance with multi-expert consensus). The high degree of reliability and accuracy suggests that the software will generalize well to multiple brain areas and eventually to large-scale brain analysis.

Algorithms↗
PubMed1997

Automatic calculation of three-dimensional margins around treatment volumes in radiotherapy planning.

Following the publication of ICRU Report 50, the concepts of GTV (gross tumour volume). CTV (clinical target volume) and PTV (planning target volume) are being used in radiotherapy planning with increasing frequency. In 3D planning, the GTV (or CTV) is normally outlined by the clinician in CT or MRI slices. The PTV is determined by adding margins to these volumes. Since manual drawing of an accurate 3D margin in a set of 2D slices is extremely time consuming, software has been developed to automate this step in the planning. The target volume is represented in a 3D matrix grid with voxel values one inside and zero outside the target volume. It is expanded by centering an ellipsoid at every matrix element within the volume. The shape of the ellipsoid reflects the size of the margins in the three main orthogonal directions. Finally, the PTV contours are determined from the 50% iso-value lines of the expanded volume. The software tool has been in clinical use since the end of 1994 and has mostly been applied to the planning of prostate irradiations. The accuracy is better than can be achieved manually and the workload has been reduced considerably (from 4 h manually to approximately 1 min automatically).

Algorithms↗
PubMed1997

Clinical protocol development using Inter/IntraNet technology: the FENARETE system.

In this work we present FENARETE, a software tool to design and distribute clinical protocols in an Inter/IntraNet framework. We consider a medical protocol as a clinical behaviour scheme, formally and clearly defined with sufficient details. Our work allows the knowledge content of any clinical protocol to be fully represented in a symbolic style. A computer based support tool that works as an interface between clinicians and the protocol knowledge base is regarded by the authors as a basic building block developing an integrated environment for medical protocols design and management. The FENARETE application has been developed in Java and it is available for any Internet-linked machine with a Java-compatible browser.

Clinical Protocols↗
PubMed2000

Prediction of exact boundaries of exons.

It is known that while the programs used to predict genes are good at determining coding nucleotides, there are considerable inaccuracies in the determination of the gene structural elements. Among them, the most notable is that of the exact boundaries of exons. In order to assess this, we had earlier reviewed various programs that predict potential splice sites and exons. The results led to the following two observations: (i) a high proportion of false positive splice sites from computational predictions occur in the vicinity of real splice sites; and (ii) current algorithms are misled to predict wrong splice sites more often when the coding potential ends within +/-25 nucleotides from real sites than when it ends at farther positions. In this report, we review decision tree models for human splice sites and the resultant software tool, namely SpliceProximalCheck, that discriminates such'proximal' false positives from real splice sites. Further presented is an integrated system (MZEF-SPC) with Splice ProximalCheck (SPC) as a front-end tool operating on the results of Michael Zhang's exon finder program. Examination of the output of the integrated program on an illustrative gene set revealed that as much as 61 of 93 MZEF-predicted false positive exons could be eliminated by SPC for a loss of only 3 out of 33 MZEF-predicted true positive exons.

Algorithms↗
PubMed2001

Clinical use of electronic portal imaging: report of AAPM Radiation Therapy Committee Task Group 58.

AAPM Task Group 58 was created to provide materials to help the medical physicist and colleagues succeed in the clinical implementation of electronic portal imaging devices (EPIDs) in radiation oncology. This complex technology has matured over the past decade and is capable of being integrated into routine practice. However, the difficulties encountered during the specification, installation, and implementation process can be overwhelming. TG58 was charged with providing sufficient information to allow the users to overcome these difficulties and put EPIDs into routine clinical practice. In answering the charge, this report provides; comprehensive information about the physics and technology of currently available EPID systems; a detailed discussion of the steps required for successful clinical implementation, based on accumulated experience; a review of software tools available and clinical use protocols to enhance EPID utilization; and specific quality assurance requirements for initial and continuing clinical use of the systems. Specific recommendations are summarized to assist the reader with successful implementation and continuing use of an EPID.

