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software_name_mentions300 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: A package for cost and critical analysis of picture archiving and communication indicating its true yield ( CAPACITY ) . The hospital - wide use of picture archiving and communication systems ( PACS ) promises a number of advantages in the future .
These benefits will only be obtained at considerable costs , however .
In view of the rapidly developing technology the costs of hardware can be expected to decrease .
The ideas about the expected moment when the benefits will exceed the costs show wide variation .
In order to get a better view on the cost comparison between PACS and the classical film - based system and also to stimulate discussions on this topic , a software package called CAPACITY ( cost and critical analysis of picture archiving and communication indicating its true yield ) has been developed by BAZIS within the scope of its IMAGIS ( image information system ) project .
CAPACITY calculates the costs in the year of introduction for both situations , conventional and PACS , based on the consumption or use of the various resources ( e.g. film , optical disks , manpower in the archive , operators , network , workstations etc .
) needed for the production of the radiological department .
These two costs are calculated for a series of years , thus giving an indication for the moment of breakeven .
User - supplied data is interrelated and checked for plausibility against a number of expert given rules of thumb by CAPACITY ' s critique module .
The first results and experiences acquired during a pilot study using a prototype version of the package will be discussed .
The CAPACITY package is available for evaluation and trial ( only distribution costs will be charged if experiences and results are returned ) .
OUTPUT:
| 2374468.txt |
software_name_mentions301 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Quantifying the characteristics of the acetabulum and proximal femur using a
semi-automated hip morphology software programme (SHIPS).
BACKGROUND: Hip-joint shape is an important factor that affects an individual's
risk of developing osteoarthritis (OA). However, validated tools to quantify
these morphological characteristics on clinical plain radiographs are few. We
developed a Matlab-based Semi-automated HIP Software programme (SHIPS) that
measures 10 morphologic characteristics of the hip that are risk factors for OA
using a plain digitised antero-posterior pelvic radiograph. In this study we
validated the accuracy and repeatability of this freeware-tool.
METHODS: Software accuracy was assessed using a test pelvic radiograph, and by
repeated measurements of an AP-pelvic radiograph digitally recreated from pelvis
computed-tomography images reformatted to create images rotated in 2-dimensions
(2.5° increments, range -15° to +15°). Intra- and inter-observer repeatability
was assessed using pelvic radiographs from 30 subjects analysed twice using the
software by two readers, and expressed as coefficient of variation (CV).
Clinical-repeatability was assessed by measuring sequential pelvic radiographs
taken on the same day after re-positioning in 23 subjects.
RESULTS: Software accuracy was within 0.1% for linear-ratios and 0.4° for
angular-measurements. Changes in pelvic inclination and rotation of ±15° resulted
in <14% change in linear-measurement ratios and <7° change in
angular-measurements. The intra-observer CV was between 0.3 to 4.1%, and
inter-
observer CV 0.7 to 9.7% with the exception of horizontal-toit-externa
(HTE, 14.6 and 24.2% respectively). Short-term clinical-repeatability varied from
0.4 to 6.1%, with the exception of HTE (37.4%).
CONCLUSION: The software showed good accuracy and repeatability for measurement
of most hip-joint morphologic risk factors for OA apart from HTE. This tool has
particular value in studying large or
retrospective datasets where
cross-sectional imaging is not feasible or available.
OUTPUT:
| 23760748.txt |
software_name_mentions302 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: [Development of analysis software package for the two kinds of Japanese
fluoro-d-glucose-positron emission tomography guideline].
Author information:
(1)Department of Radiological Technology, Faculty of Medical Science, Kyoto
College of Medical Science.
Two kinds of Japanese guidelines for the data acquisition protocol of oncology
fluoro-D-glucose-positron emission tomography (FDG-PET)/computed tomography (CT)
scans were created by the joint task force of the Japanese Society of Nuclear
Medicine Technology (JSNMT) and the Japanese Society of Nuclear Medicine (JSNM),
and published in Kakuigaku-Gijutsu 27(5): 425-456, 2007 and 29(2): 195-235, 2009.
These guidelines aim to standardize PET image quality among facilities and
different PET/CT scanner models. The objective of this study was to develop a
personal computer-based performance measurement and image quality processor for
the two kinds of Japanese guidelines for oncology (18)F-FDG PET/CT scans. We call
this software package the "PET quality control tool" (PETquact). Microsoft
Corporation's Windows(™) is used as the operating system for PETquact, which
requires 1070×720 image resolution and includes 12 different applications. The
accuracy was examined for numerous applications of PETquact. For example, in the
sensitivity application, the system sensitivity measurement results were
equivalent when comparing two PET sinograms obtained from the PETquact and the
report. PETquact is suited for analysis of the two kinds of Japanese guideline,
and it shows excellent spec to performance measurements and image quality
analysis. PETquact can be used at any facility if the software package is
installed on a laptop computer.
OUTPUT:
| 23782777.txt |
software_name_mentions303 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: FijiWings: an open source toolkit for semiautomated morphometric analysis of
insect wings.
Development requires coordination between cell proliferation and cell growth to
pattern the proper size of tissues, organs, and whole organisms. The Drosophila
wing has landmark features, such as the location of veins patterned by cell
groups and trichome structures produced by individual cells, that are useful to
examine the genetic contributions to both tissue and cell size. Wing size and
trichome density have been measured manually, which is tedious and error prone,
and although image processing and pattern-recognition software can quantify
features in micrographs, this approach has not been applied to insect wings. Here
we present FijiWings, a set of macros designed to perform semiautomated
morphophometric analysis of a wing photomicrograph. FijiWings uses plug-ins
installed in the Fiji version of ImageJ to detect and count trichomes and measure
wing area either to calculate trichome density of a defined region selected by
the user or generate a heat map of overall trichome densities. For
high-throughput screens we have developed a macro that directs a trainable
segmentation plug-in to detect wing vein locations either to measure trichome
density in specific intervein regions or produce a heat map of relative intervein
areas. We use wing GAL4 drivers and UAS-regulated transgenes to confirm the
ability of these tools to detect changes in overall tissue growth and individual
cell size. FijiWings is freely available and will be of interest to a broad
community of fly geneticists studying both the effect of gene function on wing
patterning and the evolution of wing morphology.
OUTPUT:
| 23797110.txt |
software_name_mentions304 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Gel2DE - a software tool for correlation analysis of 2D gel electrophoresis data.
BACKGROUND: Two-dimensional gel electrophoresis (2DE) is a powerful technique for
studying protein isoforms and their modifications. Existing commercial 2D image
analysis tools rely on spot detection that limits analysis of complex protein
profiles, e.g. spot appearance/disappearance or overlapping spots. Pixel-by-pixel
correlation analysis, an analysis technique for identifying relations between
protein patterns in gel images and external variables, can overcome such
limitations in spot analysis.
RESULTS: We have implemented the first publically available pixel-by-pixel
correlation analysis tool, the software Gel2DE. 2D immunoblot time course
analysis of p53 protein stabilization in response to ionizing irradiation shows
that pixel-by-pixel analysis can yield an overall activation biosignature for
p53, despite changing spots shape, size and position.
CONCLUSIONS: Pixel-by-pixel correlation of aligned 2D images permits analysis of
complex protein patterns. We anticipate that the Gel2DE correlation software will
be a useful tool for future bioinformatics discoveries through 2D gel
electrophoresis.
OUTPUT:
| 23829206.txt |
software_name_mentions305 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: The Network Modification (NeMo) Tool: elucidating the effect of white matter
integrity changes on cortical and subcortical structural connectivity.
Accurate prediction of brain dysfunction caused by disease or injury requires the
quantification of resultant neural connectivity changes compared with the normal
state. There are many methods with which to assess anatomical changes in
structural or diffusion magnetic resonance imaging, but most overlook the
topology of white matter (WM) connections that make up the healthy brain network.
Here, a new neuroimaging software pipeline called the Network Modification (NeMo)
Tool is presented that associates alterations in WM integrity with expected
changes in neural connectivity between gray matter regions. The NeMo Tool uses a
large reference set of healthy tractograms to assess implied network changes
arising from a particular pattern of WM alteration on a region- and network-wise
level. In this way, WM integrity changes can be extrapolated to the cortices and
deep brain nuclei, enabling assessment of functional and cognitive alterations.
Unlike current techniques that assess network dysfunction, the NeMo tool does not
require tractography in pathological brains for which the algorithms may be
unreliable or diffusion data are unavailable. The versatility of the NeMo Tool is
demonstrated by applying it to data from patients with Alzheimer's disease,
fronto-temporal dementia, normal pressure hydrocephalus, and mild traumatic brain
injury. This tool fills a gap in the quantitative neuroimaging field by enabling
an investigation of morphological and functional implications of changes in
structural WM integrity.
OUTPUT:
| 23855491.txt |
software_name_mentions306 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Clinical analysis of genome next - generation sequencing data using the Omicia platform .
AIMS : Next - generation sequencing is being implemented in the clinical laboratory environment for the purposes of candidate causal variant discovery in patients affected with a variety of genetic disorders .
The successful implementation of this technology for diagnosing genetic disorders requires a rapid , user - friendly method to annotate variants and generate short lists of clinically relevant variants of interest .
This report describes Omicia ' s Opal platform , a new software tool designed for variant discovery and interpretation in a clinical laboratory environment .
The software allows clinical scientists to process , analyze , interpret and report on personal genome files .
MATERIALS & METHODS : To demonstrate the software , the authors describe the interactive use of the system for the rapid discovery of disease - causing variants using three cases .
RESULTS & CONCLUSION : Here , the authors show the features of the Opal system and their use in uncovering variants of clinical significance .
