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At least 1,153 records · Page 64Linked to original sources
PubMed2000

Development of a computer software for analysis of SDS-PAGE protein fingerprints of bacterial isolates.

Protein fingerprinting is a widely used technique in epidemiological studies for typing bacterial strains. This study reports the development of a computer based gel analysis system. The system has the capability to analyse SDS-PAGE whole-cell protein profiles using digital image processing techniques. The software incorporates spatial and frequency domain operators for image enhancement, support for geometric correction of images and new algorithms for identification of strain tracks and protein bands. The system also provides facilities for correcting imaging defects for inter-gel comparison, similarity analysis, clustering and pictorial representation of results as a dendrogram. The software is highly interactive, user-friendly and can produce accurate results for differentiation of bacterial strains with minimal overhead of time.

Algorithms↗
PubMed2004

Development of public toxicogenomics software for microarray data management and analysis.

A robust bioinformatics capability is widely acknowledged as central to realizing the promises of toxicogenomics. Successful application of toxicogenomic approaches, such as DNA microarray, inextricably relies on appropriate data management, the ability to extract knowledge from massive amounts of data and the availability of functional information for data interpretation. At the FDA's National Center for Toxicological Research (NCTR), we are developing a public microarray data management and analysis software, called ArrayTrack. ArrayTrack is Minimum Information About a Microarray Experiment (MIAME) supportive for storing both microarray data and experiment parameters associated with a toxicogenomics study. A quality control mechanism is implemented to assure the fidelity of entered expression data. ArrayTrack also provides a rich collection of functional information about genes, proteins and pathways drawn from various public biological databases for facilitating data interpretation. In addition, several data analysis and visualization tools are available with ArrayTrack, and more tools will be available in the next released version. Importantly, gene expression data, functional information and analysis methods are fully integrated so that the data analysis and interpretation process is simplified and enhanced. ArrayTrack is publicly available online and the prospective user can also request a local installation version by contacting the authors.

Databases, Genetic↗
PubMed2002

An overview of the CCP4 project in protein crystallography: an example of a collaborative project.

The Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. CCP4 now distributes a large software suite and is active in developing new software. Equally importantly, CCP4 provides a focus for the whole protein crystallography community via meetings, workshops, email lists and various publications. In this Article, an overview is given of CCP4 activities and their administration. The emphasis is on generic features of the collaboration rather than details specific to protein crystallography. The CCP4 model has inspired similar developments in NMR, and it is hoped that the biological XAS community may pursue similar collaboration.

Crystallography, X-Ray↗
PubMed2005

Retinal contraction and metamorphopsia scores in eyes with idiopathic epiretinal membrane.

PURPOSE: Using M-CHARTS (Inami Co., Tokyo, Japan), which were developed by the authors to measure metamorphopsia, and image-analysis software, which was developed to quantify retinal contraction, the authors investigated the relationship between the degree of retinal contraction and the degree of metamorphopsia in eyes with idiopathic epiretinal membrane (ERM). METHODS: This study was conducted in 29 eyes with ERM (29 patients, 20 women; mean age, 62.1 +/- 8.6 years) observed for at least 3 years (mean, 3.55 +/- 0.6 years) after diagnosis. Horizontal (MH) and vertical (MV) metamorphopsia scores were obtained with the M-CHARTS. Horizontal and vertical retinal contraction due to ERM was measured by using image-analysis software developed by the authors to calculate horizontal and vertical components of changes in the locations of retinal vessels on sequential fundus images. RESULTS: There was a significant (P < 0.01) positive correlation between the degree of retinal contraction and metamorphopsia score. In addition, there were significant positive correlations between horizontal contraction of the retina and the MV score (P < 0.01) and between vertical contraction of the retina and the MH score (P < 0.05). No significant correlations were found between change in the metamorphopsia score and change in visual acuity or mean defect. CONCLUSIONS: Metamorphopsia scores correlate well with measurements of retinal contraction due to idiopathic ERM. Using M-CHARTS is a simple and useful method for quantitatively monitoring metamorphopsia in patients with ERM.

Contracture↗
PubMedDate not supplied

Microcomputer control of behavior and the acquisition of digital and analog data.

