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PubMed2006

A medical imaging and visualization toolkit in Java.

Medical imaging research and clinical applications usually require combination and integration of various techniques ranging from image processing and analysis to realistic visualization to user-friendly interaction. Researchers with different backgrounds coming from diverse areas have been using numerous types of hardware, software, and environments to obtain their results. We also observe that students often build their tools from scratch resulting in redundant work. A generic and flexible medical imaging and visualization toolkit would be helpful in medical research and educational institutes to reduce redundant development work and hence increase research efficiency. This paper presents our experience in developing a Medical Imaging and Visualization Toolkit (BIL-kit) that is a set of comprehensive libraries as well as a number of interactive tools. The BIL-kit covers a wide range of fundamental functions from image conversion and transformation, image segmentation, and analysis to geometric model generation and manipulation, all the way up to 3D visualization and interactive simulation. The toolkit design and implementation emphasize the reusability and flexibility. BIL-kit is implemented in the Java language so that it works in hybrid and dynamic research and educational environments. This also allows the toolkit to extend its usage for the development of Web-based applications. Several BIL-kit-based tools and applications are presented including image converter, image processor, general anatomy model simulator, vascular modeling environment, and volume viewer. BIL-kit is a suitable platform for researchers and students to develop visualization and simulation prototypes, and it can also be used for the development of clinical applications.

Algorithms↗
PubMedDate not supplied

Internet-based behavioral change and psychosocial care for patients with cardiovascular disease: a review of cardiac disease-specific applications.

BACKGROUND: Web-based interventions (WBIs) seem to be an efficacious method of addressing behavioral and psychosocial maladjustment among patients with chronic illness (eg, diabetes), behavioral concerns (eg, smoking cessation), and psychologic maladjustment (eg, panic disorder). Cardiology seems particularly well suited to the application of WBIs given its strong association with behavioral (eg, lifestyle) and cognitive (eg, stress and coping) factors. To date, few studies have been published that explore the use of WBIs on psychosocial and quality of life variables among populations with cardiac disease. OBJECTIVE: The purpose of this study is to review the use of WBIs in patients with cardiovascular disease to date, and to provide recommendations as to how future WBIs can be developed specifically to meet the needs of different populations with heart disease (eg, recipients of implantable cardioverter defibrillators, patients with congestive heart failure, and patients with congenital heart disease). CONCLUSIONS: We conclude that, although limitations exist, WBIs are a reasonable modus of improving patient outcomes.

Behavior↗
PubMed2004

Automated interpretation of mass spectra of complex mixtures by matching of isotope peak distributions.

Mass spectrometry is now firmly established as a powerful technique for the identification and characterization of proteins when used in conjunction with sequence databases. Various approaches involving stable-isotope labeling have been developed for quantitative comparisons between paired samples in proteomic expression analysis by mass spectrometry. However, interpretation of such mass spectra is far from being fully automated, mainly due to the difficulty of analyzing complex patterns resulting from the overlap of multiple peaks arising from the assortment of natural isotopes. In order to facilitate the interpretation of a complex mass spectrum of such a mixture, such as an MS spectrum of a stable-isotope-enriched ion species, we report on the development of a software application, 'Matching' (web accessible), that enables the automatic matching of theoretical isotope envelopes to multiple ion peaks in a raw spectrum. It is particularly useful for resolving the relative abundances of narrow-split paired peaks caused by enrichment with a stable isotope, such as 18O, 13C, 2H, or 15N.

Algorithms↗
PubMed2003

The circling behavior of the deafblind LEW-ci2 rat is linked to a segment of RNO10 containing Myo15 and Kcnj12.