OUTPUT:
| 23895124.txt |
software_name_mentions307 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: A comparison of two commercial volumetry software programs in the analysis of
pulmonary ground-glass nodules: segmentation capability and measurement accuracy.
OBJECTIVE: To compare the segmentation capability of the 2 currently available
commercial volumetry software programs with specific segmentation algorithms for
pulmonary ground-glass nodules (GGNs) and to assess their measurement accuracy.
MATERIALS AND METHODS: In this study, 55 patients with 66 GGNs underwent
unenhanced low-dose CT. GGN segmentation was performed by using 2 volumetry
software programs (LungCARE, Siemens Healthcare; LungVCAR, GE Healthcare).
Successful nodule segmentation was assessed visually and morphologic features of
GGNs were evaluated to determine factors affecting segmentation by both types of
software. In addition, the measurement accuracy of the software programs was
investigated by using an anthropomorphic chest phantom containing simulated GGNs.
RESULTS: The successful nodule segmentation rate was significantly higher in
LungCARE (90.9%) than in LungVCAR (72.7%) (p = 0.012). Vascular attachment was a
negatively influencing morphologic feature of nodule segmentation for both
software programs. As for measurement accuracy, mean relative volume measurement
errors in nodules ≥ 10 mm were 14.89% with LungCARE and 19.96% with LungVCAR. The
mean relative attenuation measurement errors in nodules ≥ 10 mm were 3.03% with
LungCARE and 5.12% with LungVCAR.
CONCLUSION: LungCARE shows significantly higher segmentation success rates than
LungVCAR. Measurement accuracy of volume and attenuation of GGNs is acceptable in
GGNs ≥ 10 mm by both software programs.
OUTPUT:
| 23901328.txt |
software_name_mentions308 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: MeltDB 2.0-advances of the metabolomics software system.
MOTIVATION: The research area metabolomics achieved tremendous popularity and
development in the last couple of years. Owing to its unique interdisciplinarity,
it requires to combine knowledge from various scientific disciplines. Advances in
the high-throughput technology and the consequently growing quality and quantity
of data put new demands on applied analytical and computational methods.
Exploration of finally generated and analyzed datasets furthermore relies on
powerful tools for data mining and visualization.
RESULTS: To cover and keep up with these requirements, we have created MeltDB
2.0, a next-generation web application addressing storage, sharing,
standardization, integration and analysis of metabolomics experiments. New
features improve both efficiency and effectivity of the entire processing
pipeline of chromatographic raw data from pre-processing to the derivation of new
biological knowledge. First, the generation of high-quality metabolic datasets
has been vastly simplified. Second, the new statistics tool box allows to
investigate these datasets according to a wide spectrum of scientific and
explorative questions.
AVAILABILITY: The system is publicly available at
https://meltdb.cebitec.uni-bielefeld.de. A login is required but freely
available.
OUTPUT:
| 23918246.txt |
software_name_mentions309 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Inter- and intra-observer variability analysis of completely automated cIMT
measurement software (AtheroEdge™) and its benchmarking against commercial
ultrasound scanner and expert Readers.
The purpose of this study was to evaluate the measurement error and inter- and
intra-observer variability of completely off-line automated and semi-automated
carotid intima-media thickness (cIMT) measurement software (AtheroEdge™). Two
hundred carotid ultrasound images from 50 asymptomatic women were analyzed.
AtheroEdge™ was benchmarked against a commercial system (Syngo, Siemens) using
automated and semi-automated modes. The measurement error and inter- and
intra-observer variability of AtheroEdge™ were tested using three readings. The
measurement error of AtheroEdge™ compared to the commercial software was
0.002±0.019mm (r=0.99) in the automated mode and -0.001±0.004mm in the
semi-automated mode (r=0.99). The measurement error of AtheroEdge™ compared to
the mean value of the three expert Readers (cIMT bias) for the automated and
semi-automated methods was -0.0004±0.158mm and -0.008±0.157mm, respectively. The
Figure-of-Merit was 99.8% and 99.9% when compared to the commercial ultrasound
scanner (using the automated and semi-automated method, respectively) and was
99.9% and 98.9% when compared to the mean value of the three expert Readers.
Regarding inter- and intra-observer variability, the intra-class correlation
coefficient of the three independent users using the semi-automated AtheroEdge™
was 0.98. AtheroEdge™ showed a measurement performance comparable to the
commercial ultrasound scanner software and the expert Readers' tracings.
AtheroEdge™ belongs to a class of automated systems that could find application
in processing large datasets for common carotid arteries, avoiding subjectivity
in cIMT measurements.
Copyright © 2013 Elsevier Ltd. All rights reserved.
OUTPUT:
| 23930821.txt |
software_name_mentions310 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Data Processing System (DPS) software with experimental design, statistical
analysis and data mining developed for use in entomological research.
A comprehensive but simple-to-use software package called DPS (Data Processing
System) has been developed to execute a range of standard numerical analyses and
operations used in experimental design, statistics and data mining. This program
runs on standard Windows computers. Many of the functions are specific to
entomological and other biological research and are not found in standard
statistical software. This paper presents applications of DPS to experimental
design, statistical analysis and data mining in entomology.
© 2012 The Authors Insect Science © 2012 Institute of Zoology, Chinese Academy of
Sciences.
OUTPUT:
| 23955865.txt |
software_name_mentions311 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Metadata - based generation and management of knowledgebases from molecular biological databases .
Present - day knowledge - based systems ( or expert systems ) and databases constitute ' islands of computing ' with little or no connection to each other .
The use of software to provide a communication channel between the two , and to integrate their separate functions , is particularly attractive in certain data - rich domains where there are already pre - existing database systems containing the data required by the relevant knowledge - based system .
Our evolving program , GENPRO , provides such a communication channel .
The original methodology has been extended to provide interactive Prolog clause input with syntactic and semantic verification .
This enables automatic generation of clauses from the source database , together with complete management of subsequent interfacing to the specified knowledge - based system .
The particular data - rich domain used in this paper is protein structure , where processes which require reasoning ( modelled by knowledge - based systems ) , such as the inference of protein topology , protein model - building and protein structure prediction , often require large amounts of raw data ( i.e. , facts about particular proteins ) in the form of logic programming ground clauses .
These are generated in the proper format by use of the concept of metadata .
OUTPUT:
| 2397635.txt |
software_name_mentions312 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: A Visual Basic simulation software tool for performance analysis of a
membrane-based advanced water treatment plant.
Erratum in
Environ Sci Pollut Res Int. 2017 May 25;:.
A Visual Basic simulation software (WATTPPA) has been developed to analyse the
performance of an advanced wastewater treatment plant. This user-friendly and
menu-driven software is based on the dynamic mathematical model for an industrial
wastewater treatment scheme that integrates chemical, biological and
membrane-based unit operations. The software-predicted results corroborate very
well with the experimental findings as indicated in the overall correlation
coefficient of the order of 0.99. The software permits pre-analysis and
manipulation of input data, helps in optimization and exhibits performance of an
integrated plant visually on a graphical platform. It allows quick performance
analysis of the whole system as well as the individual units. The software first
of its kind in its domain and in the well-known Microsoft Excel environment is
likely to be very useful in successful design, optimization and operation of an
advanced hybrid treatment plant for hazardous wastewater.
OUTPUT:
| 23982824.txt |
software_name_mentions313 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: P-TRAP: a Panicle TRAit Phenotyping tool.
BACKGROUND: In crops, inflorescence complexity and the shape and size of the seed
are among the most important characters that influence yield. For example, rice
panicles vary considerably in the number and order of branches, elongation of the
axis, and the shape and size of the seed. Manual low-throughput phenotyping
methods are time consuming, and the results are unreliable. However,
high-throughput image analysis of the qualitative and quantitative traits of rice
panicles is essential for understanding the diversity of the panicle as well as
for breeding programs.
RESULTS: This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free
open source application for high-throughput measurements of panicle architecture
and seed-related traits. The software is written in Java and can be used with
different platforms (the user-friendly Graphical User Interface (GUI) uses
Netbeans Platform 7.3). The application offers three main tools: a tool for the
analysis of panicle structure, a spikelet/grain counting tool, and a tool for the
analysis of seed shape. The three tools can be used independently or
simultaneously for analysis of the same image. Results are then reported in the
Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats.
Images of rice panicles were used to evaluate the efficiency and robustness of
the software. Compared to data obtained by manual processing, P-TRAP produced
reliable results in a much shorter time. In addition, manual processing is not
repeatable because dry panicles are vulnerable to damage. The software is very
useful, practical and collects much more data than human operators.
CONCLUSIONS: P-TRAP is a new open source software that automatically recognizes
the structure of a panicle and the seeds on the panicle in numeric images. The
software processes and quantifies several traits related to panicle structure,
detects and counts the grains, and measures their shape parameters. In short,
P-TRAP offers both efficient results and a user-friendly environment for
experiments. The experimental results showed very good accuracy compared to field
operator, expert verification and well-known academic methods.
OUTPUT:
| 23987653.txt |
software_name_mentions314 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Rapid parameterization of small molecules using the Force Field Toolkit.
The inability to rapidly generate accurate and robust parameters for novel
chemical matter continues to severely limit the application of molecular dynamics
simulations to many biological systems of interest, especially in fields such as
drug discovery. Although the release of generalized versions of common classical
force fields, for example, General Amber Force Field and CHARMM General Force
Field, have posited guidelines for parameterization of small molecules, many
technical challenges remain that have hampered their wide-scale extension. The
Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand
parameterization through algorithm and method development, automation of tedious
and error-prone tasks, and graphical user interface design. Distributed as a VMD
plugin, ffTK facilitates the traversal of a clear and organized workflow
resulting in a complete set of CHARMM-compatible parameters. A variety of tools
are provided to generate quantum mechanical target data, setup multidimensional
optimization routines, and analyze parameter performance. Parameters developed
for a small test set of molecules using ffTK were comparable to existing CGenFF
parameters in their ability to reproduce experimentally measured values for
pure-solvent properties (<15% error from experiment) and free energy of solvation
(±0.5 kcal/mol from experiment).
