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PubMed2002

An integrated computational pipeline and database to support whole-genome sequence annotation.

We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture.

Animals↗

PubMed2004

Implementing communication between Windows PCs and test equipment using RS-232 and Borland C++ Builder.

Modern experiments in the behavioral sciences frequently employ several items of electronic equipment such as computers, monitoring devices, stimulus presentation equipment, and response collection systems. In many cases it would be advantageous for these items to communicate directly with each other. Such communication may facilitate greater automation of experiments (i.e., reduced experimenter influences during the experiment), more precise experiment control (i.e., superior timing and synchronization capabilities of electronic devices), and greater accuracy of data collection (i.e., reduced ambiguity of participant responses). Many electronic experiment devices already provide external interfaces through which communication with other devices can be implemented. The most common is based on the RS-232 protocol, which is also found in all standard PCs. Therefore, Microsoft Windows based computers can be programmed to control experiments by communicating directly with electronic experiment devices. We show how to implement this RS-232 interconnection between devices and a Windows PC using currently available software tools.

Computer Communication Networks↗

PubMed2005

stam--a Bioconductor compliant R package for structured analysis of microarray data.

BACKGROUND: Genome wide microarray studies have the potential to unveil novel disease entities. Clinically homogeneous groups of patients can have diverse gene expression profiles. The definition of novel subclasses based on gene expression is a difficult problem not addressed systematically by currently available software tools. RESULTS: We present a computational tool for semi-supervised molecular disease entity detection. It automatically discovers molecular heterogeneities in phenotypically defined disease entities and suggests alternative molecular sub-entities of clinical phenotypes. This is done using both gene expression data and functional gene annotations. We provide stam, a Bioconductor compliant software package for the statistical programming environment R. We demonstrate that our tool detects gene expression patterns, which are characteristic for only a subset of patients from an established disease entity. We call such expression patterns molecular symptoms. Furthermore, stam finds novel sub-group stratifications of patients according to the absence or presence of molecular symptoms. CONCLUSION: Our software is easy to install and can be applied to a wide range of datasets. It provides the potential to reveal so far indistinguishable patient sub-groups of clinical relevance.

Calibration↗

PubMed2004

The path to enlightenment: making sense of genomic and proteomic information.

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.

Computational Biology↗

PubMed2005

Computational method for temporal pattern discovery in biomedical genomic databases.

With the rapid growth of biomedical research databases, opportunities for scientific inquiry have expanded quickly and led to a demand for computational methods that can extract biologically relevant patterns among vast amounts of data. A significant challenge is identifying temporal relationships among genotypic and clinical (phenotypic) data. Few software tools are available for such pattern matching, and they are not interoperable with existing databases. We are developing and validating a novel software method for temporal pattern discovery in biomedical genomics. In this paper, we present an efficient and flexible query algorithm (called TEMF) to extract statistical patterns from time-oriented relational databases. We show that TEMF - as an extension to our modular temporal querying application (Chronus II) - can express a wide range of complex temporal aggregations without the need for data processing in a statistical software package. We show the expressivity of TEMF using example queries from the Stanford HIV Database.

Artificial Intelligence↗

PubMedDate not supplied

HAD: an automated database tool for analyzing screening hits in drug discovery.

Collecting, organizing, and reviewing chemical information associated with screening hits are human time-consuming. The task depends highly on the individual, and human errors may result in missing leads or wasting resources. To overcome these hurdles, we have developed a decision support system, Hits Analysis Database (HAD). HAD is a software tool that automatically generates an ISIS database file containing compound structures, biological activities, calculated properties such as clogP, hazard fragment labels, structure classifications, etc. All data are processed by available software and packed into a single SD file. In addition to search capabilities, HAD provides an overview of structural classes and associated activity statistics. Chemical structures can be organized by maximum common substructure clustering. The ease of use and customized features make HAD a chief tool in lead selection processes.

Databases, Factual↗

PubMed2003

AraCyc: a biochemical pathway database for Arabidopsis.

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).

Arabidopsis↗

PubMedDate not supplied

Computer-assisted analysis of three-dimensional MR angiograms.

