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At least 1,711 records · Page 95Linked to original sources

PubMed2004

Avida: a software platform for research in computational evolutionary biology.

Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.

Biological Evolution↗

PubMed1998

Price and niche wars in a free-market economy of software agents.

One scenario of the future of computation populates the Internet with vast numbers of software agents providing, trading, and using a rich variety of information goods and services in an open, free-market economy. An essential task in such an economy is the retailing or brokering of information: gathering it from the right producers and distributing it to the right consumers. This article investigates one crucial aspect of brokers' dynamical behavior, their price-setting mechanisms, in the context of a simple information-filtering economy. We consider only the simplest cases in which a broker sets its price and product parameters based solely on the system's current state, without explicit prediction of the future. Analytical and numerical results show that the system's dynamical behavior in such "myopic" cases is generally an unending cycle of disastrous competitive "wars" in price/product space. These in turn are directly attributable to the existence of multiple peaks in the brokers' profitability landscapes, a feature whose generality is likely to extend far beyond our model.

Commerce↗

PubMed1996

Pharmaceutical inventory control software: Bhandari 2.2 (1995).

This article describes specialized software to manage pharmaceutical logistics and medicine inventories in hospitals and central/regional stores. It has been written especially for application in the developing world to support the administration of such departments. Features include ordering, inventory control, supplying, reporting and accounting.

Clinical Pharmacy Information Systems↗

PubMed1993

The surgical workstation: surgical planning using generic software.

Computer software for rendering and display of three-dimensional data is becoming readily available for all types of computers. Such programs typically accept data from any source, compute a three-dimensional volume of data, and display it with a variety of rendering options. Although not specifically designed for medical image processing, these programs can provide very detailed and finely rendered images that are useful for surgical planning. We use one such program to display data from standard computed tomography scans, which gives us a photorealistic three-dimensional view of patient anatomy. This view can be modified to render tissues transparent, translucent, or opaque, and thus allows the surgeon to selectively enhance bony architecture, tumors, or other details. Images can be rotated, sliced, and displayed in the surgical position. Image animation can be added to facilitate the display of complex anatomic relationships. Our experience with this technology suggests that such programs can provide the basis for personal surgical workstations for medical image analysis and surgical planning. Further development of such generic imaging systems should allow this useful technology to become widely available for surgical planning and education. We discuss our experience with a typical generic imaging workstation.

Brain Neoplasms↗

PubMed2001

Random effects models for HIV marker data: practical approaches with currently available software.

The analysis of marker data from HIV positive patients has been the motivation for many new developments in applied statistics. As well as reviewing these methods, this paper considers the extent to which programs to implement them are available in current software. Particular areas of development have been the joint modelling of markers and survival outcomes, non-linear random effects models that are of particular relevance for studying the efficacy of treatments and the use of Bayesian computational methods for inference from marker data. The package WinBUGS is recommended as being particularly well suited to the analysis of marker data.

Biomarkers↗

PubMed2005

Handheld computer software for school nurses.

School nurses used computers in the 1980s, the Internet in the 1990s, and are embracing handheld computers in the first decade of the 21st century to improve their practice. The purpose of this article is to provide information about handheld computers and software applications that school nurses can use in day-to-day, emergency, and disaster situations. Handheld computers help school nurses to make decisions based on accurate and up-to-date information, and to practice evidence-based nursing. Evidence-based nursing is the process by which nurses make clinical decisions using the best available research evidence, their clinical expertise, and patient preferences.

Computers, Handheld↗

PubMed1987

Serum phenobarbital concentration predictions by a personal computer software system.

The ability of a personal computer software system to predict actual serum phenobarbital concentrations (SPC) in outpatients taking phenobarbital chronically was assessed by comparing actual with predicted SPC for accuracy, bias, and precision. Data for a four-year period were collected on patients at an outpatient clinic's pharmacokinetic consultation service. The study group included 50 adults and children with at least one SPC taken at a known time after dose administration. Input variables were weight, sex, height, age, concomitant drugs and diseases, phenobarbital dosage regimen, and the time and reported value of all SPC. Initially, SIMKIN (SIMulated KINetics) simulated dosing regimens on the basis of literature estimates of pharmacokinetic parameters; SPC were then estimated for these regimens and compared with actual values. One or two additional SPC were added to the input data and analyzed, and the predicted SPC compared with actual values. Although SIMKIN's accuracy and bias as measured by regression analysis and mean prediction error, respectively, were within clinically acceptable limits, the precision was not. However, these results are limited by the population studied. Patient compliance, concomitant phenytoin therapy, changes in phenobarbital pharmacokinetic parameters with chronic dosing, and disease interactions may significantly affect predictive ability. The clinical effects of these factors need to be evaluated to further improve predictions.

Adolescent↗

PubMed1997

Interactive multimedia software design: concepts, process, and evaluation.

