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At least 757 records · Page 42Linked to original sources

PubMed2003

AMIDE: a free software tool for multimodality medical image analysis.

Amide's a Medical Image Data Examiner (AMIDE) has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI) and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

Costs and Cost Analysis↗

PubMedDate not supplied

In vitro phototoxicity testing: development and validation of a new concentration response analysis software and biostatistical analyses related to the use of various prediction models.

As demonstrated in several validation studies, the dermal phototoxic potential of chemicals in humans can be effectively assessed by in vitro methods. The core of these methods is to monitor dose-response curves of a chemical in the absence and presence of light, to quantify the difference between these two curves by appropriate measures (either the photo-irritancy factor [PIF], or the mean photo effect [MPE]), and to use these measures as predictors of in vivo phototoxicity. We present new concentration-response analysis software for in vitro phototoxicity testing, which runs on current personal computers, and takes into account all the limitations identified when using a former program. We also demonstrate the validity and robustness of this new software by applying it retrospectively to all data available from two phases of the EU/COLIPA validation trial for the 3T3 neutral red update in vitro phototoxicity test. Some frequently raised questions pertaining to the use of prediction models in phototoxicity testing are addressed, including: the necessity of using prediction models based on a cut-off; whether it is justifiable to use sharp prediction cut-off values; whether there is a biostatistical justification for the highest concentration of the test chemical; and whether repeated testing of a chemical is required.

3T3 Cells↗

PubMed2004

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.

BACKGROUND: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA) molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. RESULTS: We have developed the software package Biochemical Network Stochastic Simulator (BioNetS) for efficiently and accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous) for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solves the appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. CONCLUSIONS: We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Algorithms↗

PubMed2004

GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.

BACKGROUND: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb. RESULTS: GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences. CONCLUSIONS: GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly." AVAILABILITY: http://binf.gmu.edu/genometools.html and http://pasteur.atcc.org:8050/GeneOrder3.0.

Chromosome Mapping↗

PubMed2005

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

BACKGROUND: A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has been improved by an editor and analyzer of metabolic flux modes. Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest. RESULTS: YANA features a platform-independent, dedicated toolbox for metabolic networks with a graphical user interface to calculate (integrating METATOOL), edit (including support for the SBML format), visualize, centralize, and compare elementary flux modes. Further, YANA calculates expected flux distributions for a given Elementary Mode (EM) activity pattern and vice versa. Moreover, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomics or gene expression data give a rough indication of some individual enzyme activities, whereas the complete flux distribution in the network is often not known. As such data are noisy, YANA features a fast evolutionary algorithm (EA) for the prediction of EM activities with minimum error, including alerts for inconsistent experimental data. We offer the possibility to include further known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as an illustration example. All software and documentation are available for download at http://yana.bioapps.biozentrum.uni-wuerzburg.de. CONCLUSION: A graphical toolbox and an editor for METATOOL as well as a series of additional routines for metabolic network analyses constitute a new user-friendly software for such efforts.

Algorithms↗

PubMed2005

Graphical representation of ribosomal RNA probe accessibility data using ARB software package.

BACKGROUND: Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. RESULTS: The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI) can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool. CONCLUSION: Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page http://www.arb-home.de

Algorithms↗

PubMed2005

HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data.

BACKGROUND: Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics) is a software package designed for analysis of high dimensional biology data such as microarray data. It was initially developed for the analysis of microarray gene expression data, but it can also be used for some applications in proteomics and other aspects of genomics. HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing. RESULTS: Results generated from data preprocessing methods, quality control analysis and hypothesis testing methods are output in the form of Excel CSV tables, graphs and an Html report summarizing data analysis. CONCLUSION: HDBStat! is a platform-independent software that is freely available to academic institutions and non-profit organizations. It can be downloaded from our website http://www.soph.uab.edu/ssg_content.asp?id=1164.

Algorithms↗

PubMed2006

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.

BACKGROUND: Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets. RESULTS: OLIGOSPAWN is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but does not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it. CONCLUSION: The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OLIGOSPAWN is freely available at http://oligospawn.ucr.edu/.

Base Sequence↗

PubMedDate not supplied

FEASIBLE (I): The PC software package for feature evaluation and system inspection by logged experiments.

FEASIBLE is an MS-DOS software package which can be used for the evaluation of: Picture Archiving and Communication System (PACS) components; diagnostic image quality; and image manipulation and representation techniques. The FEASIBLE software allows the user to design any psychophysical study in detail in the fields mentioned above, to execute an arbitrary number of sessions and to statistically analyse the results by way of the Receiver Operating Characteristic (ROC) technique. FEASIBLE consists basically of three modules: DESIGN, which allows the user to set up an experiment; EXECUTION, which allows the user to execute the experimental sessions based on the design entered in the DESIGN module and stored in the program's database; and, STATISTICS, which allows various statistical analyses on the data collected during the psychophysical sessions (including the calculation of ROC curves and related parameters) and can provide a graphical presentation of the results. FEASIBLE has been designed to support experts and those who have little knowledge of psychophysical experiments. This paper discusses the background, structure and possibilities of the FEASIBLE package at this point (version 1.2, May 1988).

Hospital Information Systems↗

PubMed2003

[Development of quantification analysis software for measuring regional cerebral blood flow by the modified split-dose method with (123)I-IMP before and after acetazolamide loading].

