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PubMed2006

DyNAVacS: an integrative tool for optimized DNA vaccine design.

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL: http://miracle.igib.res.in/dynavac/.

Codon↗
PubMedDate not supplied

New technology continues to invade healthcare. What are the strategic implications/outcomes?

Healthcare technology continues to advance and be implemented in healthcare organizations. Nurse executives must strategically evaluate the effectiveness of each proposed system or device using a strategic planning process. Clinical information systems, computer-chip-based clinical monitoring devices, advanced Web-based applications with remote, wireless communication devices, clinical decision support software--all compete for capital and registered nurse salary dollars. The concept of clinical transformation is developed with new models of care delivery being supported by technology rather than driving care delivery. Senior nursing leadership's role in clinical transformation and healthcare technology implementation is developed. Proposed standards, expert group action, business and consumer groups, and legislation are reviewed as strategic drivers in the development of an electronic health record and healthcare technology. A matrix of advancing technology and strategic decision-making parameters are outlined.

Delivery of Health Care↗
PubMedDate not supplied

Utah's IBIS-PH: an innovative user interface solution for Web-based data query systems.

The ability to make good Web-based data query system (WDQS) project management decisions requires an understanding of the trade-offs inherent among various technology options. This article presents the current options available for the user interface and data display and compares the advantages and disadvantages of each for use in a WDQS. Relevant options are also discussed for back-end technologies such as Web and application servers and data storage mechanisms. We explain our decisions in developing the Indicator-based Information System for Public Health (IBIS-PH) query system to increase the probability of success and minimize risk. Finally, we compare the resulting IBIS-PH application characteristics with our original design requirements: broad public access; rich, interactive, and easy-to-use interface; portability; accessibility; maintainability of software and interface; supportability; low cost; and security.

Data Display↗
PubMed2002

Structural characterization of the human proteome.

This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.

Algorithms↗
PubMed2003

GANESH: software for customized annotation of genome regions.

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.

Animals↗
PubMed2004

MOP-UP: an online tool for finding strain-specific primers or motifs in DNA or protein alignments.

MOP-UP is a web-based application that enables efficient searching of nucleic acid or amino-acid alignments for sequences or motifs that are unique to a subset of the members represented in the alignment. This has applications in the design of assays that aim to detect particular strains or species. Since molecular-based characterisation of microbes is becoming increasingly important, MOP-UP can aid microbiologists in finding the best loci on which to base such assays. The program is accessible at: http://www.hpa.org.uk/srmd/bioinformatics/tools/mop-ups.htm.

Amino Acid Motifs↗
PubMed2005

"Where do we teach what?" Finding broad concepts in the medical school curriculum.

BACKGROUND: Often, medical educators and students do not know where important concepts are taught and learned in medical school. Manual efforts to identify and track concepts covered across the curriculum are inaccurate and resource intensive. OBJECTIVE: To test the ability of a web-based application called KnowledgeMap (KM) to automatically locate where broad biomedical concepts are covered in lecture documents in the Vanderbilt School of Medicine. METHODS: In 2003, the authors derived a gold standard set of curriculum documents by ranking 383 lecture documents as high, medium, or low relevance in their coverage of 4 broad biomedical concepts: genetics, women's health, dermatology, and radiology. We compared the gold standard rankings to KM, an automated tool that generates a variable number of subconcepts for each broad concept to calculate a relevance score for each document. Receiver operating characteristic (ROC) curves and area-under-the-curve were derived for each ranking using varying relevance score cutoffs. RESULTS: Receiver operating characteristic curve areas were acceptably high for each broad concept (range 0.74 to 0.98). At relevance scores that optimized sensitivity and specificity, 78% to 100% of highly relevant documents were identified. The best results were obtained with the application of 63 to 1437 subconcepts for a given broad concept. The search time was fast. CONCLUSIONS: The KM tool capably and automatically locates the detailed coverage of broad concepts across medical school documents in real time. Use of KM or similar tools may prove useful for other medical schools to identify broad concepts in their curricula.