Copyright © 2013 Wiley Periodicals, Inc.
OUTPUT:
| 24000174.txt |
software_name_mentions315 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: An online model composition tool for system biology models.
BACKGROUND: There are multiple representation formats for Systems Biology
computational models, and the Systems Biology Markup Language (SBML) is one of
the most widely used. SBML is used to capture, store, and distribute
computational models by Systems Biology data sources (e.g., the BioModels
Database) and researchers. Therefore, there is a need for all-in-one web-based
solutions that support advance SBML functionalities such as uploading, editing,
composing, visualizing, simulating, querying, and browsing computational models.
RESULTS: We present the design and implementation of the Model Composition Tool
(Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The
tool helps users compose systems biology models to facilitate the complex process
of merging systems biology models. We also present three tools that support the
model composition tool, namely, (1) Model Simulation Interface that generates a
visual plot of the simulation according to user's input, (2) iModel Tool as a
platform for users to upload their own models to compose, and (3) SimCom Tool
that provides a side by side comparison of models being composed in the same
pathway. Finally, we provide a web site that hosts BioModels Database models and
a separate web site that hosts SBML Test Suite models.
CONCLUSIONS: Model composition tool (and the other three tools) can be used with
little or no knowledge of the SBML document structure. For this reason, students
or anyone who wants to learn about systems biology will benefit from the
described functionalities. SBML Test Suite models will be a nice starting point
for beginners. And, for more advanced purposes, users will able to access and
employ models of the BioModels Database as well.
OUTPUT:
| 24006914.txt |
software_name_mentions316 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
With the rapid and steady increase of next generation sequencing data output, the
mapping of short reads has become a major data analysis bottleneck. On a single
computer, it can take several days to map the vast quantity of reads produced
from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we
present a new tool, DistMap - a modular, scalable and integrated workflow to map
reads in the Hadoop distributed computing framework. DistMap is easy to use,
currently supports nine different short read mapping tools and can be run on all
Unix-based operating systems. It accepts reads in FASTQ format as input and
provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and
single-end reads thereby allowing the mapping of read data produced by different
sequencing platforms. DistMap is available from http://code.google.com/p/distmap/
OUTPUT:
| 24009693.txt |
software_name_mentions317 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: BaCoCa--a heuristic software tool for the parallel assessment of sequence biases
in hundreds of gene and taxon partitions.
BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines
multiple statistical approaches (like RCFV and C value calculations) to identify
biases in aligned sequence data which potentially mislead phylogenetic
reconstructions. As a result of its speed and flexibility, the program provides
the possibility to analyze hundreds of pre-defined gene partitions and taxon
subsets in one single process run. BaCoCa is command-line driven and can be
easily integrated into automatic process pipelines of phylogenomic studies.
Moreover, given the tab-delimited output style the results can be easily used for
further analyses in programs like Excel or statistical packages like R. A
built-in option of BaCoCa is the generation of heat maps with hierarchical
clustering of certain results using R. As input files BaCoCa can handle FASTA and
relaxed PHYLIP, which are commonly used in phylogenomic pipelines. BaCoCa is
implemented in Perl and works on Windows PCs, Macs and Linux operating systems.
The executable source code as well as example test files and a detailed
documentation of BaCoCa are freely available at http://software.zfmk.de.
Copyright © 2013 Elsevier Inc. All rights reserved.
OUTPUT:
| 24076250.txt |
software_name_mentions318 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: ReportingTools: an automated result processing and presentation toolkit for
high-throughput genomic analyses.
It is common for computational analyses to generate large amounts of complex data
that are difficult to process and share with collaborators. Standard methods are
needed to transform such data into a more useful and intuitive format. We present
ReportingTools, a Bioconductor package, that automatically recognizes and
transforms the output of many common Bioconductor packages into rich,
interactive, HTML-based reports. Reports are not generic, but have been
individually designed to reflect content specific to the result type detected.
Tabular output included in reports is sortable, filterable and searchable and
contains context-relevant hyperlinks to external databases. Additionally, in-line
graphics have been developed for specific analysis types and are embedded by
default within table rows, providing a useful visual summary of underlying raw
data. ReportingTools is highly flexible and reports can be easily customized for
specific applications using the well-defined API.AVAILABILITY: The ReportingTools
package is implemented in R and available from Bioconductor (version ≥ 2.11) at
the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html.
Installation instructions and usage documentation can also be found at the above
URL.
OUTPUT:
| 24078713.txt |
software_name_mentions319 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Design and initial evaluation of a treatment planning software system for
MRI-guided laser ablation in the brain.
PURPOSE: An open-source software system for planning magnetic resonance
(MR)-guided laser-induced thermal therapy (MRgLITT) in brain is presented. The
system was designed to provide a streamlined and operator-friendly graphical user
interface (GUI) for simulating and visualizing potential outcomes of various
treatment scenarios to aid in decisions on treatment approach or feasibility.
METHODS: A portable software module was developed on the 3D Slicer platform, an
open-source medical imaging and visualization framework. The module introduces an
interactive GUI for investigating different laser positions and power settings as
well as the influence of patient-specific tissue properties for quickly creating
and evaluating custom treatment options. It also provides a common treatment
planning interface for use by both open-source and commercial finite element
solvers. In this study, an open-source finite element solver for Pennes' bioheat
equation is interfaced to the module to provide rapid 3D estimates of the
steady-state temperature distribution and potential tissue damage in the presence
of patient-specific tissue boundary conditions identified on segmented MR images.
RESULTS: The total time to initialize and simulate an MRgLITT procedure using the
GUI was [Formula: see text]5 min. Each independent simulation took [Formula: see
text]30 s, including the time to visualize the results fused with the planning
MRI. For demonstration purposes, a simulated steady-state isotherm contour
[Formula: see text] was correlated with MR temperature imaging (N = 5). The mean
Hausdorff distance between simulated and actual contours was 2.0 mm [Formula: see
text], whereas the mean Dice similarity coefficient was 0.93 [Formula: see text].
CONCLUSIONS: We have designed, implemented, and conducted initial feasibility
evaluations of a software tool for intuitive and rapid planning of MRgLITT in
brain. The retrospective in vivo dataset presented herein illustrates the
feasibility and potential of incorporating fast, image-based bioheat predictions
into an interactive virtual planning environment for such procedures.
OUTPUT:
| 24091853.txt |
software_name_mentions320 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Automated image mosaics by non-automated light microscopes: the MicroMos software
tool.
Light widefield microscopes and digital imaging are the basis for most of the
analyses performed in every biological laboratory. In particular, the
microscope's user is typically interested in acquiring high-detailed images for
analysing observed cells and tissues, meanwhile being representative of a wide
area to have reliable statistics. The microscopist has to choose between higher
magnification factor and extension of the observed area, due to the finite size
of the camera's field of view. To overcome the need of arrangement, mosaicing
techniques have been developed in the past decades for increasing the camera's
field of view by stitching together more images. Nevertheless, these approaches
typically work in batch mode and rely on motorized microscopes. Or alternatively,
the methods are conceived just to provide visually pleasant mosaics not suitable
for quantitative analyses. This work presents a tool for building mosaics of
images acquired with nonautomated light microscopes. The method proposed is based
on visual information only and the mosaics are built by incrementally stitching
couples of images, making the approach available also for online applications.
Seams in the stitching regions as well as tonal inhomogeneities are corrected by
compensating the vignetting effect. In the experiments performed, we tested
different registration approaches, confirming that the translation model is not
always the best, despite the fact that the motion of the sample holder of the
microscope is apparently translational and typically considered as such. The
method's implementation is freely distributed as an open source tool called
MicroMos. Its usability makes building mosaics of microscope images at subpixel
accuracy easier. Furthermore, optional parameters for building mosaics according
to different strategies make MicroMos an easy and reliable tool to compare
different registration approaches, warping models and tonal corrections.
© 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.
OUTPUT:
| 24111790.txt |
software_name_mentions321 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Process evaluation of software using the international classification of external
causes of injuries for collecting burn injury data at burn centers in the United
States.
Detailed information on the cause of burns is necessary to construct effective
prevention programs. The International Classification of External Causes of
Injury (ICECI) is a data collection tool that allows comprehensive categorization
of multiple facets of injury events. The objective of this study was to conduct a
process evaluation of software designed to improve the ease of use of the ICECI
so as to identify key additional variables useful for understanding the
occurrence of burn injuries, and compare this software with existing
data-collection practices conducted for burn injuries. The authors completed a
process evaluation of the implementation and ease of use of the software in six
U.S. burn centers. They also collected preliminary burn injury data and compared
them with existing variables reported to the American Burn Association's National
Burn Repository (NBR). The authors accomplished their goals of 1) creating a
data-collection tool for the ICECI, which can be linked to existing operational
programs of the NBR, 2) training registrars in the use of this tool, 3)
establishing quality-control mechanisms for ensuring accuracy and reliability, 4)
incorporating ICECI data entry into the weekly routine of the burn registrar, and
5) demonstrating the quality differences between data collected using this tool
and the NBR. Using this or similar tools with the ICECI structure or key selected
variables can improve the quantity and quality of data on burn injuries in the
United States and elsewhere and thus can be more useful in informing prevention
strategies.
OUTPUT:
| 24126473.txt |
software_name_mentions322 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: ATHENA: the analysis tool for heritable and environmental network associations.