Advances in technology and decreasing costs are enabling microcomputers to displace more traditional devices in the scientific laboratory. The availability of various approaches to software-system development for the use of microcomputers in the on-line control of experiments has contributed to the trend. This report describes a software system developed to control conditioned behavior during schedules of reinforcement while simultaneously accumulating behavioral data and physiological (analog) data using a hardware system base on the Radio Shack TRS-80 Model I microcomputer. The software utilizes a high-level interpretive language (Microsoft BASIC), assembly language and compiled BASIC to attain an acceptable execution speed and ease of programming.

Animals↗
PubMed1998

Use of the Internet for teaching in nuclear medicine.

The Internet provides several new capabilities for education in nuclear medicine, including learning at a distance, facilitation of collaboration, increased availability of training resources, and ability to develop interactive teaching materials. Dedicated case-authoring software aided development of digital teaching files at the Mallinckrodt Institute of Radiology and the Joint Program in Nuclear Medicine. Accesses to these two teaching files from sites around the world have grown rapidly. Improvements in the speed of the Internet will allow inclusion of more images at higher resolution and more extensive use of cine. Development of server-based software will allow simulation of the actual image-reading environment. A better understanding of how to use this new media will spur continued expansion in use of the Internet for nuclear medical education.

CD-ROM↗
PubMed2001

A case-acquisition and decision-support system for the analysis of group-average lactation curves.

A case-acquisition and decision-support system was developed to support the analysis of group-average lactation curves and to acquire example cases from domain specialists. This software was developed through several iterations of a three-step approach involving 1) problem analysis and formulation in consultation with two dairy nutrition specialists; 2) development of a case-acquisition and decision-support prototype by the system developer; and 3) use of the prototype by the domain specialists to analyze and classify milk-recording data from example herds. The overall problem was decomposed into three subproblems: removal of outlier tests and lactation curves of individual cows; interpretation of group-average lactation curves; and diagnosis of detected abnormalities at the herd level through the identification of potential management deficiencies. For each subproblem, a software module was developed allowing the user to analyze both graphical and numerical performance representations and classify these representations using predefined linguistic descriptors. The example-based method for the development of the program proved to be very useful, facilitating the communication between system developer and domain specialists, and allowing the specialists to explore the appropriateness of the various prototypes developed. The resulting software represents a formalization of the approach to group-average lactation curve analysis, elicited from the two domain specialists. In future research, the case-acquisition and decision-support system will be complemented with knowledge to automate identified classification tasks, which will be captured through the application of machine-learning techniques to example cases, acquired from domain specialists using the software.

Animals↗
PubMed2003

Design, development and validation of software for modelling dietary exposure to food chemicals and nutrients.

The Monte Carlo computational system for stochastic modelling of dietary exposure to food chemicals and nutrients is presented. This system was developed through a European Commission-funded research project. It is accessible as a Web-based application service. The system allows and supports very significant complexity in the data sets used as the model input, but provides a simple, general purpose, linear kernel for model evaluation. Specific features of the system include the ability to enter (arbitrarily) complex mathematical or probabilistic expressions at each and every input data field, automatic bootstrapping on subjects and on subject food intake diaries, and custom kernels to apply brand information such as market share and loyalty to the calculation of food and chemical intake.

Diet↗
PubMed1997

Data analysis using the Internet: the World Wide Web scanning probe microscopy data analysis system.

The first interactive world-wide web-based image analysis system is presented (http://pharm6.pharm.nottingham.ac.uk/processing/main. html). The system, currently tailored to scanning probe microscopy image data, has been developed to permit the use of software algorithms developed within our laboratory by researchers throughout the world. The implementation and functionality of the scanning probe microscopy server is described. Feedback from users of the facility has demonstrated its value within the research community, and highlighted key operational issues which are to be addressed. A future role of Internet-based data processing software is also discussed.

Algorithms↗
PubMed1995

Help: first aid issues.

