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PubMed2005

Automated identification of axonal growth cones in time-lapse image sequences.

The isolation and purification of axon guidance molecules has enabled in vitro studies of the effects of axon guidance molecule gradients on numerous neuronal cell types. In a typical experiment, cultured neurons are exposed to a chemotactic gradient and their growth is recorded by manual identification of the axon tip position from two or more micrographs. Detailed and statistically valid quantification of axon growth requires evaluation of a large number of neurons at closely spaced time points (e.g. using a time-lapse microscopy setup). However, manual tracing becomes increasingly impractical for recording axon growth as the number of time points and/or neurons increases. We present a software tool that automatically identifies and records the axon tip position in each phase-contrast image of a time-lapse series with minimal user involvement. The software outputs several quantitative measures of axon growth, and allows users to develop custom measurements. For, example analysis of growth velocity for a dissociated E13 mouse cortical neuron revealed frequent extension and retraction events with an average growth velocity of 0.05 +/- 0.14 microm/min. Comparison of software-identified axon tip positions with manually identified axon tip positions shows that the software's performance is indistinguishable from that of skilled human users.

Animals↗
PubMedDate not supplied

Researcher's Workbench.

The Researcher's Workbench, developed at the University of Utah College of Nursing, is a computer toolkit for nurse researchers. Workbench includes a set of software tools, most of which are commercially available, to support each stage of the research process. The tools reside on a Macintosh II desk-top computer (Apple Computer, Cupertino, CA) that houses processors to run both Macintosh and MS-DOS (Microsoft Corporation) software. The Workbench is available to all College of Nursing faculty, research associates, and graduate students. This article describes the purpose, methods, design, and implementation of the Workbench. The article assumes familiarity with personal computer terminology.

Computers↗
PubMed2006

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

BACKGROUND: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. RESULTS: We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments. CONCLUSION: Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter) and http://www.girinst.org/censor/index.php (Censor).

Animals↗
PubMed2001

Omiga: a PC-based sequence analysis tool.

Computer-based sequence analysis, notation, and manipulation are a necessity for all molecular biologists working with any but the most simple DNA sequences. As sequence data become increasingly available, tools that can be used to manipulate and annotate individual sequences and sequence elements will become an even more vital implement in the molecular biologist's arsenal. The Omiga DNA and Protein Sequence Analysis Software tool, version 2.0 provides an effective and comprehensive tool for the analysis of both nucleic acid and protein sequences that runs on a standard PC available in every molecular biology laboratory. Omiga allows the import of sequences in several common formats. Upon importing sequences and assigning them to various projects, Omiga allows the user to produce, analyze, and edit sequence alignments. Sequences may also be queried for the presence of restriction sites, sequence motifs, and other sequence features, all of which can be added into the notations accompanying each sequence. This newest version of Omiga also allows for sequencing and polymerase chain reaction (PCR) primer prediction, a functionality missing in earlier versions. Finally, Omiga allows rapid searches for putative coding regions, and Basic Local Alignment Search Tool (BLAST) queries against public databases at the National Center for Biotechnology Information (NCBI).

Humans↗
PubMed2001

Genomic sequence analysis tools: a user's guide.

The wealth of information from various genome sequencing projects provides the biologist with a new perspective from which to analyze, and design experiments with, mammalian systems. The complexity of the information, however, requires new software tools, and numerous such tools are now available. Which type and which specific system is most effective depends, in part, upon how much sequence is to be analyzed and with what level of experimental support. Here we survey a number of mammalian genomic sequence analysis systems with respect to the data they provide and the ease of their use. The hope is to aid the experimental biologist in choosing the most appropriate tool for their analyses.

Internet↗
PubMed2003

Validation of Align Technology's Treat III digital model superimposition tool and its case application.

OBJECTIVE: An assessment of the efficacy and accuracy of three-dimensional computer-based predictive orthodontic systems requires that new methods of treatment analysis be developed and validated. DESIGN: Invisalign is a digitally fabricated, removable orthodontic appliance that has been commercially available since 1999. It is made up of two main components: 1) computerized graphical images of a patient's teeth moving through a series of stages from initial to final position; 2) pressure formed clear plastic appliances made from stereolithography models of the images in the first component. SETTING AND SAMPLE POPULATION: The manufacturer of Invisalign (Align Technology, Inc.) has created a software tool that can be used to superimpose digital models to evaluate treatment outcomes in three dimensions. Using this software, research was conducted to determine if a single operator could repeatedly superimpose two identical digital models using 12 selected points from the palatal rugae over 10 trials. The tool was then applied to one subject's orthodontic treatment. EXPERIMENT VARIABLES: The output from this tool includes rotations, translations and morphological changes. For this study, translations and rotations were chosen. RESULTS: The results showed that the digital superimposition was reproducible, and that after multiple trials, the superimposition error decreased. The average error in x, y, z, Rx, Ry and Rz after 10 trials was determined to approach approximately 0.2 mm in translation and less than 1 degree in rotation, with a standard deviation of 0.15 mm and 0.7 mm, respectively. The treatment outcome from a single Invisalign-treated bicuspid extraction case was also evaluated tooth-by-tooth in x, y, z, Rx, Ry and Rz dimensions. CONCLUSION: Using the palate, as a stable reference seemed to work well and the evaluation of the single case showed that many, but not all, of the planned movements occurred.