The software tools required for postprocessing of magnetic resonance (MR) angiograms include the following functions: data handling, image visualization, and vascular analysis. A custom postprocessing software called Magnetic Resonance Angiography Computer Assisted Analysis (MARACAS) has been developed. This software combines the most commonly used three-dimensional visualization techniques with image processing methods for analysis of vascular morphology on MR angiograms. The main contributions of MARACAS are (a) implementation of a fast method for stenosis quantification on three-dimensional MR angiograms, which is clinically applicable in a personal computer-based system; and (b) portability to the most widespread platforms. The quantification is performed in three steps: extraction of the vessel centerline, detection of vessel boundaries in planes locally orthogonal to the centerline, and calculation of stenosis parameters on the basis of the resulting contours. Qualitative results from application of the method to data from patients showed that the vessel centerline correctly tracked the vessel path and that contours were correctly estimated. Quantitative results obtained from images of phantoms showed that the computation of stenosis severity was accurate.

Algorithms↗

PubMed2002

ILAB: a program for postexperimental eye movement analysis.

The recording and analysis of eye movements are fundamental to a diverse set of research applications, including studies in which reading, visual search, and both overt and covert visuospatial attention are examined. Software tools supplied with commonly available eye-tracking equipment have generally been limited in functionality and nonextensible. Because of this dearth of available software, ELAB was created to provide an extensible framework for analyzing various aspects of eye movements. The program consists of a series of open-source MATLAB functions. The program's data structures keep raw data, analysis preferences, and analyzed data separate, thus maintaining data fidelity and promoting extensibility.

Blinking↗

PubMedDate not supplied

Medial mandibular flexure and maximum occlusal force in dentate adults.

PURPOSE: Medial mandibular flexure (MMF) is the functional narrowing of the mandible during opening and protrusion movements, which may affect conventional or implant-supported prostheses. This study evaluated the association among MMF, maximum occlusal force (MOF), gender, weight, height, body mass index (BMI), and age in 80 dentate adult subjects (40 women, 40 men; age range 20 to 38 years). MATERIALS AND METHODS: Bilateral MOF was measured using a cross-arch force transducer placed in the first molar region. For MMF calculation, impressions of the mandibular occlusal surface were made with vinyl polysiloxane putty material in rest (R), maximum opening (O), and maximum protrusion (P). The impressions were scanned, and the images were processed using Adobe Photoshop software. Reference points were selected on the occlusal surface of the contralateral first molars, and the linear intermolar distance was measured using Image Tool software. MMF was calculated by subtracting the intermolar distance during opening or protrusion from the intermolar distance during rest. RESULTS: Mean values of MOF were 698.14 N for women and 1,009.48 N for men; MMF-O was 0.146 mm and MMF-Pwas 0.15 mm for the total sample. No correlation was found between MOF and MMF (r = 0.02 for MMF-O; r = 0.11 for MMF-P; P > .05) or between MMF and weight, height, BMI, or age. MOF was significantly associated (P <.001) with weight (r = 0.509), height (r = 0.459), and BMI (r = 0.423), but not with age (r = 0.009). CONCLUSION: These results suggest that MMF is not associated with MOF in this sample of dentate adults.

Adult↗

PubMed2026

Comprehensive evaluation of ACMG/AMP-based variant classification tools.

MOTIVATION: The American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines represent the gold standard for clinical variant interpretation. Despite the widespread adoption of ACMG/AMP guidelines, a comprehensive comparison of the software tools designed to implement them has been lacking. This represents a significant gap, as clinicians require evidence-based guidance on which tools to use in their practice. RESULTS: We benchmarked four ACMG/AMP-based tools (Franklin, InterVar, TAPES, Genebe) selected from 22 tools, and compared their performance with LIRICAL, a top-performing phenotype-driven tool, using 151 expert-curated datasets from Mendelian disorders. Selection criteria included free availability, VCF compatibility, operational reliability, and not being disease-specific. Our evaluation framework assessed top-N accuracy (N = 1, 5, 10, 20, 50), retention rates, precision, recall, F1 scores, and area under the curve (AUC). Statistical validation employed bootstrap confidence intervals (n = 1000) and Friedman tests. LIRICAL (68.21%) and Franklin (61.59%) demonstrated superior top-10 variant prioritization accuracy in Mendelian disorders, significantly outperforming other tools (P = .0000). Results demonstrate that tools with advanced phenotypic integration significantly outperform those relying primarily on genomic features. AVAILABILITY AND IMPLEMENTATION: All data and source code required to reproduce the findings of this study are openly available in the Code Ocean repository at https://doi.org/10.24433/CO.6562438.v1.