This article provides the health educator with a review of the design and construction of computer-based health education materials. Specifically, this review considers questions of instructional objectives as defined in the field of instructional design, a body of expertise not often deployed in the area of health education. It discusses in some detail the computer materials development process, associated documentation, and the range of personnel required. This article also briefly updates discussion of the costing process, and current costs for multimedia hardware and authoring software. The review touches on, but does not synthesize, emerging possibilities with the Internet.

Computer-Assisted Instruction↗

PubMed2003

New post-imaging software provides fast and accurate volume data from CTA surveillance after endovascular aneurysm repair.

PURPOSE: To quantify intra- and interobserver variabilities when measuring total aneurysm volume after endovascular aneurysm repair using the Vitrea 2 System and to compare it in terms of accuracy and processing time with the gold standard methods using the Easy Vision workstation. METHODS: Total aneurysm volumes from 30 postendograft CTA datasets were randomly selected from a database consisting of approximately 400 CTA datasets recorded in 89 patients. The intra- and interobserver variabilities were measured on the Vitrea workstation by 2 investigators. The intermodality variability was calculated for the same measurements using the Easy Vision workstation. The differences of each pair of measurements were plotted against their mean, and the repeatability coefficient (RC) was calculated. The mean differences were also expressed as a percentage of the first measurements. RESULTS: The intraobserver mean difference was 1.6 mL (1.4%) with an RC of 10.8 mL (10.1%) and the interobserver mean difference was -1.4 mL (-1.4%) with an RC of 11.7 mL (10.2%). The intermodality mean difference was 1.8 mL (2.0%) with an RC of 15.8 mL (11.1%). The Vitrea workstation required a median of 8 minutes (interquartile range 7-10) for 1 observer and 6 minutes (interquartile range 5-8) for the other to perform a complete volume segmentation of each patient dataset compared to an estimated average of 30 minutes using the Easy Vision workstation. CONCLUSIONS: The Vitrea workstation provides fast and accurate volume data from spiral CTA follow-up of endovascular aneurysm repair. This software may enhance the acceptability of volume surveillance in daily practice.

Aged↗

PubMed2003

Eval: a software package for analysis of genome annotations.

SUMMARY: Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another. Input is in the standard Gene Transfer Format (GTF). Eval can be run interactively or via the command line, in which case output options include easily parsable tab-delimited files. AVAILABILITY: To obtain the module package with documentation, go to http://genes.cse.wustl.edu/ and follow links for Resources, then Software. Please contact brent@cse.wustl.edu

Computational Biology↗

PubMed2005

PentaPlot: a software tool for the illustration of genome mosaicism.

BACKGROUND: Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix. RESULTS: The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families. CONCLUSION: PentaPlot is being made publicly available as an open source project at http://pentaplot.sourceforge.net.

Algorithms↗

PubMed2005

Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software.

BACKGROUND: There is an increasing need for computer-generated models that can be used for explaining the emergence and predicting the behavior of multi-protein dynamic structures in cells. Multi-agent systems (MAS) have been proposed as good candidates to achieve this goal. RESULTS: We have created 3DSpi, a multi-agent based software that we used to explore the generation of multi-protein dynamic structures. Being based on a very restricted set of parameters, it is perfectly suited for exploring the minimal set of rules needed to generate large multi-protein structures. It can therefore be used to test the hypothesis that such structures are formed and maintained by principles of self-organization. We observed that multi-protein structures emerge and that the system behavior is very robust, in terms of the number and size of the structures generated. Furthermore, the generated structures very closely mimic spatial organization of real life multi-protein structures. CONCLUSION: The behavior of 3DSpi confirms the considerable potential of MAS for modeling subcellular structures. It demonstrates that robust multi-protein structures can emerge using a restricted set of parameters and allows the exploration of the dynamics of such structures. A number of easy-to-implement modifications should make 3DSpi the virtual simulator of choice for scientists wishing to explore how topology interacts with time, to regulate the function of interacting proteins in living cells.

Cellular Structures↗

PubMed2006

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.

BACKGROUND: The biological information in genomic expression data can be understood, and computationally extracted, in the context of systems of interacting molecules. The automation of this information extraction requires high throughput management and analysis of genomic expression data, and integration of these data with other data types. RESULTS: SBEAMS-Microarray, a module of the open-source Systems Biology Experiment Analysis Management System (SBEAMS), enables MIAME-compliant storage, management, analysis, and integration of high-throughput genomic expression data. It is interoperable with the Cytoscape network integration, visualization, analysis, and modeling software platform. CONCLUSION: SBEAMS-Microarray provides end-to-end support for genomic expression analyses for network-based systems biology research.

Chromosome Mapping↗

PubMed2006

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping.

BACKGROUND: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. RESULTS: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. CONCLUSION: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.

Algorithms↗

PubMed2006

Fast index based algorithms and software for matching position specific scoring matrices.