Adult↗
PubMed2005

Congruent strategies for carbohydrate sequencing. 2. FragLib: an MSn spectral library.

A bottom-up approach to achieve full oligosaccharide and glycan characterization has been described that is based on an MSn fragment spectral library and associated tools. The library, identified as FragLib, was initiated with known standards and commercially available oligomers prepared as methylated derivatives. As a component of this effort a set of software tools has been written for storing, organizing, and comparing spectral files, including the identification of isobaric mixtures. These tools provide a facile and objective evaluation of structural details including interresidue linkage, monomer identification, anomeric configuration, and branching. The tools are components of a web-based data sharing interface for sample tracking, spectral searching, and structural confirmation. Applications have been detailed with unknown samples and previously characterized glycoconjugates.

Carbohydrate Sequence↗
PubMed1997

[Computer-assisted control of CT-guided caudo-cranial puncture access route using the triangulation method].

PURPOSE: To control the position of a puncture needle on an access route, which is not parallel to the CT-scan, using control scans not showing start and target points. METHODS: A software tool has been developed. After CT for biopsy planning x/y coordinates and table position of start and target points have to be determined on CT-scans. The software calculates x/y coordinates of the access route for every table position, which must be marked interactively on control scans. The accuracy of the programme was proven experimentally and the method was used in five patients. RESULTS: There was no difference between the calculated and measured access route in the experiment. Four of five patients were punctured successfully using our method. CONCLUSION: Our method is a promising procedure to control a CT-guided caudo-cranial biopsy access route.

Biopsy, Needle↗
PubMed2004

Optimization of combined electron and photon beams for breast cancer.

Recently, intensity-modulated radiation therapy and modulated electron radiotherapy have gathered a growing interest for the treatment of breast and head and neck tumours. In this work, we carried out a study to combine electron and photon beams to achieve differential dose distributions for multiple target volumes simultaneously. A Monte Carlo based treatment planning system was investigated, which consists of a set of software tools to perform accurate dose calculation, treatment optimization, leaf sequencing and plan analysis. We compared breast treatment plans generated using this home-grown optimization and dose calculation software for different treatment techniques. Five different planning techniques have been developed for this study based on a standard photon beam whole breast treatment and an electron beam tumour bed cone down. Technique 1 includes two 6 MV tangential wedged photon beams followed by an anterior boost electron field. Technique 2 includes two 6 MV tangential intensity-modulated photon beams and the same boost electron field. Technique 3 optimizes two intensity-modulated photon beams based on a boost electron field. Technique 4 optimizes two intensity-modulated photon beams and the weight of the boost electron field. Technique 5 combines two intensity-modulated photon beams with an intensity-modulated electron field. Our results show that technique 2 can reduce hot spots both in the breast and the tumour bed compared to technique 1 (dose inhomogeneity is reduced from 34% to 28% for the target). Techniques 3, 4 and 5 can deliver a more homogeneous dose distribution to the target (with dose inhomogeneities for the target of 22%, 20% and 9%, respectively). In many cases techniques 3, 4 and 5 can reduce the dose to the lung and heart. It is concluded that combined photon and electron beam therapy may be advantageous for treating breast cancer compared to conventional treatment techniques using tangential wedged photon beams followed by a boost electron field.

Breast↗
PubMed2006

PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments.

BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/. CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.

Database Management Systems↗
PubMed2001

A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics.

The identification of individual protein species within an organism's proteome has been optimised by increasing the information produced from mass spectral analysis through the chemical derivatisation of tryptic peptides and the development of new software tools. Peptide fragments are subjected to two forms of derivatisation. First, lysine residues are converted to homoarginine moieties by guanidination. This procedure has two advantages, first, it usually identifies the C-terminal amino acid of the tryptic peptide and also greatly increases the total information content of the mass spectrum by improving the signal response of C-terminal lysine fragments. Second, an Edman-type phenylthiocarbamoyl (PTC) modification is carried out on the N-terminal amino acid. The renders the first peptide bond highly susceptible to cleavage during mass spectrometry (MS) analysis and consequently allows the ready identification of the N-terminal residue. The utility of the procedure has been demonstrated by developing novel bioinformatic tools to exploit the additional mass spectral data in the identification of proteome proteins from the yeast Saccharomyces cerevisiae. With this combination of novel chemistry and bioinformatics, it should be possible to identify unambiguously any yeast protein spot or band from either two-dimensional or one-dimensional electropheretograms.

Databases, Factual↗
PubMedDate not supplied

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise.

Academies and Institutes↗
PubMed2006

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.

Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens.

Algorithms↗
PubMed2003

A comparative dosimetric study on tangential photon beams, intensity-modulated radiation therapy (IMRT) and modulated electron radiotherapy (MERT) for breast cancer treatment.

