Summary: The act of testing the software for compliance with a standard.
- Brudno M, Chapman M, Gottgens B, Batzoglou S, Morgenstern B. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics. 2003;4:66 pubmed..We likewise demonstrate that the DIALIGN/CHAOS combination is able to accurately align short regulatory sequences in distant orthologues. ..
- Sierk M, Pearson W. Sensitivity and selectivity in protein structure comparison. Protein Sci. 2004;13:773-85 pubmed..These results help quantify the statistical distinction between analogous and homologous structures, and provide a benchmark for structure comparison statistics. ..
- Scherf M, Klingenhoff A, Frech K, Quandt K, Schneider R, Grote K, et al. First pass annotation of promoters on human chromosome 22. Genome Res. 2001;11:333-40 pubmed..Results are available on-line at http://genomatix.gsf.de/chr22/. ..
- Shih A, Lee D, Lin L, Peng C, Chen S, Wu Y, et al. SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. BMC Bioinformatics. 2006;7:103 pubmed..With SinicView, users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment in the initial stage of sequence analysis. ..
- Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, Verschoren A, et al. SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics. 2006;7:43 pubmed..Simulation of the network scales well to large networks. The generator models different types of biological interactions and produces biologically plausible synthetic gene expression data. ..
- Subramanian A, Weyer Menkhoff J, Kaufmann M, Morgenstern B. DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics. 2005;6:66 pubmed..On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated. ..
- Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, et al. Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics. 2004;20:839-46 pubmed..Our analysis suggests that dChip is more robust and stable than the MAS5 tools for about 60% of the genes while RMAExpress is able to achieve an even greater improvement in terms of signal to noise, for more than 95% of the genes. ..
- Do C, Mahabhashyam M, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005;15:330-40 pubmed..On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource. ..
- Bader G, Hogue C. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003;4:2 pubmed..The algorithm is not affected by a known high rate of false positives in data from high-throughput interaction techniques. The program is available from ftp://ftp.mshri.on.ca/pub/BIND/Tools/MCODE. ..
- Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R, et al. Human-mouse alignments with BLASTZ. Genome Res. 2003;13:103-7 pubmed..This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results. ..
- Wessels L, Reinders M, Hart A, Veenman C, Dai H, He Y, et al. A protocol for building and evaluating predictors of disease state based on microarray data. Bioinformatics. 2005;21:3755-62 pubmed..Our training-validation protocol provides a robust methodology to evaluate the performance of new computational approaches and to objectively compare outcome predictions on different datasets. ..
- Schaefer W, Lipke C, Standke D, Kuhl H, Nowak B, Kaiser H, et al. Quantification of left ventricular volumes and ejection fraction from gated 99mTc-MIBI SPECT: MRI validation and comparison of the Emory Cardiac Tool Box with QGS and 4D-MSPECT. J Nucl Med. 2005;46:1256-63 pubmed..Nevertheless, any algorithm-inherent over- or underestimation of volumes and LVEF should be accounted for and an interchangeable use of different software packages should be avoided. ..
- Lipke C, Kuhl H, Nowak B, Kaiser H, Reinartz P, Koch K, et al. Validation of 4D-MSPECT and QGS for quantification of left ventricular volumes and ejection fraction from gated 99mTc-MIBI SPET: comparison with cardiac magnetic resonance imaging. Eur J Nucl Med Mol Imaging. 2004;31:482-90 pubmed..However, algorithm-varying underestimation of LVEF should be accounted for in the clinical context and limits interchangeable use of software. ..
- Mendes P, Sha W, Ye K. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics. 2003;19 Suppl 2:ii122-9 pubmed..The data sets and kinetic models described here are available from http://www.vbi.vt.edu/~mendes/AGN/as biochemical dynamic models in SBML and Gepasi formats. ..
- Kan Z, Rouchka E, Gish W, States D. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 2001;11:889-900 pubmed..Furthermore, the evolutionary conservation of alternative splicing between human and mouse was analyzed using an EST-based approach. (See http://stl.wustl.edu/~zkan/TAP/) ..