First aid is the initial and immediate care given to a victim outside the hospital environment, with the purpose of assuring life and avoiding worsening conditions until he/she receives qualified assistance. Providing immediate aid to someone requires tranquility and, above all, knowledge on what has to be done or not in each situation. In addition to being treated by health professionals, the chances that a victim will receive early treatment by others are large. However, in Brazil, access to information, and the possibility of reviewing it whenever necessary, may contribute greatly to the process of assimilation of this knowledge, in addition to exercises on simulated cases. Informatics has been shown as an extremely useful tool in the development of educational software, considering its multiplicity of resources and providing for the users: motivation for an interactive experience, an individualized teaching that takes into account his/her own rhythm and desired complexity level, besides making possible the user's capacity for solving problems through simulated situations. Considering that, the number of individuals of the population prepared to act as First Aid helpers in situations of life threatening accidents or sudden illness is still very scarce. The ever increasing use of the computer as a mean of spreading information in schools, enterprises, and even households and considering the advantages of an educational software for the users regarding storage and retrieval of information when needed, we proposed the creation of an interactive teaching software. This software is being developed using Storyboard live. The methodology is the following: literature review, selection of images, development of the program, application tests. The initial selected issues are: assessment of the victim, cardiorespiratory arrest and resuscitation, airway obstruction, wounds, and hemorrhages. After utilizing the program, the user should be able to solve hypothetical situations with minimal initial care and maximal physical comfort for an accident or sudden illness victim.

Computer-Assisted Instruction↗
PubMed1994

Building Internet accessible medical education software using the World Wide Web.

We describe work to enhance existing software protocols and develop a suite of new software utilities based upon a set of standards known as the World Wide Web (WWW). Specifically, we have developed an effective X-windows based WYSIWYG WWW browser/editor and a prototype for integrated wide-area authentication and authorization support for delivery and maintenance of WWW service. These software development activities, along with parallel work in content development, are empowering individuals to better use the Internet as a resource to easily author, publish, and access materials. As an illustrative application, we describe one Web-based self-instructional unit designed to increase users' knowledge of hazardous substances in the environment. This on-line monograph was adapted from a series of paper-based case studies developed by the Agency for Toxic Substances and Disease Registry of the U.S. Department of Health & Human Services. The on-line version illustrates many of the innovative features provided by the Web, and demonstrates how such materials can significantly impact medical education at all levels.

Computer Communication Networks↗
PubMed2006

Automated measurement of skin prick tests: an advance towards exact calculation of wheal size.

BACKGROUND: Using the Khoros image processing software environment, we developed a software-based system capable of extracting wheal size from skin prick tests (SPTs) in mm(2) for research and routine purposes. METHODS: At 20 min, the outlines of up to 20 wheals were marked with a pen and transferred with translucent adhesive tapes to a white paper form carrying predefined markings. The form was scanned at 200 dpi. The software automatically analysed the scanned image and calculated the sizes of the wheals. In a pilot study, serial SPTs with histamine in increasing dilutions were performed in 12 healthy volunteers in duplicate on both volar forearms. We matched the application results with a reference created from the scanned pictures. RESULTS: Bland-Altman analysis showed reference and software calculation reaching very high agreement. The comparison of reference/software resulted in a low centred coefficient of variation (COV) of 11.9%. This was superior to the conventional measurement of horizontal (COV 37.9%) or maximal/minimal diameter (COV 25.9%). CONCLUSION: We present an accurate tool for exactly calculating SPT wheal size in mm(2).

Adult↗
PubMed2003

A format for databasing and comparison of AFLP fingerprint profiles.