Curriculum↗
PubMed2006

Development of the Leapfrog methodology for evaluating hospital implemented inpatient computerized physician order entry systems.

The 1999 Institute of Medicine report raised public awareness of the frequency and cost of adverse drug events in medicine. In response, in November 2000 a coalition of healthcare purchasers announced the formation of the Leapfrog Group, an organization dedicated to making "great leaps forward" in the safety and quality of health care in America. Their first target-computerized physician order entry (CPOE)-was selected specifically for its potential to reduce harm to patients from medications. The Leapfrog inpatient CPOE standard included a requirement that the organization operating CPOE should demonstrate via a test that their inpatient CPOE system can alert physicians to at least 50% of common serious prescribing errors. This paper outlines the development of this test which evaluates the ability of implemented CPOE systems to prevent the occurrence of medication errors that have a high likelihood of leading to adverse drug events. A framework was developed to include 12 different categories of CPOE based decision support that could prevent prescribing errors leading to adverse drug events. A scoring system was developed based on the known frequency and severity of adverse drug events. Simulated test patients and accompanying simulated test medication orders were developed to evaluate the ability of a CPOE system to intercept prescribing errors in all 12 decision support categories. The test was validated at a number of inpatient sites using both commercially available and custom developed CPOE systems. A web based application was developed to allow hospitals to self-administer the evaluation.

Certification↗
PubMed2002

Glycosylation of proteins: a computer based method for the rapid exploration of conformational space of N-glycans.

Inspection of protein databases suggests that as many as 70% of proteins have potential N-glycosylation sites. Unfortunately glycoproteins often refuse to crystallize and NMR techniques do not allow an unambiguous determination of the complete conformation of the sugar part. Therefore, time-consuming complex simulation methods are often used to explore the conformational space of N-glycans. The generation of a comprehensive data base describing the conformational space of larger fragments of N-glycans taking into account the effects of branching is presented. High-temperature molecular dynamics simulations of essential N-glycan fragments are performed until conformational equilibrium has been reached. Free energy landscapes are calculated for each glycosidic linkage. All possible conformations for each N-glycan fragment are automatically assigned, ranked according to their relative population and stored in a database. These values are recalled for the generation of a complete set of all possible conformations for a given N-glycan topology. The constructed conformations are ranked according to their energy content. Since this approach allows to explore the complete conformational space of a given N-glycan within a few minutes of CPU-time on a standard PC, it is well suited to be used as a Web-Based application.

Carbohydrate Conformation↗
PubMedDate not supplied

[Automatic calculation of relative survival through the web. The WAERS project of the Catalan Institute of Oncology].

The most commonly used measure to estimate cancer survival is relative survival, defined as the ratio between observed and expected survival. Expected survival is computed on the basis of the mortality of a reference population. Mortality tables for the general population are not always available and their calculation requires specific software. For that purpose, the Catalan Institute of Oncology developed WAERS (Web-Assisted Estimation of Relative Survival), a web-based application that estimates the relative survival for a cohort of patients. The user prepares data in a specific format and sends them to a remote server located at the Catalan Institute of Oncology. This server computes relative survival and returns a file with the results to the electronic address supplied by the user. By means of this application, hospital- and population-based Spanish cancer registries and registries of other diseases can estimate relative survival of their cohorts using their reference population (province or autonomous community). This application could also be useful for cohort mortality studies.

Humans↗
PubMed2004

A SNP-centric database for the investigation of the human genome.

BACKGROUND: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. Although current genomic databases contain information on several million SNPs and are growing at a very fast rate, the true value of a SNP in this context is a function of the quality of the annotations that characterize it. Retrieving and analyzing such data for a large number of SNPs often represents a major bottleneck in the design of large-scale association studies. DESCRIPTION: SNPper is a web-based application designed to facilitate the retrieval and use of human SNPs for high-throughput research purposes. It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools. In this paper we describe the structure and organization of the SNPper database, we review the available data export and visualization options, and we describe how the architecture of SNPper and its specialized data structures support high-volume SNP analysis. CONCLUSIONS: The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research. Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome.