Biophysical Phenomena↗
PubMed2004

Software for the analysis of species-specific vocalizations.

Vocalization calls are behaviorally relevant complex sounds that typically contain several harmonics and show frequency and amplitude modulation. In this paper, an introduction to a software tool for the analysis of species-specific vocalizations is presented. The algorithm automatically or under user supervision detects time-varying amplitude and frequency parameters, which can serve for the statistical analysis of calls or as the substrate for the manipulation and synthesis of artificial calls. The described program and its results will be used in studying the representation of complex sounds in the central nervous system.

Animals↗
PubMed1999

Assessment of myocardial perfusion using multisection first-pass MRI and color-coded parameter maps: a comparison to 99mTc Sesta MIBI SPECT and systolic myocardial wall thickening analysis.

The most recently reported magnetic resonance first-pass myocardial perfusion studies were restricted to single slice imaging or a data analysis based on interactively placed regions of interest. This study was designed to investigate a new saturation recovery TurboFLASH sequence for multisection myocardial perfusion imaging and to develop a pixel-based software tool to calculate qualitative perfusion parameters. The findings of perfusion imaging were compared to percent systolic myocardial wall thickening analysis and 99mTc Sesta MIBI SPECT. Six healthy volunteers and twelve patients with proven coronary artery disease (CAD) or chronic myocardial infarction were examined. Diagnostic images were acquired for all volunteers and patients with the multisection saturation recovery TurboFLASH sequence. Perfusion defects could be visualized on parameter maps for signal intensity increase over baseline and signal intensity upslope. Sensitivity and specificity were 76.9% and 97.1% for first-pass perfusion MRI, and respectively 84.6% and 94.3% for CINE imaging. All perfusion defects determined with 99mTc Sesta MIBI SPECT were identified by the combined analysis of myocardial perfusion and wall thickening. The presented software demonstrated a pixel-based analysis of first-pass perfusion studies and simplified image interpretation in a clinical setting. The combination of perfusion and wall motion imaging provided complementary information for the treatment of patients suffering from CAD.

Adult↗
PubMed2006

[Renal transplant: color duplex ultrasound and contrast-enhanced ultrasound in the evaluation of the early postoperative phase and surgical complications].

Contrast ultrasound is a promising and straightforward method that is superior to established sonographic techniques such as conventional B-mode scanning which is used for volume measurement and hematoma demonstration. Color Doppler is important for the evaluation of rejection, the detection of perfusion defects, and complete vascularization in the diagnostic evaluation of kidney grafts. Moreover, contrast US has the potential for tumor characterization in transplanted kidneys. A single examination by contrast ultrasound can answer a variety of questions with respect to the early postoperative phase and chronic damage. New applications of contrast US will arise from the further technical development of ultrasound equipment. The rapid technical advances seen in recent years have been followed by the introduction of new software tools for the analysis of raw datasets or the improved visualization of microbubbles at very low energy. Initial studies show that efficient and early diagnosis of rejection is possible. Surgical complications like perfusion defects or hematoma can also be identified.

Animals↗
PubMed2006

Analytic webs support the synthesis of ecological data sets.

A wide variety of data sets produced by individual investigators are now synthesized to address ecological questions that span a range of spatial and temporal scales. It is important to facilitate such syntheses so that "consumers" of data sets can be confident that both input data sets and synthetic products are reliable. Necessary documentation to ensure the reliability and validation of data sets includes both familiar descriptive metadata and formal documentation of the scientific processes used (i.e., process metadata) to produce usable data sets from collections of raw data. Such documentation is complex and difficult to construct, so it is important to help "producers" create reliable data sets and to facilitate their creation of required metadata. We describe a formal representation, an "analytic web," that aids both producers and consumers of data sets by providing complete and precise definitions of scientific processes used to process raw and derived data sets. The formalisms used to define analytic webs are adaptations of those used in software engineering, and they provide a novel and effective support system for both the synthesis and the validation of ecological data sets. We illustrate the utility of an analytic web as an aid to producing synthetic data sets through a worked example: the synthesis of long-term measurements of whole-ecosystem carbon exchange. Analytic webs are also useful validation aids for consumers because they support the concurrent construction of a complete, Internet-accessible audit trail of the analytic processes used in the synthesis of the data sets. Finally we describe our early efforts to evaluate these ideas through the use of a prototype software tool, SciWalker. We indicate how this tool has been used to create analytic webs tailored to specific data-set synthesis and validation activities, and suggest extensions to it that will support additional forms of validation. The process metadata created by SciWalker is readily adapted for inclusion in Ecological Metadata Language (EML) files.

