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.

SourceResearch connectionFrom yearThrough year

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

At least 1,603 records · Page 89Linked to original sources

PubMed1985

Using computer graphics to enhance astronaut and systems safety.

Computer graphics is being employed at the NASA Johnson Space Center as a tool to perform rapid, efficient and economical analyses for man-machine integration, flight operations development and systems engineering. The Operator Station Design System (OSDS), a computer-based facility featuring a highly flexible and versatile interactive software package, PLAID, is described. This unique evaluation tool, with its expanding data base of Space Shuttle elements, various payloads, experiments, crew equipment and man models, supports a multitude of technical evaluations, including spacecraft and workstation layout, definition of astronaut visual access, flight techniques development, cargo integration and crew training. As OSDS is being applied to the Space Shuttle, Orbiter payloads (including the European Space Agency's Spacelab) and future space vehicles and stations, astronaut and systems safety are being enhanced. Typical OSDS examples are presented. By performing physical and operational evaluations during early conceptual phases. supporting systems verification for flight readiness, and applying its capabilities to real-time mission support, the OSDS provides the wherewithal to satisfy a growing need of the current and future space programs for efficient, economical analyses.

Astronauts↗

PubMed2002

Tools for the analysis of dose optimization: I. Effect-volume histogram.

With the advent of dose optimization algorithms, predominantly for intensity-modulated radiotherapy (IMRT), computer software has progressed beyond the point of being merely a tool at the hands of an expert and has become an active, independent mediator of the dosimetric conflicts between treatment goals and risks. To understand and control the internal decision finding as well as to provide means to influence it, a tool for the analysis of the dose distribution is presented which reveals the decision-making process performed by the algorithm. The internal trade-offs between partial volumes receiving high or low doses are driven by functions which attribute a weight to each volume element. The statistics of the distribution of these weights is cast into an effect-volume histogram (EVH) in analogy to dose-volume histograms. The analysis of the EVH reveals which traits of the optimum dose distribution result from the defined objectives, and which are a random consequence of under- or misspecification of treatment goals. The EVH can further assist in the process of finding suitable objectives and balancing conflicting objectives. If biologically inspired objectives are used, the EVH shows the distribution of local dose effect relative to the prescribed level.

Algorithms↗

PubMed2025

CountASAP: a lightweight, easy to use python package for processing ASAPseq data.

BACKGROUND: Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. RESULTS: To address this lack of a dedicated tool for ASAPseq data processing, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences. We directly compare the performance and user-friendliness of CountASAP to existing tools using similarly-structured data from a more common sequencing experiment: cellular indexing of transcriptomes and epitopes by sequencing (CITEseq). Further benchmarking against existing tools helps to identify proper defaults for CountASAP and assess the agreement of outputs from all tested software. A final test using a novel ASAPseq dataset provides evidence that CountASAP can generate biologically meaningful results that correlate well with paired chromatin accessibility data. CONCLUSIONS: CountASAP shows good agreement with existing, well-tested data processing tools in the analysis of similarly-structured benchmarking data. CountASAP runs efficiently on a standard laptop, has user-friendly documentation, a one-step installation, and represents the first and only tool designed specifically for the processing of ASAPseq data.

Software↗

PubMed1994

Analysing and developing object-oriented medical applications with HELIOS.

The HELIOS project promotes systematic reuse of existing software in a valuable methodological context. In order to reach this goal, the Analysis and Design Development Environment (ADDE) has been realized as a HELIOS component. This component includes the Analysis and Design sub-component (ADT), which supports the Rumbaugh's object-oriented methodology and the Insertion Retrieval Tool (IRT), which implements the reuse. The ADT sub-component enhances the quality of software development permitting a correct analysis, and design and a satisfactory documentation. The IRT Tool is dedicated to reuse by retrieving parts of existing applications (retrieve) and by qualifying elements just created or updated (insertion). A faceted system adapted to the medical domain allows an efficient search among the object database. Both tools contribute to reducing the cost of software development. This paper presents the design and the implementation of these tools in the HELIOS framework.

Database Management Systems↗

PubMed2005

[Image guided dental implantology].