MOTIVATION: Advancements in high-throughput technology have allowed researchers
to examine the genetic etiology of complex human traits in a robust fashion.
Although genome-wide association studies have identified many novel variants
associated with hundreds of traits, a large proportion of the estimated trait
heritability remains unexplained. One hypothesis is that the commonly used
statistical techniques and study designs are not robust to the complex etiology
that may underlie these human traits. This etiology could include non-linear gene
× gene or gene × environment interactions. Additionally, other levels of
biological regulation may play a large role in trait variability.
RESULTS: To address the need for computational tools that can explore enormous
datasets to detect complex susceptibility models, we have developed a software
package called the Analysis Tool for Heritable and Environmental Network
Associations (ATHENA). ATHENA combines various variable filtering methods with
machine learning techniques to analyze high-throughput categorical (i.e. single
nucleotide polymorphisms) and quantitative (i.e. gene expression levels)
predictor variables to generate multivariable models that predict either a
categorical (i.e. disease status) or quantitative (i.e. cholesterol levels)
outcomes. The goal of this article is to demonstrate the utility of ATHENA using
simulated and biological datasets that consist of both single nucleotide
polymorphisms and gene expression variables to identify complex prediction
models. Importantly, this method is flexible and can be expanded to include other
types of high-throughput data (i.e. RNA-seq data and biomarker measurements).
AVAILABILITY: ATHENA is freely available for download. The software, user manual
and tutorial can be downloaded from
http://ritchielab.psu.edu/ritchielab/software.
OUTPUT:
| 24149050.txt |
software_name_mentions323 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Developing software to "track and catch" missed follow-up of abnormal test
results in a complex sociotechnical environment.
BACKGROUND: Abnormal test results do not always receive timely follow-up, even
when providers are notified through electronic health record (EHR)-based alerts.
High workload, alert fatigue, and other demands on attention disrupt a provider's
prospective memory for tasks required to initiate follow-up. Thus, EHR-based
tracking and reminding functionalities are needed to improve follow-up.
OBJECTIVES: The purpose of this study was to develop a decision-support software
prototype enabling individual and system-wide tracking of abnormal test result
alerts lacking follow-up, and to conduct formative evaluations, including
usability testing.
METHODS: We developed a working prototype software system, the Alert Watch And
Response Engine (AWARE), to detect abnormal test result alerts lacking documented
follow-up, and to present context-specific reminders to providers. Development
and testing took place within the VA's EHR and focused on four cancer-related
abnormal test results. Design concepts emphasized mitigating the effects of high
workload and alert fatigue while being minimally intrusive. We conducted a
multifaceted formative evaluation of the software, addressing fit within the
larger socio-technical system. Evaluations included usability testing with the
prototype and interview questions about organizational and workflow factors.
Participants included 23 physicians, 9 clinical information technology
specialists, and 8 quality/safety managers.
RESULTS: Evaluation results indicated that our software prototype fit within the
technical environment and clinical workflow, and physicians were able to use it
successfully. Quality/safety managers reported that the tool would be useful in
future quality assurance activities to detect patients who lack documented
follow-up. Additionally, we successfully installed the software on the local
facility's "test" EHR system, thus demonstrating technical compatibility.
CONCLUSION: To address the factors involved in missed test results, we developed
a software prototype to account for technical, usability, organizational, and
workflow needs. Our evaluation has shown the feasibility of the prototype as a
means of facilitating better follow-up for cancer-related abnormal test results.
OUTPUT:
| 24155789.txt |
software_name_mentions324 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Tripal v1.1: a standards-based toolkit for construction of online genetic and
genomic databases.
Tripal is an open-source freely available toolkit for construction of online
genomic and genetic databases. It aims to facilitate development of
community-driven biological websites by integrating the GMOD Chado database
schema with Drupal, a popular website creation and content management software.
Tripal provides a suite of tools for interaction with a Chado database and
display of content therein. The tools are designed to be generic to support the
various ways in which data may be stored in Chado. Previous releases of Tripal
have supported organisms, genomic libraries, biological stocks, stock collections
and genomic features, their alignments and annotations. Also, Tripal and its
extension modules provided loaders for commonly used file formats such as FASTA,
GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic
templates were provided for common views of biological data, which could be
customized using an open Application Programming Interface to change the way data
are displayed. Here, we report additional tools and functionality that are part
of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site
curator to import data stored in a custom tab delimited format; (ii) full support
of every Chado table for Drupal Views (a powerful tool allowing site developers
to construct novel displays and search pages); (iii) new modules including
'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural
Diversity' modules. Tutorials, mailing lists, download and set-up instructions,
extension modules and other documentation can be found at the Tripal website
located at http://tripal.info. DATABASE URL: http://tripal.info/.
OUTPUT:
| 24163125.txt |
software_name_mentions325 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: ConfocalCheck--a software tool for the automated monitoring of confocal
microscope performance.
Laser scanning confocal microscopy has become an invaluable tool in biomedical
research but regular quality testing is vital to maintain the system's
performance for diagnostic and research purposes. Although many methods have been
devised over the years to characterise specific aspects of a confocal microscope
like measuring the optical point spread function or the field illumination, only
very few analysis tools are available. Our aim was to develop a comprehensive
quality assurance framework ranging from image acquisition to automated analysis
and documentation. We created standardised test data to assess the performance of
the lasers, the objective lenses and other key components required for optimum
confocal operation. The ConfocalCheck software presented here analyses the data
fully automatically. It creates numerous visual outputs indicating potential
issues requiring further investigation. By storing results in a web browser
compatible file format the software greatly simplifies record keeping allowing
the operator to quickly compare old and new data and to spot developing trends.
We demonstrate that the systematic monitoring of confocal performance is
essential in a core facility environment and how the quantitative measurements
obtained can be used for the detailed characterisation of system components as
well as for comparisons across multiple instruments.
OUTPUT:
| 24224017.txt |
software_name_mentions326 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: HCI∧2 framework: a software framework for multimodal human-computer interaction
systems.
This paper presents a novel software framework for the development and research
in the area of multimodal human-computer interface (MHCI) systems. The proposed
software framework, which is called the HCI∧2 Framework, is built upon
publish/subscribe (P/S) architecture. It implements a shared-memory-based data
transport protocol for message delivery and a TCP-based system management
protocol. The latter ensures that the integrity of system structure is maintained
at runtime. With the inclusion of bridging modules, the HCI∧2 Framework is
interoperable with other software frameworks including Psyclone and ActiveMQ. In
addition to the core communication middleware, we also present the integrated
development environment (IDE) of the HCI∧2 Framework. It provides a complete
graphical environment to support every step in a typical MHCI system development
process, including module development, debugging, packaging, and management, as
well as the whole system management and testing. The quantitative evaluation
indicates that our framework outperforms other similar tools in terms of average
message latency and maximum data throughput under a typical single PC scenario.
To demonstrate HCI∧2 Framework's capabilities in integrating heterogeneous
modules, we present several example modules working with a variety of hardware
and software. We also present an example of a full system developed using the
proposed HCI∧2 Framework, which is called the CamGame system and represents a
computer game based on hand-held marker(s) and low-cost camera(s).
OUTPUT:
| 24235258.txt |
software_name_mentions327 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: ASSIST: a fast versatile local structural comparison tool.
MOTIVATION: Structural genomics initiatives are increasingly leading to the
determination of the 3D structure of target proteins whose catalytic function is
not known. The aim of this work was that of developing a novel versatile tool for
searching structural similarity, which allows to predict the catalytic function,
if any, of these proteins.
RESULTS: The algorithm implemented by the tool is based on local structural
comparison to find the largest subset of similar residues between an input
protein and known functional sites. The method uses a geometric hashing approach
where information related to residue pairs from the input structures is stored in
a hash table and then is quickly retrieved during the comparison step. Tests on
proteins belonging to different functional classes, done using the Catalytic Site
Atlas entries as targets, indicate that the algorithm is able to identify the
correct functional class of the input protein in the vast majority of the cases.
AVAILABILITY AND IMPLEMENTATION: The application was developed in Java SE 6, with
a Java Swing Graphic User Interface (GUI). The system can be run locally on any
operating system (OS) equipped with a suitable Java Virtual Machine, and is
available at the following URL:
http://www.computationalbiology.it/software/ASSISTv1.zip.
OUTPUT:
| 24243934.txt |
software_name_mentions328 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: RaTrav: a tool for calculating mean first-passage times on biochemical networks.
BACKGROUND: The concept of mean first-passage times (MFPTs) occupies an important
place in the theory of stochastic processes, with the methods of their
calculation being equally important in theoretical physics, chemistry and
biology. We present here a software tool designed to support computational
biology studies where Markovian dynamics takes place and MFPTs between initial
and single or multiple final states in network-like systems are used. Two methods
are made available for which their efficiency is strongly dependent on the
topology of the defined network: the combinatorial Hill technique and the Monte
Carlo simulation method.
RESULTS: After a brief introduction to RaTrav, we highlight the utility of MFPT
calculations by providing two examples (accompanied by Additional file 1) where
they are deemed to be of importance: analysis of a protein-protein docking funnel
and interpretation of the free energy transduction between two coupled enzymatic
reactions controlled by the dynamics of transition between enzyme conformational
states.
CONCLUSIONS: RaTrav is a versatile and easy to use software tool for calculating
MFPTs across biochemical networks. The user simply prepares a text file with the
structure of a given network, along with some additional basic parameters such as
transition probabilities, waiting probabilities (if any) and local times (weights
of edges), which define explicitly the stochastic dynamics on the network. The
RaTrav tool can then be applied in order to compute desired MFPTs. For the
provided examples, we were able to find the favourable binding path within a
protein-protein docking funnel and to calculate the degree of coupling for two
chemical reactions catalysed simultaneously by the same protein enzyme. However,
the list of possible applications is much wider.
