Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “software tools”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24Linked to original sources
PubMed2005

NAV: a tool for producing presentation quality animations of graphical cognitive model dynamics.

Computational models of cognition often exhibit complex dynamics that are difficult to discern without the use of visualization tools. Current tools often provide insight only to the modeling expert, however, and they provide limited functionality for communicating model dynamics to the nonexpert, as is needed during scientific presentations and in educational settings. We present NAV, the Node Activity Visualizer, an easy-to-use and portable software tool that interactively transforms the output of cognitive modeling simulators into presentation quality animations of model performance.

Cognition↗
PubMed1990

[The definition and realization of a computerized archive for radiological data of scientific interest].

The general requirements are analyzed of a system designed to acquire and manage radiological data of scientific interest. These requirements consist in: easy implementation, to develop the system in the same environment where it is going to be used; easy use, to avoid excessive needs and resources for the system to be managed in practice; reduced implementation cost, in terms of resources required for its implementation; user-oriented approach, in the sense of meeting the radiologists' requirements, and flexibility, for the system to be an effective tool for the widest range of possible applications. Two actual applications of this general approach are then discussed, one relative to breast investigations data, and the other to digital procedures (US, CT, DSA, MR) data. For each application the software tools employed are analyzed, together with the archive structures and the used codes, the collecting data procedures and the programs. For the breast investigations archive the possibility of obtaining standard periodic reports is pointed out. These reports summarize the global department activity in this area during selected periods (six months-one year). They allow interesting clinical conclusions to be drawn. As for the digital procedures archive, the possibility is stressed of searching different combinations of scientific data out of tens of thousands of cases in just a few minutes.

Computer Systems↗
PubMed2000

Artificial neural network based identification of environmental bacteria by gas-chromatographic and electrophoretic data.

Chemotaxonomic identification techniques are powerful tools for environmental micro-organisms, for which poor diagnostic schemes are available. Whole cellular fatty acid methyl esters (FAME) content is a stable bacterial profile, the analysis method is rapid, cheap, simple to perform and highly automated. Whole-cell protein is an even more powerful tool because it yields information at or below the species level. The description of new species and genera and subsequent continuous rearrangement provide large amounts of data, resulting in large databases. In order to set up suitable software tools to work on such large databases artificial neural network (ANN) based programs have been used to classify and identify marine bacteria at genus and species levels, starting from the fatty acid profiles and protein profiles respectively. We analysed 50 certified strains belonging to Halomonas, Marinomonas, Marinospirillum, Oceanospirillum and Pseudoalteromonas genera. Both supervised and unsupervised ANNs provide a correct classification of the marine strains analyzed. Moreover, a set of 73 marine fresh isolates were used as an example of identification using ANNs. We propose supervised and unsupervised ANNs as a reliable tool for classification of bacteria by means of their FAME and of whole-protein analyses and as a sound basis for a comprehensive artificial intelligence based system for polyphasic taxonomy.

Bacteria↗
PubMed2003

SoFAR: software for fully automatic evaluation of real-time PCR data.

Quantitative real-time PCR has proven to be an extremely useful technique in life sciences for many applications. Although a lot of attention has been paid to the optimization of the assay conditions, the analysis of the data acquired is often done with software tools that do not make optimum use of the information provided by the data. Particularly, this is the case for high-throughput analysis, which requires a careful characterization and interpretation of the complete data by suitable software. Here we present a software solution for the robust, reliable, accurate, and fast evaluation of real-time PCR data, called SoFAR. The software automatically evaluates the data acquired with the LightCycler system. It applies new algorithms for an adaptive background correction of signal trends, the calculation of the effective signal noise, the automated identification of the exponential phases, the adaptive smoothing of the raw data, and the correction of melting curve data. Finally, it provides information regarding the validity of the results obtained. The SoFAR software minimizes the time required for evaluation and increases the accuracy and reliability of the results. The software is available upon request.

Algorithms↗
PubMed2006

Visual setup of logical models of signaling and regulatory networks with ProMoT.

BACKGROUND: The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networks using this formalism. Even though there is a large number of tools to set up models describing biological networks using a biochemical (kinetic) formalism, however, they do not support logical models. RESULTS: Herein we present a flexible framework for setting up large logical models in a visual manner with the software tool ProMoT. An easily extendible library, ProMoT's inherent modularity and object-oriented concept as well as adaptive visualization techniques provide a versatile environment. Both the graphical and the textual description of the logical model can be exported to different formats. CONCLUSION: New features of ProMoT facilitate an efficient set-up of large Boolean models of biochemical interaction networks. The modeling environment is flexible; it can easily be adapted to specific requirements, and new extensions can be introduced. ProMoT is freely available from http://www.mpi-magdeburg.mpg.de/projects/promot/.

Animals↗
PubMedDate not supplied

Designing a flexible user interface for both users and programmers.