The LEW/Ztm-ci2 rat is an autosomal recessive mutant that displays circling behavior, deafness, progressive retinopathy, locomotor hyperactivity, ataxia, and opisthotonus. We performed a genome-wide scan of a (LEW/Ztm-ci2 x BN/Ztm) F1 x LEW/Ztm-ci2 backcross population with anonymous microsatellite markers to analyze the genetics of this mutant rat. This linkage analysis demonstrated a very strong association of RNO10 SSLP markers to the phenotype with a core region in the central part of the chromosome. The knowledge of genes mapping to this part of the rat genome and their linkage to SSLP markers is still poor. We developed SSLP markers closely linked to genes, which might be responsible for the mutant phenotype by using the growing amount of rat-specific DNA sequences available at World Wide Web databases. Application of this method facilitated the search for candidate genes for the phenotype of the LEW-ci2 rat. We were able to map Myo15 and its neighboring genes, Znf179 and Aldh3a1, to the region of interest and Myo1c to a more distal location on RNO10. Further rat BAC clones were used to create a physical map of the region of interest. This map revealed the position of further genes. Among those is Kcnj12. Owing to their localization on RNO10 and their involvement in a similar pathology in human and mouse, Myo15 and Kcnj12 can be regarded as candidate genes for the deafblind phenotype of the LEW-ci2 rat.

Animals↗
PubMed2006

Enabling collaborative medical diagnosis over the Internet via peer-to-peer distribution of electronic health records.

Recent developments in networking and computing technologies and the expansion of the electronic health record system have enabled the possibility of online collaboration between geographically distributed medical personnel. In this context, the paper presents a Web-based application, which implements a collaborative working environment for physicians by enabling the peer-to-peer exchange of electronic health records. The paper treats technological issues such as Video, Audio and Message Communication, Workspace Management, Distributed Medical Data Management and exchange, while it emphasizes on the Security issues arisen, due to the sensitive and private nature of the medical information. In the paper, we present initial results from the system in practice and measurements regarding transmission times and bandwidth requirements. A wavelet based image compression scheme is also introduced for reducing network delays. A number of physicians were asked to use the platform for testing purposes and for measuring user acceptance. The system was considered by them to be very useful, as they found that the platform simulated very well the personal contact between them and their colleagues during medical meetings.

Computer Communication Networks↗
PubMed2006

Radiology education: a glimpse into the future.

The digital revolution in radiology continues to advance rapidly. There are a number of interesting developments within radiology informatics which may have a significant impact on education and training of radiologists in the near future. These include extended functionality of handheld computers, web-based skill and knowledge assessment, standardization of radiological procedural training using simulated or virtual patients, worldwide videoconferencing via high-quality health networks such as Internet2 and global collaboration of radiological educational resources via comprehensive, multi-national databases such as the medical imaging resource centre initiative of the Radiological Society of North America. This article will explore the role of e-learning in radiology, highlight a number of useful web-based applications in this area, and explain how the current and future technological advances might best be incorporated into radiological training.

Clinical Competence↗
PubMed2006

Expression mapping of tetracycline-responsive prion protein promoter: digital atlasing for generating cell-specific disease models.

We present a digital atlas system that allows mapping of molecular expression patterns at cellular resolution through large series of histological sections. Using this system, we have mapped the distribution of a distinct marker, encoded by the LacZ reporter gene driven by the tetracycline-responsive prion protein promoter in double transgenic mice. The purpose is to evaluate the suitability of this promoter mouse line for targeting genes of interest to specific brain regions, essential for construction of inducible transgenic disease models. Following processing to visualize the promoter expression, sections were counterstained to simultaneously display cytoarchitectonics. High-resolution mosaic images covering entire coronal sections were collected through the mouse brain at intervals of 200 microm. A web-based application provides access to a customized virtual microscopy tool for viewing and navigation within and across the section images. For each section image, the nearest section in a standard atlas is defined, and annotations of key structures and regions inserted. Putative categorization of labeled cells was performed with use of distribution patterns, followed by cell size and shape, as parameters that were compared to legacy data. Among the ensuing results were expression of this promoter in putative glial cells in the cerebellum (and not in Purkinje cells), in putative glial cells in the substantia nigra, in pallidal glial cells or interneurons, and in distinct cell layers and regions of the hippocampus. The study serves as a precursor for a database resource allowing evaluation of the suitability of different promoter mouse lines for generating disease models.