- Zafar N, Mazumder R, Seto D. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinformatics. 2002;3:12 pubmed..This web resource is available at http://pumpkins.ib3.gmu.edu:8080/CoreGenes or http://www.bif.atcc.org/CoreGenes. ..
- Gomis M, Gall C, Brahmi F. Web-based citation management compared to EndNote: options for medical sciences. Med Ref Serv Q. 2008;27:260-71 pubmed publisher..The search results indicated it would be appropriate to search databases via citation management software for citation verification tasks and for cursory keyword searching. ..
- Struckmann S, Esch D, Scholer H, Fuellen G. Visualization and exploration of conserved regulatory modules using ReXSpecies 2. BMC Evol Biol. 2011;11:267 pubmed publisher..Our tool is designed to analyze transcription factor binding site predictions considering their common pattern of occurrence, highlighting their evolutionary history. ..
- Jonsson G, Anguera M, Blanco Villaseñor A, Losada J, Hernández Mendo A, Ardá T, et al. Hidden patterns of play interaction in soccer using SOF-CODER. Behav Res Methods. 2006;38:372-81 pubmed..The results suggest that it is possible to identify new kinds of profiles for both individuals and teams on the basis of observational criteria and a further analysis of temporal behavioral patterns detected within the performances. ..
- Bazzocchi A, Diano D, Battista G, Albisinni U, Rossi C, Guglielmi G. New dual-energy X-ray absorptiometry equipment in the assessment of vertebral fractures: technical limits and software accuracy. Skeletal Radiol. 2012;41:823-9 pubmed publisher..This study provides new and interesting information about the accuracy, reliability, and imaging quality provided by iDXA in the assessment of VFs. ..
- Abhari K, de Ribaupierre S, Peters T, Eagleson R. Evaluation of a VR and stereo-endoscopic tool to facilitate 3rd ventriculostomy. Stud Health Technol Inform. 2011;163:1-7 pubmed
- Yanagawa M, Tanaka Y, Kusumoto M, Watanabe S, Tsuchiya R, Honda O, et al. Automated assessment of malignant degree of small peripheral adenocarcinomas using volumetric CT data: correlation with pathologic prognostic factors. Lung Cancer. 2010;70:286-94 pubmed publisher..0007, 0.0027), vascular invasion (p=0.003, 0.012), and pleural invasion (p=0.021, 0.025). Using our custom-developed software, it is feasible to predict the pathological prognostic factors of small peripheral adenocarcinomas. ..
- GARVIN J, DuVall S, South B, Bray B, Bolton D, Heavirland J, et al. Automated extraction of ejection fraction for quality measurement using regular expressions in Unstructured Information Management Architecture (UIMA) for heart failure. J Am Med Inform Assoc. 2012;19:859-66 pubmed publisher..9% (95% CI 91.2% to 92.7%). An EF value of <40% can be accurately identified in VA echocardiogram reports. An automated information extraction system can be used to accurately extract EF for quality measurement. ..
- Xue Y, Ren J, Gao X, Jin C, Wen L, Yao X. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics. 2008;7:1598-608 pubmed publisher..Thus, the GPS 2.0 is a useful tool for predicting protein phosphorylation sites and their cognate kinases and is freely available on line. ..
- Dai Q, Wang T. Use of linear regression model to compare RNA secondary structures. J Theor Biol. 2008;253:854-60 pubmed publisher..The results have shown the effectiveness of the proposed models. Moreover, the time complexity of our models is favorable by comparing with that of the existing methods which solve the similar problem. ..
- Girasis C, Schuurbiers J, Muramatsu T, Aben J, Onuma Y, Soekhradj S, et al. Advanced three-dimensional quantitative coronary angiographic assessment of bifurcation lesions: methodology and phantom validation. EuroIntervention. 2013;8:1451-60 pubmed publisher..30). Advances in the methodology of 3-D reconstruction and quantitative analysis for bifurcation lesions translated into highly accurate, precise and reproducible measures of diameter, length and BA. ..