The design of a user interface for computers is examined from both the end user's and the programmer's point of view. Different methods of menu selection and user feedback are discussed. A graphics interface using pull down menus and dialog boxes is ideal for simplifying user interaction and program organization. This style of interface also provides for a modular program development environment, reduced program development time, program portability, and reduced maintenance. Software tools for programming the user interface are explored and pseudo-code examples are given.

Feedback↗
PubMed2006

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

BACKGROUND: Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. RESULT: WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. CONCLUSION: This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Computer Graphics↗
PubMed2003

Modeling hospital information systems. Part 1: The revised three-layer graph-based meta model 3LGM2.

OBJECTIVES: Not only architects but also information managers need models and modeling tools for their subject of work. Especially for supporting strategic information management in hospitals, the meta model 3LGM2 is presented as an ontological basis for modeling the comprehensive information system of a hospital (HIS). METHODS: In a case study, requirements for modeling HIS have been deduced. Accordingly 3LGM2 has been designed to describe HIS by concepts on three layers. The domain layer consists of enterprise functions and entity types, the logical tool layer focuses on application components and the physical tool layer describes physical data processing components. In contrast to other approaches a lot of inter-layer-relationships exist. 3LGM2 is defined using the Unified Modeling Language (UML). RESULTS: Models of HIS can be created which comprise not only technical and semantic aspects but also computer-based and paper-based information processing. A software tool supporting the creation of 3LGM2 compliant models in a graphical way has been developed. The tool supports in detecting those shortcomings at the logical or the physical tool layers which make it impossible to satisfy the information needs at the domain layer. 3LGM2 can also be used as an ontology for describing HIS in natural language. CONCLUSIONS: Strategic information management even in large hospitals should be and can be supported by dedicated methods and tools. Although there have been good experiences with 3LGM2 concerning digital document archiving at the Leipzig University Hospital, which are presented in part 2, the benefit of the proposed method and tool has to be further evaluated.

Hospital Information Systems↗
PubMed2004

Objective evaluation of three-dimensional image registration algorithms--tools for optimization and evaluation.

OBJECTIVE: The registration of medical volume data sets plays an important role when different images or modalities are used during computer-assisted surgical procedures. Nevertheless, it is often questionable how robust and accurate the underlying algorithms really are. Therefore, the goal is to foster the establishment of methods for an objective evaluation. METHOD: To reliably calculate the accuracy of registration algorithms, a reference transformation must be known. Due to the unknown perfect registration for real clinical data, the simulation of realistic data and successive affine transformations are employed. The simulation is based on models of the respective imaging modality where the dominant physical effects are taken into account. This gives the user full control over all simulation and transformation parameters. Finally, suitable quality measures are applied which allow a systematic evaluation of image registration accuracy by comparing the known theoretical result and the transformation calculated by the algorithm under investigation. RESULTS: During the development of a new registration algorithm, the presented method proved to be a very valuable tool for optimization and evaluation of registration accuracy, since it allows objective numerical comparison of the calculated results. CONCLUSIONS: The presented method can be used during the development of algorithms for optimization and for quantitative comparison of different registration schemes. The respective software tool can automatically generate and transform simulated but realistic data. Employing suitable numerical quality measures, an objective evaluation of registration results can be easily obtained. Still, the validity of the relatively simple models has to be verified to draw reliable conclusions with respect to real data.

Algorithms↗
PubMed2004

Tools for loading MEDLINE into a local relational database.

BACKGROUND: Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. RESULTS: We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated. CONCLUSIONS: Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu.

Database Management Systems↗
PubMed2006

SNAP: Combine and Map modules for multilocus population genetic analysis.

We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) for working with DNA sequences sampled from populations. SNAP Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding insertions or deletions, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype-phenotype associations. SNAP Combine merges multiple DNA sequence alignments into a single multiple alignment file. The resulting file can be the union or intersection of the input files. SNAP Combine currently reads from and writes to several sequence alignment file formats including both sequential and interleaved formats. Combine also keeps track of the start and end positions of each separate alignment file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

Algorithms↗
PubMed1990

Computerizing medical records: software criteria for systems to document patient encounters.

It is difficult to design and build computer systems to document medical care, especially if the entries are to be made by health care professionals. Not all software approaches are equally well suited to the task. Twenty-one specific software characteristics were identified that promote efficient development and support clinical needs. Using a software tool that satisfied these characteristics, we developed a computerized medical chart system that physicians can use to write notes and document patient encounters. The success of this system was due to a good fit between the basic capabilities of the software approach and the requirements of the project. These criteria can serve as the starting point for evaluating or developing other software applications that depend on physician input of clinical information.

Documentation↗
PubMedDate not supplied

Getting the most out of your practice--the Practice Health Atlas and business modelling opportunities.