Databases, Genetic↗
PubMed2005

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.

BACKGROUND: Prediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective way to combine the individual predictors, at will, to a single consensus prediction method. RESULTS: We assess the statistical significance of the performance of each prediction scheme and conclude that Hidden Markov Model based methods, HMM-B2TMR, ProfTMB and PRED-TMBB, are currently the best predictors, according to either the per-residue accuracy, the segments overlap measure (SOV) or the total number of proteins with correctly predicted topologies in the test set. Furthermore, we show that the available predictors perform better when only transmembrane beta-barrel domains are used for prediction, rather than the precursor full-length sequences, even though the HMM-based predictors are not influenced significantly. The consensus prediction method performs significantly better than each individual available predictor, since it increases the accuracy up to 4% regarding SOV and up to 15% in correctly predicted topologies. CONCLUSIONS: The consensus prediction method described in this work, optimizes the predicted topology with a dynamic programming algorithm and is implemented in a web-based application freely available to non-commercial users at http://bioinformatics.biol.uoa.gr/ConBBPRED.

Algorithms↗
PubMed2006

VANTED: a system for advanced data analysis and visualization in the context of biological networks.

BACKGROUND: Recent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes. RESULTS: We present VANTED, a tool for the visualization and analysis of networks with related experimental data. Data from large-scale biochemical experiments is uploaded into the software via a Microsoft Excel-based form. Then it can be mapped on a network that is either drawn with the tool itself, downloaded from the KEGG Pathway database, or imported using standard network exchange formats. Transcript, enzyme, and metabolite data can be presented in the context of their underlying networks, e. g. metabolic pathways or classification hierarchies. Visualization and navigation methods support the visual exploration of the data-enriched networks. Statistical methods allow analysis and comparison of multiple data sets such as different developmental stages or genetically different lines. Correlation networks can be automatically generated from the data and substances can be clustered according to similar behavior over time. As examples, metabolite profiling and enzyme activity data sets have been visualized in different metabolic maps, correlation networks have been generated and similar time patterns detected. Some relationships between different metabolites were discovered which are in close accordance with the literature. CONCLUSION: VANTED greatly helps researchers in the analysis and interpretation of biochemical data, and thus is a useful tool for modern biological research. VANTED as a Java Web Start Application including a user guide and example data sets is available free of charge at http://vanted.ipk-gatersleben.de.

Algorithms↗
PubMed2006

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

BACKGROUND: Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. DESCRIPTION: Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html CONCLUSION: The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.

Database Management Systems↗
PubMed2006

Exploration of biological network centralities with CentiBiN.

BACKGROUND: The elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements. Centrality analysis ranks network elements according to their importance within the network structure and different centrality measures focus on different importance concepts. Central elements of biological networks have been found to be, for example, essential for viability. RESULTS: CentiBiN (Centralities in Biological Networks) is a tool for the computation and exploration of centralities in biological networks such as protein-protein interaction networks. It computes 17 different centralities for directed or undirected networks, ranging from local measures, that is, measures that only consider the direct neighbourhood of a network element, to global measures. CentiBiN supports the exploration of the centrality distribution by visualising central elements within the network and provides several layout mechanisms for the automatic generation of graphical representations of a network. It supports different input formats, especially for biological networks, and the export of the computed centralities to other tools. CONCLUSION: CentiBiN helps systems biology researchers to identify crucial elements of biological networks. CentiBiN including a user guide and example data sets is available free of charge at http://centibin.ipk-gatersleben.de/. CentiBiN is available in two different versions: a Java Web Start application and an installable Windows application.

Computer Graphics↗
PubMed2006

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

BACKGROUND: We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable. RESULTS: We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the Project Manager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping. CONCLUSION: The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.

Animals↗
PubMed2006

PathSys: integrating molecular interaction graphs for systems biology.

BACKGROUND: The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. RESULTS: Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae) and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. CONCLUSION: Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

Computer Graphics↗