OUTPUT:
| 24261882.txt |
software_name_mentions329 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins.
BACKGROUND: Disulfide engineering is an important biotechnological tool that has
advanced a wide range of research. The introduction of novel disulfide bonds into
proteins has been used extensively to improve protein stability, modify
functional characteristics, and to assist in the study of protein dynamics.
Successful use of this technology is greatly enhanced by software that can
predict pairs of residues that will likely form a disulfide bond if mutated to
cysteines.
RESULTS: We had previously developed and distributed software for this purpose:
Disulfide by Design (DbD). The original DbD program has been widely used;
however, it has a number of limitations including a Windows platform dependency.
Here, we introduce Disulfide by Design 2.0 (DbD2), a web-based,
platform-independent application that significantly extends functionality,
visualization, and analysis capabilities beyond the original program. Among the
enhancements to the software is the ability to analyze the B-factor of protein
regions involved in predicted disulfide bonds. Importantly, this feature
facilitates the identification of potential disulfides that are not only likely
to form but are also expected to provide improved thermal stability to the
protein.
CONCLUSIONS: DbD2 provides platform-independent access and significantly extends
the original functionality of DbD. A web server hosting DbD2 is provided at
http://cptweb.cpt.wayne.edu/DbD2/.
OUTPUT:
| 24289175.txt |
software_name_mentions330 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: ISRNA: an integrative online toolkit for short reads from high-throughput
sequencing data.
Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing
high-throughput small RNA sequencing data. Besides the high-speed genome mapping
function, ISRNA provides statistics for genomic location, length distribution and
nucleotide composition bias analysis of sequence reads. Number of reads mapped to
known microRNAs and other classes of short non-coding RNAs, coverage of short
reads on genes, expression abundance of sequence reads as well as some other
analysis functions are also supported. The versatile search functions enable
users to select sequence reads according to their sub-sequences, expression
abundance, genomic location, relationship to genes, etc. A specialized genome
browser is integrated to visualize the genomic distribution of short reads. ISRNA
also supports management and comparison among multiple datasets.AVAILABILITY:
ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at
http://omicslab.genetics.ac.cn/ISRNA/.
OUTPUT:
| 24300438.txt |
software_name_mentions331 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: ITEP: an integrated toolkit for exploration of microbial pan-genomes.
BACKGROUND: Comparative genomics is a powerful approach for studying variation in
physiological traits as well as the evolution and ecology of microorganisms.
Recent technological advances have enabled sequencing large numbers of related
genomes in a single project, requiring computational tools for their integrated
analysis. In particular, accurate annotations and identification of gene presence
and absence are critical for understanding and modeling the cellular physiology
of newly sequenced genomes. Although many tools are available to compare the gene
contents of related genomes, new tools are necessary to enable close examination
and curation of protein families from large numbers of closely related organisms,
to integrate curation with the analysis of gain and loss, and to generate
metabolic networks linking the annotations to observed phenotypes.
RESULTS: We have developed ITEP, an Integrated Toolkit for Exploration of
microbial Pan-genomes, to curate protein families, compute similarities to
externally-defined domains, analyze gene gain and loss, and generate draft
metabolic networks from one or more curated reference network reconstructions in
groups of related microbial species among which the combination of core and
variable genes constitute the their "pan-genomes". The ITEP toolkit consists of:
(1) a series of modular command-line scripts for identification, comparison,
curation, and analysis of protein families and their distribution across many
genomes; (2) a set of Python libraries for programmatic access to the same data;
and (3) pre-packaged scripts to perform common analysis workflows on a collection
of genomes. ITEP's capabilities include de novo protein family prediction,
ortholog detection, analysis of functional domains, identification of core and
variable genes and gene regions, sequence alignments and tree generation,
annotation curation, and the integration of cross-genome analysis and metabolic
networks for study of metabolic network evolution.
CONCLUSIONS: ITEP is a powerful, flexible toolkit for generation and curation of
protein families. ITEP's modular design allows for straightforward extension as
analysis methods and tools evolve. By integrating comparative genomics with the
development of draft metabolic networks, ITEP harnesses the power of comparative
genomics to build confidence in links between genotype and phenotype and helps
disambiguate gene annotations when they are evaluated in both evolutionary and
metabolic network contexts.
OUTPUT:
| 24387194.txt |
software_name_mentions332 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Microarray Inspector: tissue cross contamination detection tool for microarray
data.
Microarray technology changed the landscape of contemporary life sciences by
providing vast amounts of expression data. Researchers are building up
repositories of experiment results with various conditions and samples which
serve the scientific community as a precious resource. Ensuring that the sample
is of high quality is of utmost importance to this effort. The task is
complicated by the fact that in many cases datasets lack information concerning
pre-experimental quality assessment. Transcription profiling of tissue samples
may be invalidated by an error caused by heterogeneity of the material. The risk
of tissue cross contamination is especially high in oncological studies, where it
is often difficult to extract the sample. Therefore, there is a need of
developing a method detecting tissue contamination in a post-experimental phase.
We propose Microarray Inspector: customizable, user-friendly software that
enables easy detection of samples containing mixed tissue types. The advantage of
the tool is that it uses raw expression data files and analyses each array
independently. In addition, the system allows the user to adjust the criteria of
the analysis to conform to individual needs and research requirements. The final
output of the program contains comfortable to read reports about tissue
contamination assessment with detailed information about the test parameters and
results. Microarray Inspector provides a list of contaminant biomarkers needed in
the analysis of adipose tissue contamination. Using real data (datasets from
public repositories) and our tool, we confirmed high specificity of the software
in detecting contamination. The results indicated the presence of adipose tissue
admixture in a range from approximately 4% to 13% in several tested surgical
samples.
OUTPUT:
| 24432313.txt |
software_name_mentions333 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Microcomputer collection and analysis of RR - interval data in the BB - rat .
An analog to digital converter and microcomputer system for the collection of real - time RR - interval data in the BB - rat is described .
Calculation of the statistic R is discussed and a commented program listing in Microsoft basic , for performing this transformation , is included as an appendix .
OUTPUT:
| 2625042.txt |
software_name_mentions334 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: GENCOV : a Fortran program that generates randomly censored survival data with covariates .
We present a Fortran program for simulating censored survival data with covariates under the assumption of random censoring .
The program generates times distributed according to the uniform distribution , the generalized Gamma distribution , the log - normal distribution and Pettitt ' s generalized logistic distribution with Box - Cox transformation of the time variable .
Covariates can be introduced in the definition of the survival time , resulting in the generalized log - gamma , log - normal and Pettitt ' s regression models .
Thereby the program provides the means for generating censored survival data according to parametric versions of three common regression models for censored survival data : the Accelerated Failure Time , the Proportional Hazards and the Proportional Odds models .
OUTPUT:
| 2714079.txt |
software_name_mentions335 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Simplifying record linkage : software and strategy .
Although the methodology of record linkage is fairly well developed , there is a need for less expensive methods and simpler software to facilitate trying out different tactics to generate good linkages .
The present work has built on a fourth generation language SAS ( Statistical Analysis System ) with accompanying macroprocessor , to develop a user - friendly and flexible system for both exact and probabilistic matching .
The major features of the LINKS system are presented and illustrated using 1979 - 1984 information from the Manitoba Health Services Commission ( MHSC ) registry file with the Canadian Mortality Data Base .
Initial runs with exact , then probabilistic , matching linked approximately 91 % of the Vital Statistics records to corresponding MHSC records .
Subsequent modification of parameters improved the linkage to 95 % .
OUTPUT:
| 3665453.txt |
software_name_mentions336 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: DATAC : a multipurpose biological data analysis program based on a mathematical interpreter .
The use of a mathematical command interpreter combined with the structural facility of the C - language allowed us to design a data treatment program having considerable flexibility and being able to handle any types of data ( electrophysiological , biochemical and theoretical data ) . Ensembles of data are treated by the interpreter as if they were simple variables so that an elaborate computation can be performed on the spot by simply writing the appropriate equation on the terminal .
These facilities combined with the ability of editing macrocommands at run time provide the user with data treatment possibilities that extend far beyond the possibilities actually implemented in the program .
The originality of this program is that the user can easily implement the commands he most often needs , writing them in a language that most scientists will know , algebra .
OUTPUT:
| 3755121.txt |
software_name_mentions337 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Automated data acquisition and analysis of neural evoked potentials .
A software system to collect , analyze and store trains of neural evoked potentials is presented .
Real - time waveform capture permits sampling of a variable - duration data window of 6 to 399.6 ms with a sample delay accurately adjustable up to 1 001 ms ( 20 microseconds resolution ) . The digitized representation of each waveform is stored for individual analysis .
Off - line processing determines 17 parameters of each waveform , including an arrow - selected amplitude and time .
Individual processing of waveforms preserves all degrees of freedom for statistical analysis across waveforms .
Ensemble averages may optionally be formed from the individual waveforms with processing performed on the averaged responses .
The software provides MENU - selectable support functions including stimulus - to - artifact timing , storage and retrieval of data and calculated parameters , digital display of waveforms , data calibration and gain modification , table referenced data editing , file management , simple statistics , hardcopy output , and optional database interfacing with output formatted for compatibility with a statistics package ( SAS ) .
OUTPUT:
| 3849376.txt |
software_name_mentions338 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: PLASMAP : an interactive computational tool for storage , retrieval and device - independent graphic display of conventional restriction maps .
We describe an interactive computational tool , PLASMAP , which allows the user to electronically store , retrieve , and display circular restriction maps .