Software↗

PubMed2006

Genetic algorithm for multi-objective experimental optimization.

A new software tool making use of a genetic algorithm for multi-objective experimental optimization (GAME.opt) was developed based on a strength Pareto evolutionary algorithm. The software deals with high dimensional variable spaces and unknown interactions of design variables. This approach was evaluated by means of multi-objective test problems replacing the experimental results. A default parameter setting is proposed enabling users without expert knowledge to minimize the experimental effort (small population sizes and few generations).

Algorithms↗

PubMed1995

RNA secondary structure prediction using highly parallel computers.

An RNA secondary structure prediction method using a highly parallel computer is reported. We focus on finding thermodynamically stable structures of a single-stranded RNA molecule. Our approach is based on a parallel combinatorial method which calculates the free energy of a molecule as the sum of the free energies of all the physically possible hydrogen bonds. Our parallel algorithm finds many highly stable structures all at once, while most of the conventional prediction methods find only the most stable structure. The important idea in our algorithm is search tree pruning, with dynamic load balancing across the processor elements in a parallel computer. Software tools for visualization and classification of secondary structures are also presented using the sequence of cadang-cadang coconut viroid as an example. Our software system runs on CM-5.

Algorithms↗

PubMed2006

Modeling end-users' acceptance of a knowledge authoring tool.

OBJECTIVES: Knowledge bases comprise a vital component in the classic medical expert system model, yet the knowledge acquisition process by which they are created has been characterized as highly iterative and labor-intensive. The difficulty of this process underscores the importance of knowledge authoring tools that satisfy the demands of end-users. The authors hypothesize that the acceptability of a knowledge authoring tool for the creation of medical knowledge base content can be predicted by an accepted model in the information technology (IT) field, specifically the Technology Acceptance Model (TAM). METHODS: An online survey was conducted amongst knowledge base authors who had previously established experience with the authoring tool software. The Likert-based questions in the survey were patterned directly after accepted TAM constructs with minor modifications to particularize them to the software being used. The results were analyzed using structural equation modeling. RESULTS: The TAM performed well in predicting endusers' behavioral intentions to use the knowledge authoring tool. Five out of seven goodness-of-fit statistics indicate that the model represents the behavioral intentions of the authors well. All but one of the hypothesized relationships specified by the TAM were significant with p values less than 0.05. CONCLUSIONS: The TAM provides an adequate means by which development teams can anticipate and better understand what aspects of a knowledge authoring tool are most important to their target audience. Further research involving other behavioral models and an expanded user base will be necessary to better understand the scope of issues that factor into acceptability.

Attitude↗

PubMed2006

GOurmet: a tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions.

BACKGROUND: The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize effectively. Software tools have been recently developed to use the distribution of gene ontology (GO) terms associated with the genes in an EP to identify specific biological functions or processes that are over- or under-represented in that EP relative to other EPs. Additionally, it is possible to use the distribution of GO terms inherent to each EP to relate that EP as a whole to other EPs. Because GO term annotation is organized in a tree-like cascade of variable granularity, this approach allows the user to relate (e.g., by hierarchical clustering) EPs of varying length and from different platforms (e.g., GeneChip, SAGE, EST library). RESULTS: Here we present GOurmet, a software package that calculates the distribution of GO terms represented by the genes in an individual expression profile (EP), clusters multiple EPs based on these integrated GO term distributions, and provides users several tools to visualize and compare EPs. GOurmet is particularly useful in meta-analysis to examine EPs of specified cell types (e.g., tissue-specific stem cells) that are obtained through different experimental procedures. GOurmet also introduces a new tool, the Targetoid plot, which allows users to dynamically render the multi-dimensional relationships among individual elements in any clustering analysis. The Targetoid plotting tool allows users to select any element as the center of the plot, and the program will then represent all other elements in the cluster as a function of similarity to the selected central element. CONCLUSION: GOurmet is a user-friendly, GUI-based software package that greatly facilitates analysis of results generated by multiple EPs. The clustering analysis features a dynamic targetoid plot that is generalizable for use with any clustering application.