BACKGROUND: Amplified fragment length polymorphism (AFLP) is a PCR-based technique that involves restriction of genomic DNA followed by ligation of adaptors to the fragments generated and selective PCR amplification of a subset of these fragments. The amplified fragments are separated on a sequencing gel and visualized by autoradiography or fluorescent sequencing equipment. AFLP allows high-resolution genotyping but the lack of a format for databasing and comparison of AFLP fingerprint profiles limits its wider applications in profiling large numbers of biological samples. RESULTS: A scheme is described to represent a DNA fingerprint profile with a nucleotide sequence-like format in which the information line contains the minimal necessary details to interpret an AFLP DNA fingerprint profile. They include technique used, information on restriction enzymes, primer combination, biological source for DNA materials, fragment sizing and annotation. The bodylines contain information on size and relative intensity of DNA fragments by a string of defined alphabets or symbols. Algorithms for normalizing raw data, binning of fragments and comparing AFLP DNA fingerprint profiles are described. Firstly, the peak heights are normalized against their average and then represented by five symbols according to their relative intensities. Secondly, a binning algorithm based loosely on common springs and rubber bands is applied, which positions sequence fragments into their best possible integer approximations. A BLAST-like reward-penalty concept is used to compare AFLP fingerprint profiles by matching peaks using two metrics: score and percentage of similarity. A software package was developed based on our scheme and proposed algorithms. Example of use this software is given in evaluating novelty of a new tropical orchid cultivar by comparing its AFLP fingerprint profile against those of related commercial cultivars in a database. CONCLUSIONS: AFLP DNA fingerprint profiles can be databased and compared effectively with software developed based on our scheme and algorithms. It will facilitate wider use of this DNA fingerprinting technique in areas such as forensic study, intellectual property protection for biological materials and biodiversity management. Moreover, the same concepts can be applied to databasing and comparing DNA fingerprint profiles obtained with other DNA fingerprint techniques.

Algorithms↗
PubMed2004

TOSCA-Imaging--developing Internet based image processing software for screening and diagnosis of diabetic retinopathy.

The primary aim of TOSCA-Imaging, which was a part of the TOSCA Project financed by EU's Fifth Framework IST Programme, was to develop Internet based software and image data bases for screening and diagnosis of diabetic retinopathy and implementing it into a real life situation. The work consisted of: 1) Construction of an Internet based communication platform for transmitting and analyzing retinal images. 2) Implementation of routines for detecting the first microaneurysm (transition from normal to pathologic), detecting patients needing referral for treatment (presence of venous beading or hard exudates near the fovea), and for serial analysis (image alignment). 3) Construction of a reference image data base. A preliminary validation showed that decisions that depended on a precise detection of individual lesions, e.g. the detection of normality, had a sensitivity and specificity of around 80%, whereas decisions that depended on the detection of lesion patterns, e.g. clinically significant macular oedema, had a sensitivity and specificity of more than 95%. Validation of the reference image data base by double grading by two expert graders suggested a sensitivity and a specificity of just below 90% for any lesion and of more than 95% for predicting the overall retinopathy grade. TOSCA-Imaging has succeeded in its primary aim of developing Internet based software and implementing it into a real life situation, integrating work within image processing done in four different European countries (England, Germany, Ireland, and Denmark) to be accessed from one Internet web site.

Algorithms↗
PubMed1991

User-friendly image processing software tools: general purpose features and application to the correlation of PET-CT brain images.

An interactive software package, performing some useful general purpose image processing operations and being used as a tool for the problem of the anatomical correlation of PET brain images, is under development. The software is developed as a comprehensive tool with a graphic user-interface allowing the display of the processed images through the use of a variety of colormaps. The implemented routines perform a lot of processing operations on the images: a) Local image processing, i.e. smoothing and sharpening, contours extraction, interactive expansion, shrinking and thresholding of the gray scale, histogram equalization. b) ROI handling, i.e., ROI drawing and computing, transformation of an image to a ROI, ROI editing. c) Additional operators include frequency space image processing such as FFT.

Brain↗
PubMed2000

Octamer-primed sequencing technology: development of primer identification software.

Octamer sequencing technology (OST) is a primer-directed sequencing strategy in which an individual octamer primer is selected from a pre-synthesized octamer primer library and used to sequence a DNA fragment. However, selecting candidate primers from such a library is time consuming and can be a bottleneck in the sequencing process. To accelerate the sequencing process and to obtain high quality sequencing data, a computer program, electronic OST or eOST, was developed to automatically identify candidate primers from an octamer primer library. eOST integrates the base calling software PHRED to provide a quality assessment for target sequences and identifies potential primer binding sites located within a high quality target region. To increase the sequencing success rate, eOST includes a simple dynamic folding algorithm to automatically calculate the free energy and predict the secondary structure within the template in the vicinity of the octamer-binding site. Several parameters were found to be important, including base quality threshold, the window size of the template sequence segment, and the threshold [Delta] G value. OST, coupled with the eOST software, can be used to sequence short DNA fragments or in the finishing assembly stage of large-scale sequencing of genomic DNA.

Algorithms↗