BACKGROUND: The Practice Health Atlas (PHA) is a decision support tool for general practice, designed by the Adelaide Western Division of General Practice (AWDGP). OBJECTIVE: This article describes the features of the PHA and its potential role in enhancing health care. DISCUSSION: In developing the PHA, the AWDGP utilises a range of software tools and consults with a practice to understand its clinical data management approach. The PHA comprises three sections: epidemiology, business and clinical modelling systems, access to services. The objectives include developing a professional culture around quality health data and synthesis of aggregated de-identified general practice data at both practice and divisional level (and beyond) to assist with local health needs assessment, planning, and funding. Evaluation occurs through group feedback sessions and from the general practitioners and staff. It has demonstrated its potential to fulfill the objectives in outcome areas such as data quality and management, team based care, pro-active practice population health care, and business systems development, thereby contributing to improved patient health outcomes.

Adolescent↗
PubMed1989

Computer-assisted resonance assignments.

Investigation of NMR spectra by automatic procedures began only a few years ago. Many projects are still in progress and results have not been published; completed projects, with published results, have not yet found their final form. Other approaches might be incorporated. One example is the simulation of cross-peaks. These calculations explicitly take into account spectral parameters set for data acquisition and processing. They thus allow realistic simulations of expected peak patterns. Comparison of experimentally obtained peaks with a collection of simulated peaks helps characterize the spin system and determine coupling constants, especially in strongly coupled systems. Whereas automatic assignment procedures will require improvement for quite some time, it seems that useful and time-saving software tools complementing pure computer graphics will be available in the very near future.

Algorithms↗
PubMed2002

Beyond guidelines: tool arms physicians with critical knowledge at the point of care.

Any generalist knows that it is virtually impossible to stay on top of all new developments that impact management of chronic disease. Further, the complexity involved with individual cases makes optimal care an even tougher challenge. However, a growing number of practitioners and organizations are addressing this problem by making use of a unique software tool that matches current knowledge and advice with specific patients at the point of care. Early studies show the approach can go a long way toward making sure evidence-based guidelines are followed while offering the potential for substantial cost savings.

Decision Support Systems, Clinical↗
PubMed2026

Ten quick tips for spatial transcriptomics analysis.

Spatial transcriptomics (ST) enables genome-wide gene expression profiling while retaining spatial context within tissue sections. Since the foundational work by Ståhl et al. in 2016, the field has expanded rapidly, with diverse platforms now spanning sequencing-based (e.g., Visium, Visium HD, Slide-seq, Stereo-seq, and Seq-Scope) and imaging-based (e.g., MERFISH, Xenium, and CosMx SMI) approaches. The breadth of platforms, data structures, and computational tools, however, can be daunting for newcomers. Here, we present ten quick tips spanning the entire ST research workflow: whether ST suits a given biological question, how to select a platform aligned with study objectives, how to understand and process ST data, and which software tools to employ for analysis and visualization. We further discuss interpreting spatial patterns in biological context, integrating complementary modalities such as single-cell RNA sequencing and spatial proteomics, and leveraging public datasets and sharing results. Finally, we highlight current limitations of ST, particularly the challenge of reconstructing three-dimensional tissue architecture from serial tissue sections. This review provides biologists, bioinformaticians, and clinician-scientists with a concise, platform-neutral roadmap for incorporating ST into research, from experimental design to biological discovery.

Spatial Transcriptomics↗
PubMed2006

P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.

UNLABELLED: The software tool P2BAT provides a massive parallel and user friendly implementation of the PBAT-analysis tools for family-based association tests (FBATs) in large-scale studies, including genome-wide association studies with several thousand subjects. Built on the original PBAT-implementation of the Lange-Van Steen algorithm to bypass the multiple testing problem in family-based association studies, P2BAT integrates all PBAT-analysis tools for binary and complex traits into R and makes them accessible through a user-friendly GUI. The genome-wide analysis tools are fully automated and can be ran massively parallel directly through the GUI. P2BAT is fully documented and contains graphical output tools for time-to-onset analysis. P2BAT also features the ability to test for gene and environment/drug interaction. AVAILABILITY: The P2BAT package is available as the R package 'pbatR' which can be downloaded from http://cran.r-project.org/. The PBAT-software is available at http://www.biostat.harvard.edu/~clange/.

Algorithms↗
PubMed1994

Integration of data driven decision support into the HELIOS environment.

The development of large-scale, clinically accepted decision support systems (DSS) calls for powerful and commonly available methods and tools for knowledge acquisition, system realisation, and knowledge base maintenance. The paper addresses problems associated with the integration of knowledge-based systems within the clinical setting with special reference to (i) data driven decision support, (ii) the Arden Syntax as a knowledge representation format and, (iii) the HELIOS software engineering environment. Architecture of a DSS based on Arden Syntax and its integration in the HELIOS environment are presented. Realisation of the DSS is discussed in relation to client-server architecture and object-oriented databases, which are essential concepts of the HELIOS environment. Sharability and reusability of the knowledge, together with commonality of used software tools are also discussed.

Database Management Systems↗