Data Collection↗
PubMed2006

Computer-assisted analysis of 4D cardiac MR image sequences after myocardial infarction.

OBJECTIVES: Spatial-temporal MR image sequences of the heart contain information about shape and motion changes and pathological structures after myocardial infarction. In this paper a Heart Analysis Tool (HeAT) for the quantitative analysis of 4D MR image sequences of infarct patients is presented. METHODS: HeAT supports interactive segmentation of anatomical and pathological structures. Registration of Cine- and DE-MR image data is applied to enable their combined evaluation during the analysis process. Partitioning of the myocardium in segments enables the analysis with high local resolution. Corresponding segments are generated and used for inter/intrapatient comparison. Quantitative parameters were extracted and visualized. RESULTS: Parameters like endocard movement in the infarcted area of six infarct patients were computed in HeAT. Parameters in the infarct area show the expected dysfunctional characteristics. Based on theses parameters passive endocardial movement and myocardial areas with decreased contraction could be identified. CONCLUSION: In contrast to other software tools HeAT supports the combination of contour information of Cine-MR and DE-MR, local analysis with high resolution and inter/intra patient comparison. HeAT enables an observer-independent evaluation of the complex cardiac image data. Using HeAT in further studies can increase the understanding of left ventricle (LV) remodeling.

Algorithms↗
PubMed2005

Gene discovery in neuropharmacological and behavioral studies using Affymetrix microarray data.

We describe methods and software tools for doing data analysis based on Affymetrix microarray data, emphasizing often neglected issues. In our experience with neuroscience studies, experimental design and quality assessment are vital. We also describe in detail the pre-processing methods we have found useful for Affymetrix data. Finally, we summarize the statistical literature and describe some pitfalls in the post-processing analysis.

Animals↗
PubMed2003

MAVG: locating non-overlapping maximum average segments in a given sequence.

SUMMARY: MAVG is a software tool for finding k non-overlapping maximum-average segments that are sufficiently long in a given sequence of real numbers, for any k > 0. It has applications in several areas of biomolecular sequence analysis including locating GC-rich regions and CpG islands in a genomic sequence, and annotating multiple sequence alignments. AVAILABILITY: http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/.

Algorithms↗
PubMed1991

A Hypercard program for the identification of biological specimens.

A Hypercard-based software tool developed to provide help in the identification of biological specimens is presented. The package implements a matching algorithm that compares alphanumeric strings and runs on Macintosh computers, though its simple architecture can be transferred to other computers and/or other programming environments. The overall performance of the program and its easy customization to specific problems are demonstrated by discussing at length one application in the field of earthworm identification.

Algorithms↗
PubMed2003

Pathways database system: an integrated system for biological pathways.

MOTIVATION: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. RESULTS: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data. AVAILABILITY: Available on request from the authors.

Database Management Systems↗
PubMed2005

Sociomics! Using the IssueCrawler to map, monitor and engage with the global proteomics research network.

We invite comment upon an experiment to locate proteomics on the WWW using a software tool called the IssueCrawler. We call our research "sociomics" because, like the bioscience omics, it is a semi-automated, computerised approach to the global analysis of data, whose computerised results can be integrated towards the development of a new "systems sociology" approach to the study of society. Our findings are that proteomics on the web is a scale-free network whose nodes display considerable "dynamic range".

Cluster Analysis↗