Dental implants insertion is a predictable surgical procedure with very high success rates. An optimal implants placement requires excellent surgical skills and good prosthetic perception. Performing an inaccurate implantation can lead to irreversible surgical damage on the one hand or a prosthetic failure on the other hand. Planning software provide the surgeon with good planning tool; existing navigation systems allow for translating them into performance by semi-active or passive guidance. The later allows for flexibility in the implant location during the operation and real-time tracking of drill position. All of these tools are helpful in avoiding damage to anatomical structures by performing the implantation in close relation to the CT scan. But the solutions that provide most possible advantages requires CT with special markers, long and expansive preoperative preparations and most of all a very high initial cost. These, in addition to a very long learning curve are the reason for these systems not to become a popular working tool. The most important challenges of the next generation systems in dental implants navigation are lower price, smaller size, good performance and reliability and ease of use. This kind of image guided system should allow for preplanning of implants locations, and guided insertion by minimal invasive procedure.

Computer Simulation↗

PubMed2005

Does PET/CT render software registration obsolete?

It was the success of software-based image registration that eventually led to the introduction of hardware-based concepts for image fusion, such as combined PET/CT tomographs. A prototype PET/CT was first presented in 1998, with various commercial designs to follow since 2000. PET/ CT is used primarily as a diagnostic modality in the field of extra-cerebral oncology imaging. The major advantage of combined imaging over retrospective software registration is the nearly identical position of the patient during both complementary examination, and therefore tomograms of identical parts of the body can be provided in spatially-corresponding slices. Despite the availability of hardware combinations of complementary imaging modalities software-based image registration, however, still inherits a major role in subsequent data processing, in particular when individual imaging modalities other than combined PET/CT are being used during patient workup. Furthermore, software is likely to become an important tool for the correction of residual motion-induced mis-registration within combined PET/CT data sets, and for follow-up studies involving, for example, CT, PET, and PET/CT. Therefore, flexible algorithms that utilize non-linear interpolation schemes implemented on fast computer systems are needed, and will continue to contribute to successful image registration and fusion in clinical practice.

Brain↗

PubMed1997

Computer-based surgical audit programs: a review of three current options.

BACKGROUND: In order to find the most useful computerized auditing system for the needs of the QE II Hospital surgical department three surgical auditing software programs were assessed. METHODS: The Otago University Surgical Auditing Program, the Australian Surgical Auditing Program, and RACS-Audit were trialled for a period of 1 month each. The software programs were evaluated to find the time requirements for data entry, the level of surgical knowledge needed for effective audit information entry, and the perceived usefulness of the generated reports. RESULTS: It was found that the Otago University program best suited the needs of the department. This system was designed for use in a hospital environment with multiple users. The method of data collection was simple and rapid. Entry of data into the program was logical, well structured and able to be performed by both junior medical staff and clerical staff. Reports generated by this system included information in an appropriate format for the departments' morbidity and mortality meetings. CONCLUSION: Personal computers are an ideal tool for the undertaking of surgical audit. Software programs are designed for different uses and should be critically assessed to ensure that the method of data entry, the time involved, and the reports generated enable an efficient and effective audit to be carried out.

General Surgery↗

PubMed2004

Specially adapted interactive tools for an improved 3D-segmentation of the spine.

For imaging purposes of the spine, segmented image data provides the basis for a variety of modern clinical applications. However, the anatomical complex structure of the spine as well as the extensive degenerative bony deformations apparent in the clinical situation, generally complicate the application of a fully automated segmentation. To serve the special needs for image segmentation of the spine anatomy a newly developed software system is presented, that implements specially adapted interactive tools, taking its 'axis'-skeletal structure into account. A standardized protocol combines the newly developed interactive tools (rotation transformation, warped dissection plane) with standard segmentation tools to provide both a fast and accurate segmentation procedure. The introduced software environment has been valuable for the segmentation of cervical, thoracic and lumbar spines segments based on clinical routine and research images.

Computers↗

PubMed2004

[Computer-assisted anatomical study of nasofrontal region].