Animals↗
PubMed2026

Structure-centric searching enables global mapping of the public metabolome.

Searching and learning from aggregated public metabolomics data spanning thousands of studies remained largely inaccessible. Here we present StructureMASST, a web-based application enabling scalable, structure-centric searches across public metabolomics repositories using molecule names or chemical representations. It queries a precomputed knowledgebase of 2.19 billion spectral matches and 420 million metadata links, supports modification-tolerant and mass-shift searches, and maps chemical structures across taxonomy, biological context and environmental conditions to accelerate discovery.

Journal Article↗
PubMed2001

Twelve tips on choosing web teaching software.

Experimentation with the new technology of web-based teaching has meant that many medical schools are using more than one software system for delivery. In the medical faculty at the University of New South Wales at the end of 1999, three different software packages (WebTeach, Top Class and Learning Space) were used for mediating teaching and learning on the web. The type of applications for which web-based teaching is used also varied widely. They ranged from a distance-education coursework masters programme delivered via the web, to the provision of additional resource materials and case discussions to supplement undergraduate classes on campus. Once web-based teaching moves out of the experimental phase and into the mainstream there is usually pressure to standardize on one software system. This has the advantage of limiting costs for training and support but it may require some compromise on functionality. Faced with the need to limit the number of software packages in use at UNSW the published comparisons of web software (Landon, 2001; University of California at Berkeley; 2001; Marshall University, 2001; Murdoch University, 2001) were first investigated. These show in broad terms what each package will do but often lack sufficient detail to determine whether the package will meet specific requirements. To get a better idea of how different software packages operate under the pressure of day-to-day teaching, 15 academic course coordinators, instructional designers and educational developers from six Australian universities who are involved in designing and delivering web courses were interviewed. The authors also joined online user groups and asked questions of international users. The aim was to find out what strengths and weaknesses they had found in the packages they used and whether they would make the same choice again. The authors were particularly interested to find out what questions they would ask when considering a new package. The twelve tips that follow summarize their advice to those considering the choice of a web teaching package.

Journal Article↗
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↗
PubMed2004

Enhanced quality and quantity of retrieval of Critically Appraised Topics using the CAT Crawler.

As healthcare moves towards the implementation of Evidence-Based Medicine (EBM), Critically Appraised Topics (CATs) become useful in helping physicians to make clinical decisions. A number of academic and healthcare organizations have set up web-based CAT libraries. The primary objective of the presented work is to provide a one-stop search and download site that allows access to multiple CAT libraries. A web-based application, namely the CAT Crawler, was developed to serve physicians with an adequate access to available appraised topics on the Internet. Important information is extracted automatically and regularly from CAT websites, and consolidated by checking the uniqueness and availability. The principle of meta-search is incorporated into the implementation of the search engine, which finds relevant topics following keyword input. The retrieved result directs the physician to the original resource page. A full-text article of a particular topic can be converted into a proper format for downloading to Personal Digital Assistant (PDA) devices. In summary, the application provides physicians with a common interface to retrieve relevant CATs on particular clinical topics from multiple resources, and thus speeds up the decision making process.

Algorithms↗
PubMed2002

SNPper: retrieval and analysis of human SNPs.

MOTIVATION: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for the study of the human genome. SNPs can be used as markers to create high-density genetic maps, as causal candidates for diseases, or to reconstruct the history of our genome. SNP-based studies rely on the availability of large numbers of validated, high-frequency SNPs whose position on the chromosomes is known with precision. Although large collections of SNPs exist in public databases, researchers need tools to effectively retrieve and manipulate them. RESULTS: We describe the implementation and usage of SNPper, a web-based application to automate the tasks of extracting SNPs from public databases, analyzing them and exporting them in formats suitable for subsequent use. Our application is oriented toward the needs of candidate-gene, whole-genome and fine-mapping studies, and provides several flexible ways to present and export the data. The application has been publicly available for over a year, and has received positive user feedback and high usage levels.