PLASMAP permits users to construct libraries of plasmid restriction maps as a set of files which may be edited in the laboratory at any time .
The display feature of PLASMAP quickly generates device - independent , artist - quality , full - color or monochrome , hard copies or CRT screens of complex , conventional circular restriction maps .
OUTPUT:
| 6320096.txt |
software_name_mentions339 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: CHROMPAC III : an improved package for microcomputer - assisted analysis of karyotypes .
An improved package of BASIC computer programs designed to facilitate complete analysis of karyotypes is described .
The package ' s many functions include facilities for measurement of chromosomes , analysis of data , pairing of homologues , designation of sex chromosomes and supernumeraries , storage and recall of data , and generation of idiograms and karyograms .
OUTPUT:
| 6546940.txt |
software_name_mentions340 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: The HELP system .
OUTPUT:
| 6688267.txt |
software_name_mentions341 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Flux analysis of microbial metabolic pathways using a visual programming environment .
This paper describes the use of a visual programming environment ( LabVIEW ) for the flux analysis of metabolic pathways .
Representations of metabolic pathways are constructed in software from individual reaction elements ( icons ) which are linked together to indicate potential flux routes .
Off - line bioprocess data are then used to supply the inputs and outputs to the metabolic pathway and the pathway fluxes are calculated .
The metabolic system can be modelled at different levels of complexity and new pathways can be inserted into existing models .
To illustrate this , flux analyses are performed on three Escherichia coli mutants with metabolic pathway deletions and insertions .
The first analysis looks at organic acid production and the second at the effect of the presence in E .
coli of an engineered pathway for toluene degradation .
OUTPUT:
| 7576534.txt |
software_name_mentions342 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: The use of microsoft excel as a user interface for biological simulations .
We used Microsoft Excel 4.0 for Windows running on a PC - 486 to develop a user interface for two biological simulation models : a lung fluid balance model and a fractal model of the pulmonary circulation .
The simulation programs were written in the C programming language , while the user interface was written in the macro language of Excel .
The interface builds input data files for the simulation programs and provides a mechanism for displaying relevant information from output files produced from the simulations .
Input fields are partially protected so that the user cannot modify certain portions of the spreadsheet .
The Excel interface is used to build models from different available components and to select appropriate parameters for these models .
The developed interface was also useful for running models in the batch mode .
After selecting changes in lung fluid balance parameters , the interface allows users to find new steady state values by automatically running the model and adjusting initial conditions .
Several different graphical options allow users to easily investigate the effects of selecting particular models and parameters .
Techniques used in developing our user interface can be extended to most biological simulation programs which manipulate input and output data files .
OUTPUT:
| 7614822.txt |
software_name_mentions343 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Two - graph receiver operating characteristic ( TG - ROC ) : a Microsoft - EXCEL template for the selection of cut - off values in diagnostic tests .
TG - ROC , a template for Microsoft - EXCEL , represents a novel , easy - to - handle approach for selecting cut - off values in quantitative diagnostic tests .
In addition to graphical representations of test efficiency , Youden index and likelihood ratios as functions of the preselected cut - off value , the software supports the definition of an intermediate range of test results .
For this purpose , two cut - off values are established that realise a pre - selected accuracy level ( e.g. , 90 or 95 % sensitivity and specificity ) which can be specified by the user .
OUTPUT:
| 7665897.txt |
software_name_mentions344 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Microsoft Excel Program for creating attractive survival curves .
This paper describes the design of a Microsoft Excel Program which interactively creates attractive and outstanding survival curves .
This program enables medical researchers to easily create quality presentation graphs of survival curves and obtain high quality slides and prints , which can be inserted in papers or used directly at medical meetings .
Through the use of vertical bars , this program can display the exact points where censored cases occur on survival curves , making it possible to monitor censoring patterns between groups .
Furthermore , this program can also create survival curves based on the proportional hazards model for specific patterns of covariate values , given estimated regression coefficients and baseline survival function .
This program may be a most useful and effective tool in creating medical research papers containing survival analysis .
OUTPUT:
| 7861102.txt |
software_name_mentions345 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: An Excel program for calculating and plotting receiver - operator characteristic ( ROC ) curves , histograms and descriptive statistics .
Receiver - operator characteristic ( ROC ) curves have been used increasingly to assess the performance of clinical laboratory tests and to determine suitable positive / negative threshold values .
The Microsoft Excel 4.0 program Plot .
ROC was designed to provide formatted , publication quality output with minimal user involvement .
It asks for a few parameters at the beginning and then runs autonomously , creating ROC charts , histograms and descriptive statistics for each test chosen , and a cumulative ROC chart to compare tests .
Output can easily be formatted further using Excel ' s graphics and text formatting capabilities .
OUTPUT:
| 7924261.txt |
software_name_mentions346 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: A CAD analysis programme for prosthetics and orthotics .
A CAD ( computer aided design ) analysis software package ( CADVIEW ) was designed for use with prosthetic and orthotic CAD CAM ( computer aided design / computer aided manufacture ) systems .
Using the Microsoft Windows 3.1 environment , CADVIEW provides a series of anatomical shape viewing and analysis tools .
These tools include simultaneous display of multiple sockets and multiple views , two dimensional ( 2D ) and three dimensional ( 3D ) measurement , shape statistics , multi - shape alignment , cross - sectional comparison , colour coded 3D comparison , resolution enhancement , and image copying capabilities .
This programme should be of benefit to clinicians and researchers who wish to assess and / or compare CAD data generated by MS - DOS based CAD CAM systems .
OUTPUT:
| 7991360.txt |
software_name_mentions347 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: SEQSEE : a comprehensive program suite for protein sequence analysis .
SEQSEE ( SEQuence SEEker ) is a multi - purpose , menu - driven suite of programs designed to provide a fully integrated , state - of - the - art package for the analysis and display of protein sequences and protein databases .
It is currently configured to run on most UNIX - based machines including Sun , SGI and NeXT workstations with conversion to other architectures ( e.g .
Vax or Cray ) being a relatively simple task .
SEQSEE is capable of performing nearly all of the analytical and comparative tasks found in most comprehensive commercially available software packages .
These include sequence / database searching , sequence retrieval , sequence entry and editing , statistical sequence analysis , multiple sequence alignment , flexible pattern matching , and secondary structure prediction .
SEQSEE also integrates a number of unique databases which allow it to perform many additional functions such as structure - based sequence alignments and homology - based secondary structure prediction .
Additional enhancements to many previously published algorithms have substantially improved the performance of SEQSEE over that found for most other commercial products .
The source code , the documentation and all of the required databases for SEQSEE are freely available and may be obtained by anonymous ftp .
OUTPUT:
| 8019859.txt |
software_name_mentions348 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: FarFetch - - an Internet - based sequence entry server .
This communication is to announce the availability of a network server for biological sequence database entries which will allow scientists to fetch entries in a desired format directly into their file store .
This server will use TCP / IP protocols allowing any user with an Internet connection to participate .
FarFetch will allow users to obtain sequence entries in a directly usable form as opposed to conventional e - mail based sequence retrievers .
This server also differs from Gopher and WAIS servers in that the sequence entry is written into the user ' s file store in a format that is immediately usable .
Clients for the OpenVMS , Unix and Macintosh operating systems have been written and are available via anonymous ftp .
Development of MS - DOS and Windows clients is planned .
There will be no usage fees associated with the server .
OUTPUT:
| 8019871.txt |
software_name_mentions349 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: NM - Win : a personal computer - based Microsoft Windows front - end to NONMEM IV .
A Microsoft Windows - based front - end , NM - Win , has been written to provide a more user - friendly environment to do nonlinear mixed effect modeling with the NONMEM program .
NM - Win utilizes an object - oriented interface design which allows users to view and edit control , PRED , and / or data files using Windows Notepad .
In addition , calls made to the Microsoft FORTRAN compiler and linker which generate the final NONMEN executable are performed simply by clicking the " Run NONMEN " button .
During the executive step , interactions can be viewed in a window to check the progress of the run .
Errors encountered while NONMEN or NM - TRAN is running are brought to a window for ease in debugging .
Advanced options allow the user the flexibility of compiling user - written PRED files and creating linker response files .
While the PC platform is not optimal for large data set or complex models , it does permit easier debugging and offers multitasking while Windows is running .
OUTPUT:
| 8058641.txt |
software_name_mentions350 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Object - oriented design of medical imaging software .
A special software package for interactive display and manipulation of medical images was developed at the University Hospital of Geneva , as part of a hospital wide Picture Archiving and Communication System ( PACS ) . This software package , called Osiris , was especially designed to be easily usable and adaptable to the needs of noncomputer - oriented physicians .
The Osiris software has been developed to allow the visualization of medical images obtained from any imaging modality .
It provides generic manipulation tools , processing tools , and analysis tools more specific to clinical applications .
This software , based on an object - oriented paradigm , is portable and extensible .
Osiris is available on two different operating systems : the Unix X - 11 / OSF - Motif based workstations , and the Macintosh family .
OUTPUT:
| 8168050.txt |
software_name_mentions351 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Improved sensitivity of profile searches through the use of sequence weights and gap excision .
Position - specific substitution matrices , known as profiles , derived from multiple sequence alignments are currently used to search sequence databases for distantly related members of protein families .
The performance of the database searches is enhanced by using ( i ) a sequence weighting scheme which assigns higher weights to more distantly related sequences based on branch lengths derived from phylogenetic trees , ( ii ) exclusion of positions with mainly padding characters at sites of insertions or deletions and ( iii ) the BLOSUM62 residue comparison matrix .
A natural consequence of these modifications is an improvement in the alignment of new sequences to the profiles .