OBJECTIVE: To evaluate the value of Advantage Windows 3.1 (AW 3.1) software for anatomical study of nasofrontal region, and to study the CT characteristics of nasofrontal region which related to the frontal sinus surgery. METHODS: Eighty patients underwent axial consecutive computed tomography scans and these data were studied with AW 3.1 software which provided reconstructional imaging of continuous coronal, sagittal, axial sections. Some related structures of nasofrontal region were studied and measured. RESULTS: AW 3.1 software could identify and measure the following structures accurately: The diameter of frontal sinus was (22.5 +/- 8.6) mm in height, (16.3 +/- 6.8) mm in depth, (23.8 +/- 9.8) mm in breadth. The diameter of frontal sinus ostium: the anterior-posterior diameter was (7.3 +/- 1.7) mm, the transverse diameter was (8.5 +/- 1.9) mm. The width of nasal beak of frontal bone(5.9 +/- 1.4 ) mm. The distance of frontal sinus ostium to the floor of columella nasi and the corresponding angle to the nasal floor were (60.8 +/- 4.2) mm and (70.1 +/- 4.7) degrees. The superior attachment sites of the uncinate process were as follows: lamina papyracea 41%, posteromedial wall of agger nasi cell 11%, middle turbinate 19%, anterior skull base 16%, superior bifurcation 13%. The cells could impinge on the frontal recess to cause obstruction (terminal recess 38.8%, anterior ethmoid cell 27.6%, agger nasi cells 24.5%). The accessory cells could impinge on the frontal sinus (perifrontal cells 32.7%, superaorbital cells 38.8%, intersinus septal cells 32.0%). There was significant difference between two groups of characteristics of nasofrontal region. CONCLUSIONS: AW 3.1 software is a helpful and powerful new tool for anatomical study of nasofrontal region and for preoperative evaluation. The structures of nasofrontal region are complex and various, frontal sinusitis almost always results from the obstruction of frontal sinus outflow tract. These results of anatomical study of nasofrontal region are helpful in directing the functional endoscopic surgery in frontal sinus.

Adult↗

PubMed1991

A software system for interactive and quantitative visualization of multidimensional biomedical images.

A comprehensive software system called ANALYZE has been developed which permits detailed investigation and evaluation of 3-D biomedical images. The software can be used with any 2-D or 3-D imaging modality, including x-ray computed tomography, radionuclide emission tomography, ultrasound tomography, magnetic resonance imaging and both light and electron microscopy. The package is unique in its synergistic integration of fully interactive modules for direct display, manipulation and measurement of multidimensional image data. Several original algorithms are included which improve image display efficiency and quality. One of the most versatile and powerful algorithms is interactive volume rendering, which is optimized to be fast without compromising image quality. An important advantage of this technique is to display 3-D images directly from the original data and to provide on-the-fly combinations of selected image transformations and/or volume set operations (union, intersection, difference, etc.). The inclusion of a variety of interactive editing and quantitative mensuration tools significantly extends the usefulness of the software. Any curvilinear path or region-of-interest can be manually specified and/or automatically segmented for numerical determination and statistical analyses of distances, areas, volumes, shapes, densities and textures. ANALYZE is written entirely in "C" and runs on several standard UNIX workstations. It is being used in a variety of applications by over 40 institutions around the world, and has been licensed by Mayo to several imaging companies. The software architecture permits systematic enhancements and upgrades which has fostered development of a readily expandable package. ANALYZE comprises a powerful "visualization workshop" for rapid prototyping of specific application packages, including applications to interactive surgery simulation and radiation treatment planning. ANALYZE offers the potential to accurately and reproducibly examine, from images, the structure and function of any cell, tissue, limb, organ or organ system of the body, much like a surgeon or pathologist might do in real life, but entirely non-invasively, without pain or destruction of tissue. These capabilities promise exciting new insights into the basic processes of life, and major advances in health care delivery through improved diagnosis and treatment of disease.

Computer Graphics↗

PubMed2006

High performance GRID based implementation for genomics and protein analysis.

Starting from the genomic and proteomic sequence data, a complex computational infrastructure as been established with the objective to develop a GRID based system to to automate the analysis, prediction and annotation processes of genomic DNA. To support of this type of analysis, several algorithms as been used to recognize biological signals involved in the identification of genes and proteins. The system implemented can be use to analyse the content of the large number of genomic sequences. For this reason, the system realized is capable of using a computational architecture specifically designed for intensive computing based on GRID technologies developed throughout the BIOINFOGRID European project. We developed a GRID based workflow to correlate different kind of Bioinformatics data, going from the Genomics Nucleotide to the Protein Sequence. The first step in the workflow consists of submitting a nucleotide sequence that is elaborated by a specific software for gene prediction. In particular this tool performs a search in the nucleotide sequence to find out the key components of gene. The predicted gene is then translated in the corresponding protein sequence. Based on protein sequence is then possible to identify the domains that characterize the protein functionality using specific tools of domain prediction. Protein domains classification are very important in the analysis of the macromolecular functionality. To analyze a whole protein family from large genome of various organism means to elaborate a large amount of data that requires huge computational resources. To analyze all this data we suggest the use of a high performance platform based on grid technology. We have implemented our applications on a wide area grid platform for scientific applications [http://www.grid.it and http://grid-it.cnaf.infn.it] composed of about 1000 CPU's. The grid infrastructure consists in a collection of computing elements and storage elements that jointly concur to define a platform for high performance elaboration. In this study a grid based application is presented to compute the protein domain analysis in a distributed way. This approach has high performance because the protein domains are checked with different software in parallel in different grid sites.