Recently, energy- and intensity-modulated electron radiotherapy (MERT) has garnered a growing interest for the treatment of superficial targets. In this work. we carried out a comparative dosimetry study to evaluate MERT, photon beam intensity-modulated radiation therapy (IMRT) and conventional tangential photon beams for the treatment of breast cancer. A Monte Carlo based treatment planning system has been investigated, which consists of a set of software tools to perform accurate dose calculation, treatment optimization, leaf sequencing and plan analysis. We have compared breast treatment plans generated using this home-grown treatment optimization and dose calculation software forthese treatment techniques. The MERT plans were planned with up to two gantry angles and four nominal energies (6, 9, 12 and 16 MeV). The tangential photon treatment plans were planned with 6 MV wedged photon beams. The IMRT plans were planned using both multiple-gantry 6 MV photon beams or two 6 MV tangential beams. Our results show that tangential IMRT can reduce the dose to the lung, heart and contralateral breast compared to conventional tangential wedged beams (up to 50% reduction in high dose volume or 5 Gy in the maximum dose). MERT can reduce the maximum dose to the lung by up to 20 Gy and to the heart by up to 35 Gy compared to conventional tangential wedged beams. Multiple beam angle IMRT can significantly reduce the maximum dose to the lung and heart (up to 20 Gy) but it induces low and medium doses to a large volume of normal tissues including lung, heart and contralateral breast. It is concluded that MERT has superior capabilities to achieve dose conformity both laterally and in the depth direction, which will be well suited for treating superficial targets such as breast cancer.

Breast Neoplasms↗
PubMed2002

Genetic programming approach for the optimal selection of combinations of neuronal networks to classify sleep stages by QUISI.

The usefulness of a new way to optimize the cooperation of trained neural networks for automatic one-channel sleep stage analysis using genetic programming and performance evaluation by including the interrater reliability are the focus of our paper. The one-channel sleep classification could be significantly improved by the optimization. The software tool HENNE, with its genetic programming compartment was developed for this purpose. The tool has proved to be useful for searching for optima in difficult goal surfaces. To contribute to the general discussion about the benefit of the automatic one-channel sleep analysis on the basis of the frontal site, we tried to evaluate our results before the background of the interrater variability. Comparing the kappa statistics of different independent studies with our results, we concluded that there are no dramatic differences as a rule and that QUISI is a useful device as a presleep laboratory and ambulatory diagnostic tool.

Humans↗
PubMed2004

Interactive DNA sequence and structure design for DNA nanoapplications.

DNA sequence and structure design is very important for DNA nanoapplications. A computer-aided design tool is needed for exploring DNA sequence and structure of interests before experimental synthesis, which is a time- and labor-consuming process. In this paper, an interactive DNA sequence and structure design software tool called DNA shop is proposed and implemented. The visualization tool can generate DNA structures by specifying, selecting, and moving DNA sequences around and display corresponding structures. Using the tool, DNA sequence and structure can be visually inspected in three-dimensional space before experimental studies.

Algorithms↗
PubMed2005

The use of microarrays to study the anaerobic response in Arabidopsis.

BACKGROUND AND AIMS: The use of microarrays to characterize the transcript profile of Arabidopsis under various experimental conditions is rapidly expanding. This technique provides a huge amount of expression data, requiring bioinformatics tools to allow the proposal of working hypotheses. The aim of this study was to test the usefulness of this approach to examine the anaerobic response of Arabidopsis by evaluating the reliability of microarray data sets and by interrogation of microarray databases for the expression data of a set of anoxia-inducible genes. METHODS: User-driven software tools that display large gene expression datasets onto diagrams of metabolic pathways were used. The Genevestigator software was used to explore the expression of anoxia-inducible genes throughout the life cycle of Arabidopsis as well as relative to plant organs. T-DNA tagged mutants for selected genes identified from our microarray analysis were searched in the Arabidopsis thaliana Insertion Database, looking for insertional mutants from the Salk collection. KEY RESULTS: The results indicate that microarray data can provide the basis for new hypotheses in the field of plant responses to anaerobiosis and also provide knowledge for a targeted screening of Arabidopsis mutants. CONCLUSIONS: Research on plant responses to anaerobiosis can enormously benefit from the microarray technology.

Anaerobiosis↗
PubMed2001

Transcript-based computer animation of movement: evaluating a new tool for nonverbal behavior research.

A new approach for the use of computer animation in experimental nonverbal research is introduced. The method was evaluated in a pilot study comparing video recordings of movement in dyadic interactions with computer animations based on transcripts of the behavior, to determine whether similar impression effects could be obtained. At the core of our development is a software tool allowing for the conversion of so-called position time-series protocols of movement into animation scripts for a professional computer animation platform. Our software combines computer-assisted movement transcription and editing with state-of-the-art 3-D animation technology. We present empirical evidence indicating remarkable overall correspondence between video recordings and computer animations. Due to the lack of facial activity in the computer animations, a decline in visual attention for the face area could be observed, which did not, however, affect the impression ratings.

Adolescent↗