However , the accuracy of the alignments can be further increased by employing a similarity residue comparison matrix .
These developments are implemented in a program called PROFILEWEIGHT which runs on Unix and Vax computers .
The only input required by the program is the multiple sequence alignment .
The output from PROFILEWEIGHT is a profile designed to be used by existing searching and alignment programs .
Test results from database searches with four different families of proteins show the improved sensitivity of the weighted profiles .
OUTPUT:
| 8193951.txt |
software_name_mentions352 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: fastDNAmL : a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood .
We have developed a new tool , called fastDNAml , for constructing phylogenetic trees from DNA sequences .
The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems , and is available from the Ribosomal Database Project ( RDP ) by anonymous FTP .
Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein ' s dnaml program .
Several enhancements , including algorithmic changes , significantly improve performance and reduce memory usage , making it feasible to construct even very large trees .
Trees containing 40 - 100 taxa have been easily generated , and phylogenetic estimates are possible even when hundreds of sequences exist .
We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes .
OUTPUT:
| 8193955.txt |
software_name_mentions353 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: DNA modeller : an interactive program for modelling stacks of DNA base pairs on a microcomputer .
DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement .
It calculates the van der Waals and electrostatic energies of base - base interactions using the AMBER potential , minimizes the energy with respect to the pair ( buckle , propeller , opening , shear , stretch , stagger ) and step ( tilt , roll , twist , shift , slide , rise ) parameters , calculates lengths of the canonical hydrogen bonds between the complementary bases , and calculates interatomic distances between the successive base pairs .
Input / output files are simple lists of the step and pair parameters or lists of the atom specifications ( N1 , C2 , etc .
) and their Cartesian coordinates ( compatible with the Desktop Molecular Modeller * .
mol files ) . The program is supplied with a readbrk utility which transforms PDB / NDB to the * .
mol format readable by DNA Modeller .
The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed , and their bases visualized and interactively manipulated .
In addition , DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies .
A plotter utility creates wire mono or stereo pictures of the bases .
This program is designed for IBM - compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge ( SCO Unix DOS emulator ) .
OUTPUT:
| 8193957.txt |
software_name_mentions354 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Life after conversion to mainframe Unix .
OUTPUT:
| 8201885.txt |
software_name_mentions355 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: A veterinary anatomy tutoring system .
A veterinary anatomy tutoring system was developed by using Knowledge Pro , an object - oriented software development tool with hypermedia capabilities , and MS Access , a relational database .
Communication between them is facilitated by using the Structured Query Language ( SQL ) . The architecture of the system is based on knowledge sets , each of which covers four different descriptions of an organ , namely gross anatomy ( general description ) , gross anatomy ( comparative features ) , histology , and embryology , which constitute the knowledge units .
These knowledge units are linked with three global variables that define the animals , the topographies , and the system to which this organ belongs , creating three data - bases .
These three data - bases are interrelated through the organ field in order to establish a relational model .
This system allows versatility in the student ' s navigation through the information space by offering different modes for information location and presentation .
These include course mode , review mode , reference mode , dissection mode , and comparison mode .
In addition , the system provides a self - evaluation mode .
OUTPUT:
| 8205800.txt |
software_name_mentions356 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: GEPASI : a software package for modelling the dynamics , steady states and control of biochemical and other systems .
GEPASI is a software system for modelling chemical and biochemical reaction networks on computers running Microsoft Windows .
For any system of up to 45 metabolites and 45 reactions , each with any user - defined or one of 35 predefined rate equations , one can produce trajectories of the metabolite concentrations and obtain a steady state ( if it does exist ) . When steady - state solutions are produced , elasticity and control coefficients , as defined in metabolic control analysis , are calculated .
GEPASI also allows the automatic generation of a sequence of simulations with different combinations of parameter values , effectively scanning a hyper - solid in parameter space .
Together with the ability to produce user - defined columnar data files , these features allow for both very quick and systematic study of biochemical pathway models .
The source code ( in C ) is available on request from the author , and while the user interface is dependent on having MS - Windows as the operating system , the numerical part is portable to other operating systems .
GEPASI is suitable both for research and educational purposes .
Although GEPASI was written with biochemical pathways in mind , it can equally be used to stimulate other dynamical systems .
OUTPUT:
| 8293329.txt |
software_name_mentions357 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: SIGNAL SCAN 3.0 : new database and program features .
SIGNAL SCAN is a program that utilizes a transcription factor database to find potential transcription factor binding sites in DNA sequences .
The program is now in its third version .
The SIGNAL SCAN transcription factor database format has changed and the program output format has been improved .
New features allow the user to update the SIGNAL SCAN database automatically , to retrieve original journal citations and to develop user signal databases .
The program now uses an indexing algorithm , improving scanning speed by a factor of 3. SIGNAL SCAN is now network compatible and is available for IBM - compatible PC , Unix and VMS platforms .
OUTPUT:
| 8435761.txt |
software_name_mentions358 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Renal function tests for windows - - a model for the development and distribution of medical software on the Internet .
A computer application ( Renal Function Tests for Windows ) was developed to calculate and sort data for quantitative renal function testing using the Microsoft Visual Basic for Windows programming language .
The following diagnostic indices are computed : Measured creatinine clearance - - The rate at which serum is cleared of creatinine .
Standardized clearance - - Creatinine clearance scaled by body surface area .
Estimated creatinine clearance - - Renal creatinine clearance estimated from serum creatinine Renal failure index - - To distinguish prerenal azotemia from oliguric acute renal failure .
Renal free water clearance - - Net volume per min of free water excreted by the kidneys .
Fractional excretion of filtered sodium - - To distinguish prerenal azotemia from acute renal failure .
Renal Function Tests for Windows ( RFT ) allows the user to choose to enter only the data that is available .
The program will then calculate all the possible results from the given data .
Upon request , the program will also inform the user of data that is missing for those results that cannot be calculated .
The flexibility of this program allows the user to perform ' what if ' analysis through the manipulation of input data .
Distribution of this program was accomplished using the Internet File Transfer Protocol ( FTP ) service .
The effectiveness of mode of distributing medical software awaits feedback from users on the Internet .
OUTPUT:
| 8557407.txt |
software_name_mentions359 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: FDDI information management system for centralizing interactive , computerized multimedia clinical experiences in pediatric rheumatology / Immunology .
This paper describes the design , authoring , and development of interactive , computerized , multimedia clinical simulations in pediatric rheumatology / immunology and related musculoskeletal diseases , the development and implementation of a high speed information management system for their centralized storage and distribution , and analytical methods for evaluating the total system ' s educational impact on medical students and pediatric residents .
An FDDI fiber optic network with client / server / host architecture is the core .
The server houses digitized audio , still - image video clips and text files .
A host station houses the DB2 / 2 database containing case - associated labels and information .
Cases can be accessed from any workstation via a customized interface in AVA / 2 written specifically for this application .
OS / 2 Presentation Manager controls , written in C , are incorporated into the interface .
This interface allows SQL searches and retrievals of cases and case materials .
In addition to providing user - directed clinical experiences , this centralized information management system provides designated faculty with the ability to add audio notes and visual pointers to image files .
Users may browse through case materials , mark selected ones and download them for utilization in lectures or for editing and converting into 35 mm slides .
OUTPUT:
| 8591407.txt |
software_name_mentions360 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: The micrograph data processing program .
MDPP is a fully featured general - purpose image processing package primarily written to support research in structural biology using data gathered by electron microscopy .
It has focused on the analysis of images using Fourier techniques , particularly periodic plane - layer and helical structures , but has extensive tools for other processing options ( e.g. , point - counting , image quantitation , DNA sequencing , and display ) . Three - dimensional reconstruction methods are supported , including iterative deconvolution schemes for light micrographs .
The basic program is command line - driven , but the user can choose to write sophisticated command scripts and use a menu - driven full - screen or Motif interface to call them .
Color images are supported with both color palette and RGB options .
Extensive documentation is accessible from within the program as online HELP and also as HTML .
Care has been taken to support interfaces to other image processing packages , e.g. , MacIntosh applications via the TIFF image format , and other EM - targeted image processing packages .
The paper provides an overview of the program , its design , and implementation and outlines future plans for software development .
Some general issues concerning image processing program design are discussed .
OUTPUT:
| 8742720.txt |
software_name_mentions361 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: IVE ( Image Visualization Environment ) : a software platform for all three - dimensional microscopy applications .
IVE ( Image Visualization Environment ) is a software platform designed from the outset to handle all aspects of modern computerized multidimensional microscopy .
This platform provides users with an execution environment in which 5D data ( XYZ , wavelength , and time ) can be easily manipulated for the purpose of data collection , processing , display , and analysis .
During the entire process , powerful data display functions are readily available for extracting complicated three - dimensional information through data visualization .
By employing both the shared memory and multitasking features of the UNIX operation system , individual functions can be implemented as separate programs , and multiple programs can access the same data pool simultaneously .
This enables users to combine the functionalities of different programs to facilitate each unique data analysis task .
Furthermore , by defining an appropriate program execution model , commonly shared functional components such as data display , data I / O and user interface , etc .
can be implemented using simple IVE library calls .
This dramatically reduces the program development time and ensures consistency throughout the entire software system .
As a result , users can quickly master the microscopy software system and new functions can be easily integrated , as different functional requirements arise for different research projects .
OUTPUT:
| 8742723.txt |
software_name_mentions362 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Spike - train acquisition , analysis and real - time experimental control using a graphical programming language ( LabView ) . A solution is described for the acquisition on a personal computer of standard pulses derived from neuronal discharge , measurement of neuronal discharge times , real - time control of stimulus delivery based on specified inter - pulse interval conditions in the neuronal spike train , and on - line display and analysis of the experimental data .