- Tsiflikas I, Biermann C, Thomas C, Ketelsen D, Claussen C, Heuschmid M. Carotid artery stenosis: performance of advanced vessel analysis software in evaluating CTA. Eur J Radiol. 2012;81:2255-9 pubmed publisher..via (Siemens Healthcare, Forchheim, Germany) provides a high rate of reproducibility in assessment of carotid artery stenosis. Furthermore a significant time saving in comparison to standard image interpretation is achievable. ..
- Zubaran C, Tres I. The use of the computerized version of quality of life and health status questionnaires in a community sample in southern Brazil. Sao Paulo Med J. 2011;129:36-40 pubmed..Health-related issues were significantly correlated with the overall experience of wellbeing and quality of life. The computerized versions of the PHS and MQLI are valid tools for research and clinical use in Brazil. ..
- Olch A. Evaluation of the accuracy of 3DVH software estimates of dose to virtual ion chamber and film in composite IMRT QA. Med Phys. 2012;39:81-6 pubmed publisher..This is also a necessary although not sufficient condition for validation of the accuracy of 3DVH predictions of the 3D dose using beam-by-beam measurements. ..
- Christe A, Leidolt L, Huber A, Steiger P, Szucs Farkas Z, Roos J, et al. Lung cancer screening with CT: evaluation of radiologists and different computer assisted detection software (CAD) as first and second readers for lung nodule detection at different dose levels. Eur J Radiol. 2013;82:e873-8 pubmed publisher..03). Combination of a human observer with any of the tested CAD systems provide optimal sensitivity for lung nodule detection even at reduced dose at 25 mAs/80 kVp. ..
- Pepper S, Saunders E, Edwards L, Wilson C, Miller C. The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics. 2007;8:273 pubmed..0 was found to have performance approaching that of its peers. When used alongside detection calls, MAS5 is a sensitive and selective algorithm for identifying differentially expressed genes. ..
- Taylor R, Yegin G, Rogers D. Benchmarking brachydose: Voxel based EGSnrc Monte Carlo calculations of TG-43 dosimetry parameters. Med Phys. 2007;34:445-57 pubmed..Overall, calculations made with Brachydose show good agreement with calculations made with PTRAN although there are some exceptions. ..
- Gillette T, Grefenstette J. On comparing neuronal morphologies with the constrained tree-edit-distance. Neuroinformatics. 2009;7:191-4 pubmed publisher..However, other more efficient algorithms may make use of it as a gold standard for direct morphological comparison. ..
- Manninen T, Mäkiraatikka E, Ylipaa A, Pettinen A, Leinonen K, Linne M. Discrete stochastic simulation of cell signaling: comparison of computational tools. Conf Proc IEEE Eng Med Biol Soc. 2006;1:2013-6 pubmed..The present study is one of the first evaluations of stochastic simulation tools for realistic signal transduction pathways. ..
- Khan H. SCEW: a Microsoft Excel add-in for easy creation of survival curves. Comput Methods Programs Biomed. 2006;83:12-7 pubmed..The advantages of this program are simple data input, minimal procedural steps and the creation of survival curves in the familiar confines of Excel. ..
- Ye Y, Park J, Kim S, Choi J, Hur G, Lee H, et al. Clinical evaluation of the computerized chronic urticaria-specific quality of life questionnaire in Korean patients with chronic urticaria. Clin Exp Dermatol. 2012;37:722-8 pubmed publisher..The computerized CU-QOL is a convenient and valid tool for measuring QOL in patients with CU. This study suggests that UAS, dermatographism and emotional stress are strong CU-QOL predictors in Korean patients with CU. ..
- Dong Q, Wilkerson M, Brendel V. Tracembler--software for in-silico chromosome walking in unassembled genomes. BMC Bioinformatics. 2007;8:151 pubmed..A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations. ..
- Sentelle C, Anagnostopoulos G, Georgiopoulos M. Efficient revised simplex method for SVM training. IEEE Trans Neural Netw. 2011;22:1650-61 pubmed publisher..In addition, we show competitive performance of the proposed algorithm against two popular SVM training algorithms, SVMLight and LIBSVM. ..