Database Management Systems↗
PubMed2025

SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences.

SUMMARY: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often restricted to experts in programming and mathematics. This is due to the need to implement entire models and solvers from the mathematical notation models are normally presented as. Here, we present SBMLtoOdin, an R package that translates differential equation models in SBML format from the BioModels database into executable R code using the R package odin, allowing researchers to easily reuse models. We also present Menelmacar, a web-based application that provides interactive visualisations of these models by solving their differential equations in the browser. This platform allows non-experts to simulate and investigate models using an easy-to-use interface. AVAILABILITY AND IMPLEMENTATION: SBMLtoOdin is published under the open source Apache 2.0 licence at https://github.com/bacpop/SBMLtoOdin and can be installed as an R package. The code for the Menelmacar website is published under the MIT License at https://github.com/bacpop/odinviewer, and the website can be found at https://biomodels.bacpop.org/.

Software↗
PubMed2003

MARAN: normalizing micro-array data.

SUMMARY: MARAN is a web-based application for normalizing microarray data. MARAN comprises a generic ANOVA model, an option for Loess fitting prior to ANOVA analysis, and a module for selecting genes with significantly changing expression. AVAILABILITY: http://www.esat.kuleuven.ac.be/maran/.

Algorithms↗
PubMed2004

Decoupling dynamical systems for pathway identification from metabolic profiles.

RATIONALE: Modern molecular biology is generating data of unprecedented quantity and quality. Particularly exciting for biochemical pathway modeling and proteomics are comprehensive, time-dense profiles of metabolites or proteins that are measurable, for instance, with mass spectrometry, nuclear magnetic resonance or protein kinase phosphorylation. These profiles contain a wealth of information about the structure and dynamics of the pathway or network from which the data were obtained. The retrieval of this information requires a combination of computational methods and mathematical models, which are typically represented as systems of ordinary differential equations. RESULTS: We show that, for the purpose of structure identification, the substitution of differentials with estimated slopes in non-linear network models reduces the coupled system of differential equations to several sets of decoupled algebraic equations, which can be processed efficiently in parallel or sequentially. The estimation of slopes for each time series of the metabolic or proteomic profile is accomplished with a 'universal function' that is computed directly from the data by cross-validated training of an artificial neural network (ANN). CONCLUSIONS: Without preprocessing, the inverse problem of determining structure from metabolic or proteomic profile data is challenging and computationally expensive. The combination of system decoupling and data fitting with universal functions simplifies this inverse problem very significantly. Examples show successful estimations and current limitations of the method. AVAILABILITY: A preliminary Web-based application for ANN smoothing is accessible at http://bioinformatics.musc.edu/webmetabol/. S-systems can be interactively analyzed with the user-friendly freeware PLAS (http://correio.cc.fc.ul.pt/~aenf/plas.html) or with the MATLAB module BSTLab (http://bioinformatics.musc.edu/bstlab/), which is currently being beta-tested.

Algorithms↗
PubMed2004

Defining 3D residue environment in protein structures using SCORPION and FORMIGA.

SUMMARY: Two web-based applications to analyze amino acids three-dimensional (3D) local environment within protein structures-SCORPION and FORMIGA-are presented. SCORPION and FORMIGA produce a graphical presentation for simple statistical data showing the frequency of residue occurrence within a given sphere (defined here as the 3D contacts). The center of that sphere is placed at the Calpha and at the last heavy atom in the side chain of the selected amino acid. Further depth of detail is given in terms of a secondary structure to which the profiled amino acid belongs. Results obtained with those two applications are relevant for estimating the importance of the amino acid 3D local environment for protein folding and stability. Effectively, SCORPION and FORMIGA construct knowledge-based force fields. The difference between SCORPION and FORMIGA is in that the latter operates on protein interfaces, while the former only functions for a single protein chain. Both applications are implemented as stand-alone components of STING Millennium Suite. AVAILABILITY: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org/SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS. [options: Scorpion, Formiga]

Algorithms↗