Artificial Intelligence↗

PubMed1995

The cumulative verification image analysis tool for offline evaluation of portal images.

PURPOSE: Daily portal images acquired using electronic portal imaging devices contain important information about the setup variation of the individual patient. The data can be used to evaluate the treatment and to derive correction for the individual patient. The large volume of images also require software tools for efficient analysis. This article describes the approach of cumulative verification image analysis (CVIA) specifically designed as an offline tool to extract quantitative information from daily portal images. METHODS AND MATERIALS: The user interface, image and graphics display, and algorithms of the CVIA tool have been implemented in ANSCI C using the X Window graphics standards. The tool consists of three major components: (a) definition of treatment geometry and anatomical information; (b) registration of portal images with a reference image to determine setup variation; and (c) quantitative analysis of all setup variation measurements. The CVIA tool is not automated. User interaction is required and preferred. Successful alignment of anatomies on portal images at present remains mostly dependent on clinical judgment. Predefined templates of block shapes and anatomies are used for image registration to enhance efficiency, taking advantage of the fact that much of the tool's operation is repeated in the analysis of daily portal images. RESULTS: The CVIA tool is portable and has been implemented on workstations with different operating systems. Analysis of 20 sequential daily portal images can be completed in less than 1 h. The temporal information is used to characterize setup variation in terms of its systematic, random and time-dependent components. The cumulative information is used to derive block overlap isofrequency distributions (BOIDs), which quantify the effective coverage of the prescribed treatment area throughout the course of treatment. Finally, a set of software utilities is available to facilitate feedback of the information for treatment plan recalculation and to test various decision strategies for treatment adjustment. CONCLUSIONS: The CVIA tool provides comprehensive analysis of daily images acquired with electronic portal imaging devices. Its offline approach allows characterization of the nature of setup variation for the individual patient that would have been difficult to deduce using only a few daily or weekly portal images. Distribution of the tool will help establish an important database of setup variation from many clinics. The information derived from CVIA can also serve as the foundation to integrate treatment verification, treatment planning, and treatment delivery.

Computer Peripherals↗

PubMed1999

Estimating medical resources required following a nuclear event.

Large quantities of medical resources are necessary for the treatment of patients suffering from acute radiation syndrome in combination with blast and thermal injuries (combined injuries). So far, however, there is no tool available for evaluating the resources required for the treatment of combined injuries. The purpose of this manuscript is to describe the scientific basis for a newly developed software tool designed to estimate the medical resources needed for treating the combined injuries of individuals/high numbers of casualties who may be involved in civil defense, emergency medical care and various military activities (namely out of area) in the case of a nuclear event.

Blast Injuries↗

PubMed2006

New angiographic measurement tool for analysis of small cerebral vessels: application to a subarachnoid haemorrhage model in the rat.

INTRODUCTION: Exact quantification of vasospasm by angiography is known to be difficult especially in small vessels. The purpose of the study was to develop a new method for computerized analysis of small arteries and to demonstrate feasibility on cerebral angiographies of rats acquired on a clinical angiography unit. METHODS: A new software tool analysing grey values and subtracting background noise was validated on a vessel model. It was tested in practice in animals with subarachnoid haemorrhage (SAH). A total of 28 rats were divided into four groups: SAH untreated, SAH treated with local calcium antagonist, SAH treated with placebo, and sham-operated. The diameters of segments of the internal carotid, caudal cerebral, middle cerebral, rostral cerebral and the stapedial arteries were measured and compared to direct measurements of the diameters on magnified images. RESULTS: There was a direct correlation between the cross-sectional area of vessels measured in a phantom and the measurements acquired using the new image analysis method. The spread of repeated measurements with the new software was small compared to the spread of direct measurements of vessel diameters on magnified images. Application of the measurement tool to experimental SAH in rats showed a statistically significant reduction of vasospasm in the SAH groups treated with nimodipine-releasing pellets in comparison to all the other groups combined. CONCLUSION: The presented computerized method for analysis of small intracranial vessels is a new method allowing precise relative measurements. Nimodipine-releasing subarachnoidal pellets reduce vasospasm, but further testing with larger numbers is necessary. The tool can be applied to human angiography without modification and offers the promise of substantial progress in the diagnosis of vasospasm after SAH.

Animals↗