- He T, Wu Y, Du K. [Medical device software requirements and evaluation]. Zhongguo Yi Liao Qi Xie Za Zhi. 2011;35:379-82 pubmed..And it discusses the methods on evaluating medical device software from two aspects, the design and development process of the software and software products. ..
- Chevalier A, Cegarra J. A constraint-satisfaction approach to studying the management of multiple objectives in design problem-solving. Psychol Rep. 2006;99:488-93 pubmed..Possible methodological generalizations are discussed. ..
- Conway C, O Shea D, O Brien S, Lawler D, Dodrill G, O Grady A, et al. The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line. BMC Bioinformatics. 2006;7:256 pubmed
- Dzintars E, Stathakis S, Mavroidis P, Sadeghi A, Papanikolaou N. Performance of independent dose calculation in helical tomotherapy: implementation of the MCSIM code. Australas Phys Eng Sci Med. 2012;35:423-38 pubmed publisher..By comparing point doses and dose profiles, the EGS4/MCSIM Monte Carlo environment was seen to provide an accurate independent dose calculation. ..
- Henne E, Anderson J, Lowe N, Kesten S. Comparison of human lung tissue mass measurements from ex vivo lungs and high resolution CT software analysis. BMC Pulm Med. 2012;12:18 pubmed publisher..56%. The degree of concordance between the software mass quantification to physical mass measurements provides substantial evidence that the software method represents an appropriate non-invasive means to determine lung tissue mass. ..
- Johnson C. Why did that happen? Exploring the proliferation of barely usable software in healthcare systems. Qual Saf Health Care. 2006;15 Suppl 1:i76-81 pubmed
- Martz H, Kozioziemski B, Lehman S, Hau Riege S, Schneberk D, Barty A. Validation of radiographic simulation codes including x-ray phase effects for millimeter-size objects with micrometer structures. J Opt Soc Am A Opt Image Sci Vis. 2007;24:169-78 pubmed..We conclude that the multislice method is not required for accurate simulation of greater than or equal to 8 keV x-ray radiographs of millimeter-size objects with micrometer structures. ..
- Ishiyama H, Nakamura R, Satoh T, Tanji S, Teh B, Uemae M, et al. Matched-pair analysis and dosimetric variations of two types of software for interstitial permanent brachytherapy for prostate cancer. Med Dosim. 2012;37:84-6 pubmed publisher..Our results showed that use of different software could lead to different dosimetric results, which might affect the clinical outcomes. ..
- Lartizien C, Kuntner C, Goertzen A, Evans A, Reilhac A. Validation of PET-SORTEO Monte Carlo simulations for the geometries of the MicroPET R4 and Focus 220 PET scanners. Phys Med Biol. 2007;52:4845-62 pubmed
- Meloun M, Bordovská S. Benchmarking and validating algorithms that estimate pK(a) values of drugs based on their molecular structures. Anal Bioanal Chem. 2007;389:1267-81 pubmed..The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules. ..
- Dowell N, Tofts P. Fast, accurate, and precise mapping of the RF field in vivo using the 180 degrees signal null. Magn Reson Med. 2007;58:622-30 pubmed..The experiment utilizes an existing MR sequence supplied by the scanner manufacturer. The technique is validated experimentally and a theoretical investigation into the optimum experimental parameters is presented. ..
- Ashraf H, de Hoop B, Shaker S, Dirksen A, Bach K, Hansen H, et al. Lung nodule volumetry: segmentation algorithms within the same software package cannot be used interchangeably. Eur Radiol. 2010;20:1878-85 pubmed publisher..It is crucial even in the same software package to choose identical parameters for follow-up. ..
- Gortzis L. Designing and redesigning medical telecare services: a forces-oriented model. Methods Inf Med. 2007;46:27-35 pubmed..The optimal parameter combination must be chosen according to the aim of each telecare procedure. Further research is needed to determine the minimum parameters to support telecare service design. ..