BACKGROUND: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task. RESULTS: We present a new non-heuristic algorithm, called ESAsearch, to efficiently find matches of PSSMs in large databases. Our approach preprocesses the search space, e.g., a complete genome or a set of protein sequences, and builds an enhanced suffix array that is stored on file. This allows the searching of a database with a PSSM in sublinear expected time. Since ESAsearch benefits from small alphabets, we present a variant operating on sequences recoded according to a reduced alphabet. We also address the problem of non-comparable PSSM-scores by developing a method which allows the efficient computation of a matrix similarity threshold for a PSSM, given an E-value or a p-value. Our method is based on dynamic programming and, in contrast to other methods, it employs lazy evaluation of the dynamic programming matrix. We evaluated algorithm ESAsearch with nucleotide PSSMs and with amino acid PSSMs. Compared to the best previous methods, ESAsearch shows speedups of a factor between 17 and 275 for nucleotide PSSMs, and speedups up to factor 1.8 for amino acid PSSMs. Comparisons with the most widely used programs even show speedups by a factor of at least 3.8. Alphabet reduction yields an additional speedup factor of 2 on amino acid sequences compared to results achieved with the 20 symbol standard alphabet. The lazy evaluation method is also much faster than previous methods, with speedups of a factor between 3 and 330. CONCLUSION: Our analysis of ESAsearch reveals sublinear runtime in the expected case, and linear runtime in the worst case for sequences not shorter than the absolute value of A(m) + m - 1, where m is the length of the PSSM and A a finite alphabet. In practice, ESAsearch shows superior performance over the most widely used programs, especially for DNA sequences. The new algorithm for accurate on-the-fly calculations of thresholds has the potential to replace formerly used approximation approaches. Beyond the algorithmic contributions, we provide a robust, well documented, and easy to use software package, implementing the ideas and algorithms presented in this manuscript.

Algorithms↗

PubMed2006

BioMoby extensions to the Taverna workflow management and enactment software.

BACKGROUND: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. RESULTS: The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. CONCLUSION: With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.

Biology↗

PubMed2006

Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP.

BACKGROUND: Confocal laser scanning microscopy (CLSM) is the method of choice to study interfacial biofilms and acquires time-resolved three-dimensional data of the biofilm structure. CLSM can be used in a multi-channel modus where the different channels map individual biofilm components. This communication presents a novel image quantification tool, PHLIP, for the quantitative analysis of large amounts of multichannel CLSM data in an automated way. PHLIP can be freely downloaded from http://phlip.sourceforge.net. RESULTS: PHLIP is an open source public license Matlab toolbox that includes functions for CLSM imaging data handling and ten image analysis operations describing various aspects of biofilm morphology. The use of PHLIP is here demonstrated by a study of the development of a natural marine phototrophic biofilm. It is shown how the examination of the individual biofilm components using the multi-channel capability of PHLIP allowed the description of the dynamic spatial and temporal separation of diatoms, bacteria and organic and inorganic matter during the shift from a bacteria-dominated to a diatom-dominated phototrophic biofilm. Reflection images and weight measurements complementing the PHLIP analyses suggest that a large part of the biofilm mass consisted of inorganic mineral material. CONCLUSION: The presented case study reveals new insight into the temporal development of a phototrophic biofilm where multi-channel imaging allowed to parallel monitor the dynamics of the individual biofilm components over time. This application of PHLIP presents the power of biofilm image analysis by multi-channel CLSM software and demonstrates the importance of PHLIP for the scientific community as a flexible and extendable image analysis platform for automated image processing.

Biofilms↗

PubMed2006

Development and evaluation of an open source software tool for deidentification of pathology reports.

BACKGROUND: Electronic medical records, including pathology reports, are often used for research purposes. Currently, there are few programs freely available to remove identifiers while leaving the remainder of the pathology report text intact. Our goal was to produce an open source, Health Insurance Portability and Accountability Act (HIPAA) compliant, deidentification tool tailored for pathology reports. We designed a three-step process for removing potential identifiers. The first step is to look for identifiers known to be associated with the patient, such as name, medical record number, pathology accession number, etc. Next, a series of pattern matches look for predictable patterns likely to represent identifying data; such as dates, accession numbers and addresses as well as patient, institution and physician names. Finally, individual words are compared with a database of proper names and geographic locations. Pathology reports from three institutions were used to design and test the algorithms. The software was improved iteratively on training sets until it exhibited good performance. 1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and note those that were not removed. RESULTS: 1254 (69.7 %) of 1800 pathology reports contained identifiers in the body of the report. 3439 (98.3%) of 3499 unique identifiers in the test set were removed. Only 19 HIPAA-specified identifiers (mainly consult accession numbers and misspelled names) were missed. Of 41 non-HIPAA identifiers missed, the majority were partial institutional addresses and ages. Outside consultation case reports typically contain numerous identifiers and were the most challenging to deidentify comprehensively. There was variation in performance among reports from the three institutions, highlighting the need for site-specific customization, which is easily accomplished with our tool. CONCLUSION: We have demonstrated that it is possible to create an open-source deidentification program which performs well on free-text pathology reports.

Computer Security↗