Computational Biology↗

PubMed2005

NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae.

BACKGROUND: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications:a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c) Pairwise sequence comparison with a range of different methods. d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments. RESULTS: Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons. DISCUSSION: This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol. AVAILABILITY: The program is freely available at http://bio.ifom-firc.it/NTFootPrinter.

Animals↗

PubMed2005

RNAshapes: an integrated RNA analysis package based on abstract shapes.

We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.

Algorithms↗

PubMed1995

PLANET: a phage library analysis expert tool.

In recent years random peptide libraries displayed on filamentous phage have been widely used and new ideas and techniques are continuously developing in the field (1-5). Notwithstanding this growing interest in the technique and in its promising results, and the enormous increase in usage and scope, very little effort has been devoted to the implementation of software able to handle and analyze the growing number of phage library-derived sequences. In our laboratory, phage libraries are extensively used and peptide sequences are continuously produced, so that the need arose of creating a database (6) to collect all the experimental results in a format compatible with GCG sequence analysis packages (7). We present here the description of an XWindow-based software package named PLANET (Phage Library ANalysis Expert Tool) devoted to the maintenance and statistical analysis of the database.

Bacteriophages↗

PubMed1995

NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

Magnetic Resonance Spectroscopy↗

PubMed1989

Linear array test tool.

A new linear array test tool is presented. It is easily used to directly measure an image acquisition parameter: the transmit/receive aperture. The aperture measurement gives important information concerning the functioning of the real-time multielement transducer and the equipment's signal-processing hardware and software. A feasibility test of the new test tool demonstrated that it can be easily used by clinical personnel to (1) determine the variation of the transmit/receive aperture with image depth; (2) document the operation of the equipment in each of the operator selectable focusing schemes; (3) perform quick checks of equipment performance when in doubt; and (4) test for and document the existence of nonfunctioning elements in linear, curved linear (convex), and phased arrays.

Acoustics↗

PubMed2005

Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC.

Comparative analysis of genomic sequences is a powerful approach to discover functional sites in these sequences. Herein, we present a WWW-based software system for multiple alignment of genomic sequences. We use the local alignment tool CHAOS to rapidly identify chains of pairwise similarities. These similarities are used as anchor points to speed up the DIALIGN multiple-alignment program. Finally, the visualization tool ABC is used for interactive graphical representation of the resulting multiple alignments. Our software is available at Göttingen Bioinformatics Compute Server (GOBICS) at http://dialign.gobics.de/chaos-dialign-submission.

Computer Graphics↗

PubMed2005

Assessing team performance in the operating room: development and use of a "black-box" recorder and other tools for the intraoperative environment.

BACKGROUND: The objective of this research was to develop a digital system to archive the complete operative environment along with the assessment tools for analysis of this data, allowing prospective studies of operative performance, intraoperative errors, team performance, and communication. Ability to study this environment will yield new insights, allowing design of systems to avoid preventable errors that contribute to perioperative complications. STUDY DESIGN: A multitrack, synchronized, digital audio-visual recording system (RATE tool) was developed to monitor intraoperative performance, including software to synchronize data and allow assignment of independent observational scores. Cases were scored for technical performance, participants' situational awareness (knowledge of critical information), and their comfort and satisfaction with the conduct of the procedure. RESULTS: Laparoscopic cholecystectomy (n = 10) was studied. Technical performance of the RATE tool was excellent. The RATE tool allowed real time, multitrack data collection of all aspects of the operative environment, while permitting digital recording of the objective assessment data in a time synchronized and annotated fashion during the procedure. The mean technical performance score was 73% +/- 28% of maximum (perfect) performance. Situational awareness varied widely among team members, with the attending surgeon typically the only team member having comprehensive knowledge of critical case information. CONCLUSIONS: The RATE tool allows prospective analysis of performance measures such as technical judgments, team performance, and communication patterns, offers the opportunity to conduct prospective intraoperative studies of human performance, and allows for postoperative discussion, review, and teaching. This study also suggests that gaps in situational awareness might be an underappreciated source of operative adverse events. Future uses of this system will aid teaching, failure or adverse event analysis, and intervention research.

Cholecystectomy, Laparoscopic↗