The hardware consisted of an Apple Macintosh IIci computer and a plug - in card ( National Instruments NB - MIO16 ) that supports A / D , D / A , digital I / O and timer functions .
The software was written in the object - oriented graphical programming language LabView .
Essential elements of the source code of the LabView program are presented and explained .
The use of the system is demonstrated in an experiment in which the reflex responses to muscle stretch are assessed for a single motor unit in the human masseter muscle .
OUTPUT:
| 8750090.txt |
software_name_mentions363 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Spreadsheet macro for setting up PCR assay tubes .
This article describes a Microsoft Excel macro designed to calculate PCR master mix amounts based on variations in the DNA template amounts added to each tube , the total number of PCR assay tubes being set up or both .
This macro uses a dynamic dialog box to quickly calculate and display the new component volumes after changes in one or both of the variables .
The PCR assay mix protocol can then be printed in a format suitable for record keeping .
This macro was designed for use with the Windows version of Excel but will also run on Macintosh computers .
OUTPUT:
| 8780879.txt |
software_name_mentions364 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Design of a high resolution image cytometer with open software architecture .
A relatively inexpensive , non - proprietary high resolution color pathology workstation is described .
Hardware consists of a JVC frame capture camera with adjustable resolution up to 4416 x 3456 , matching frame grabber and a Unix workstation .
Analytic software was developed using Khoros 1.0.5 , a powerful and flexible system for the development of image analysis applications that is based on a visual programming language .
Applications have been developed for DNA ploidy , quantitative immunohistochemistry and texture and shape analysis .
The instrument ' s software is uniquely extensible and transparent , and has been made publicly available over the Internet .
OUTPUT:
| 8789265.txt |
software_name_mentions365 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Multimedia clinical examination : the time honoured art and science mirrored digitally .
In the recent years , multimedia has exhibited a tremendous presence in the personal computer market and it has exerted an influence in our homes and teaching institutions as well .
To define it very simply , a multimedia PC is a personal computer capable of producing images and sound of reasonable quality by means of software toggles .
This paper presents an Asymetrix Multimedia Toolbook application entitled Multimedia Clinical Examination ( MCE ) which harnesses the ability of affordable computers to create and display a variety of audiovisual media to supplement ' bed - side teaching ' of elementary clinical methods which includes history taking and physical examination .
MCE comprises a history taking module which helps in keeping track of the possible differential diagnoses and a physical examination module which shows digital videos of appropriate examination steps .
The application runs on the Microsoft Windows platform .
OUTPUT:
| 8847118.txt |
software_name_mentions366 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: NCOMP - - a windows - based computer program for noncompartmental analysis of pharmacokinetic data .
The computer program NCOMP performs noncompartmental analysis of pharmacokinetic data obtained from iv bolus , continuous infusion , and oral modes of administration .
Integration of area - under - the - curve and area - under - the - first - moment - curve is done by either Lagrange polynomials or the hybrid method of Purves , which uses parabola - through - the - origin and log trapezoidal algorithms .
Written for Microsoft Windows , NCOMP is designed to be used in conjunction with a spreadsheet program for graphical display and handling of data .
NCOMP interactively aids the user in determining how best to extrapolate the areas to time infinity and in estimating the time zero concentration for iv bolus data .
OUTPUT:
| 8901075.txt |
software_name_mentions367 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Software for microbial fingerprinting by means of the infrared spectra .
Two computer programs were designed for helping in library handling and microbial identification by means of their infrared spectra .
The program ' Transform ' runs in the IR Data Manager environment and produces ASCII files containing transformed data from infrared absorbance spectra .
The program ' WinSpectra ' is written in Visual Basic v. 3.0 .
It imports the ASCII files created with ' Transform ' , and is able to handle , analyse and identify them by their mathematical comparison with a library of microbial spectra .
Both programs run in graphical , menu - driven interface ( GEM and MS Windows , for IBM - PC compatibles , with extensive on - line help .
OUTPUT:
| 8902362.txt |
software_name_mentions368 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Sensitivity and selectivity in protein similarity searches : a comparison of Smith - Waterman in hardware to BLAST and FASTA .
To predict the functions of a possible protein product of any new or uncharacterized DNA sequence , it is important first to detect all significant similarities between the encoded amino acid sequence and any accumulated protein sequence data .
We have implemented a set of queries and database sequences and proceeded to test and compare various similarity search methods and their parameterizations .
We demonstrate here that the Smith - Waterman ( S - W ) dynamic programming method and the optimized version of FASTA are significantly better able to distinguish true similarities from statistical noise than is the popular database search tool BLAST .
Also , a simple " log - length normalization " of S - W scores based on the query and target sequence lengths greatly increased the selectivity of the S - W searches , exceeding the default normalization method of FASTA .
An implementation of the modified S - W algorithm in hardware ( the Fast Data Finder ) is able to match the accuracy of software versions while greatly speeding up its execution .
We present here the selectivity and sensitivity data from these tests as well as results for various scoring matrices .
We present data that will help users to choose threshold score values for evaluation of database search results .
We also illustrate the impact of using simple - sequence masking tools such as SEG or XNU .
OUTPUT:
| 8954800.txt |
software_name_mentions369 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Evaluation of VoiceType Dictation for Windows for the radiologist .
The accuracy of the radiology vocabulary domain of the IBM VoiceType Dictation for Windows speech recognition system for use in a clinical setting was evaluated .
Six men and one woman dictated a case report under several conditions .
The impact of vocabulary domain , microphone position , personal enrollment , and background noise were assessed .
The dictations were exported to Microsoft Word 6.0 , printed , and graded for accuracy .
The data were expressed as a percentage correct .
The enrollment and training processes took an average of 5 hours to complete .
The accuracy of VoiceType Dictation was significantly reduced by speech volume and background noise level so that it could not be used to dictate clinical information accurately in a hospital setting .
Although IBM ' s VoiceType Dictation with the radiology vocabulary domain has improved speech recognition , it is not a reliable dictation system for accurate and efficient clinical dictation in a hospital setting .
OUTPUT:
| 9110274.txt |
software_name_mentions370 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: BEAUTY : an enhanced BLAST - based search tool that integrates multiple biological information resources into sequence similarity search results .
BEAUTY ( BLAST enhanced alignment utility ) is an enhanced version of the NCBI ' s BLAST data base search tool that facilitates identification of the functions of matched sequences .
We have created new data bases of conserved regions and functional domains for protein sequences in NCBI ' s Entrez data base , and BEAUTY allows this information to be incorporated directly into BLAST search results .
A Conserved Regions Data Base , containing the locations of conserved regions within Entrez protein sequences , was constructed by ( 1 ) clustering the entire data base into families , ( 2 ) aligning each family using our PIMA multiple sequence alignment program , and ( 3 ) scanning the multiple alignments to locate the conserved regions within each aligned sequence .
A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez , PROSITE , BLOCKS , and PRINTS data bases .
BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and / or annotated domains .
BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate , for each matched sequence , a schematic display that allows one to directly compare the relative locations of ( 1 ) the conserved regions , ( 2 ) annotated domains and sites , and ( 3 ) the locally aligned regions matched in the BLAST search .
In addition , BEAUTY search results include World - Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences .
This convenient integration of protein families , conserved regions , annotated domains , alignment displays , and World - Wide Web resources greatly enhances the biological informativeness of sequence similarity searches .
BEAUTY searches can be performed remotely on our system using the " BCM Search Launcher " World - Wide Web pages ( URL is < http : / / gc.bcm.tmc.edu : 8088 / search - launcher / launcher.html > ) .
OUTPUT:
| 9132271.txt |
software_name_mentions371 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: Left ventricular pressure and volume data acquisition and analysis using LabVIEW .
To automate analysis of left ventricular pressure - volume data , we used LabVIEW to create applications that digitize and display data recorded from conductance and manometric catheters .
Applications separate data into cardiac cycles , calculate parallel conductance , and calculate indices of left ventricular function , including end - systolic elastance , preload - recruitable stroke work , stroke volume , ejection fraction , stroke work , maximum and minimum derivative of ventricular pressure , heart rate , indices of relaxation , peak filling rate , and ventricular chamber stiffness .
Pressure - volume loops can be graphically displayed .
These analyses are exported to a text - file .
These applications have simplified and automated the process of evaluating ventricular function .
OUTPUT:
| 9158920.txt |
software_name_mentions372 | Instruction: Given an abstract identity all software names from it by highlighting within <mark> and </mark> tags. Also, apply these guidelines to help with accuracy:
1.Longest noun phrase where one explicit software name is the head noun should be marked
2.If the noun phrase contains more than one explicit software name, the explicit software names should be marked individually
3.Software name tagging should NOT include the description or content of software
4.Full software name and its following acronym within parenthesis should be marked as a whole
5.Acronym type of software name and its following full name within parenthesis should be marked as a whole
6.Software name and its following version number should be marked as a whole
INPUT: The teaching of computer programming and digital image processing in radiography .
The increased use of digital processing techniques in Medical Radiations imaging modalities , along with the rapid advance in information technology has resulted in a significant change in the delivery of radiographic teaching programs .
This paper details a methodology used to concurrently educate radiographers in both computer programming and image processing .
The students learn to program in visual basic applications ( VBA ) , and the programming skills are contextualised by requiring the students to write a digital subtraction angiography ( DSA ) package .
Program code generation and image presentation interface is undertaken by the spreadsheet Microsoft Excel .
The user - friendly nature of this common interface enables all students to readily begin program creation .
The teaching of programming and image processing skills by this method may be readily generalised to other vocational fields where digital image manipulation is a professional requirement .
OUTPUT:
| 9726504.txt |