We developed a quantification analysis software program for measuring regional cerebral blood flow (rCBF) at rest and under acetazolamide (ACZ) stress by the modified split-dose (MSD) method with iodine-123 N-isopropyl-p-iodoamphetamine (IMP) and compared the rCBF values measured by the MSD method and by the split dose (123)I-IMP SPECT (SD) method requiring one continuous withdrawal of arterial blood. Since the MSD method allows the input of two arterial blood sampling parameter values, the background subtraction procedure for obtaining ACZ-induced images in the MSD method is not identical to the procedure in the SD method. With our software program for rCBF quantification, the resting rCBF values determined by the MSD method were closely correlated with the values measured by the SD method (r=0.94), and there was also a good correlation between the ACZ-induced rCBF values obtained by the MSD method and by the SD method (r=0.81). The increase in rCBF under ACZ stress was estimated to be approximately 26% by the SD method and 38% by the MSD method, suggesting that the MSD method tends to overestimate the increase in rCBF under ACZ stress in comparison with the SD method, but the variability of the rCBF values at rest and during ACZ stress analyzed by the MSD method was smaller than the variability with the SD method. Further clinical studies are required to validate our rCBF quantification analysis program for the MSD method.

Acetazolamide↗

PubMed2002

[Development and evaluation of QA software for the monitor chamber of an accelerator].

The monitor chamber of a radiotherapy system needs to be calibrated once a week. Because the calibration procedure requires a large variety of complicated calculations, we have developed software that facilitates calculation and enables comparison and storage of data. According to the standard measurement of absorbed dose, we used Visual Basic 6.0 (Microsoft Corp.) to establish the calibration method. This new technique has simplified the conventional intricate calculation required for calibration of the monitor chamber and enabled automatic processing of calculated results. We have confirmed the usefulness of this software in calibrating the monitor chamber. In the routine inspection, we can compare the current data with former results. Because of this advantage, it is possible to eliminate serious accidents such as overdosing and underdosing.

Calibration↗

PubMed1997

An example of usability measurement in clinical software procedures.

As a consequence of the dramatic improvements achieved in information technology standards in terms of single hardware and software components, efforts in the evaluation processes have been focused on the assessment of critical human factors, such as work-flow organisation, man-machine interaction and, in general, quality of use, or usability. This trend is particularly valid when applied to medical informatics, since the human component is the basis of the information processing system in health care context. With the aim to establish an action-research project on the evaluation and assessment of clinical software procedures which constitute an integrated Hospital Information System, the authors adopted this strategy and considered the measurement of perceived usability as one of the main goals of the project itself: the paper reports the results of this experience.

Attitude of Health Personnel↗

PubMed1997

Software quality assessment for health care systems.

The problem of defining a quality model to be used in the evaluation of the software components of a Health Care System (HCS) is addressed. The model, based on the ISO/IEC 9126 standard, has been interpreted to fit the requirements of some classes of applications representative of Health Care Systems, on the basis of the experience gained both in the field of medical Informatics and assessment of software products. The values resulting from weighing the quality characteristics according to their criticality outline a set of quality profiles that can be used both for evaluation and certification.

Delivery of Health Care↗

PubMed1998

The software challenge for the next decade: the global objects scenario.

This paper discusses the advantages of developing software as pattern-based components. The design and implementation of a pattern-based suite of software components specially constructed for the electronic patient record is presented. The methodology and the lessons learned in the development of these components are discussed. Finally, some comments about the globalization and the need for more integration among component developers in a worldwide basis is discussed.

Humans↗

PubMed2002

FDA final guidance on software validation.

The United States Food and Drug Administration (FDA) places considerable importance on the validation of software contained in and used to design, develop, or manufacture medical devices. This article discusses a recently published final FDA guidance document on software validation and the reasons for its importance.

Computer Systems↗

PubMed2000

[Development and application of the software measuring the size of injured body surface].

A software to measure the area, length and angle of injured body surface is introduced. It is suitable for evaluating injury degrees with 2 or 3 dimension measurement. The software is developed by Visual Basic 6.0 on Windows 98 terrace, supporting digital video camera, digital camera and scanner input. It is easy to use and has been applied in more than 200 cases.

Diagnosis, Computer-Assisted↗

PubMed2001

[The research on applications of diagnostic software in single photon emission computed tomography].

In this paper, the structure of software system, the principles of overlay programming and the running mechanism of the programs for the Single Photon Emission Computed Tomography(SPECT) made by French SOPHA MEDICAL Corp. are analyzed in detail. On this basis, a method of extending functions of the system is introduced too. All the results of the extension in software functions for organ volume determination and of the measurements for living animals have proved the correctness and reliability of the method.

Software↗

PubMedDate not supplied

[Basic principles of system software maintenance for multi-functional non-invasive spectrophotometric diagnostic devices and complexes].

Due to the promotion of methods and devices of non-invasive spectrophotometric diagnostics in the sphere of medicine, software support for such diagnostic systems has been growing to be a topical issue. The general ideology of designing the system software support for multi-function spectrophotometric diagnostic tools is under discussion in the paper. The need in a multi-stratum structure of presenting, analyzing and processing the diagnostic findings, i.e. beginning from physical result interpretation to its common medical interpretation, is substantiated.

Diagnosis, Computer-Assisted↗