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Selecting Software Phase Markers with Code Structure Analysis
International Symposium on Code Generation and Optimization (CGO'06)
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In this paper, we present an automated profiling approach to identify code locations whose executions correlate with phase changes. ...
These "software phase markers" can be used to easily detect phase changes across different inputs to a program without hardware support. ...
Acknowledgments We would like to Xipeng Shen and Chen Ding for providing us with data and their cache simulation infrastructure, we thank Michael Huang for answering our questions about EX-PERT, and we ...
doi:10.1109/cgo.2006.32
dblp:conf/cgo/LauPC06
fatcat:my73agashvdpzpkzp44sbxrbyi
GEVALT: An integrated software tool for genotype analysis
2007
BMC Bioinformatics
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GEVALT combines the strong visual abilities of Haploview with our quick and powerful algorithms for genotypes phasing (GERBIL), tag SNP selection (STAMPA) and permutation testing for evaluating significance ...
Conclusion: GEVALT is an integrated viewer that uses state of the art phasing and tag SNP selection algorithms. ...
We are grateful to the Haploview Team for making their software and source code available to us, and to Eran Halperin who codeveloped Stampa. ...
doi:10.1186/1471-2105-8-36
pmid:17270038
pmcid:PMC1797190
fatcat:gth5ynvxhzc2hov4b4ngmgtvq4
Development of PCR based markers in Terpene synthase genes for marker assisted selection of high resin yielders in Pinus roxburghii Sarg
2015
Silvae Genetica
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With the help of bioinformatics tools, we were able to associate some markers with resin yield. This study holds a key promise for the conservation of pine germplasm in natural habitat. ...
Primers were designed based on the related coding sequences to target these regions using Primer 3 software to amplify and isolate related genomic loci in chir pine genotypes. ...
Genetic structure analysis using STRUCTURE software The model based clustering algorithm was applied to identify subgroups with distinct allele frequencies (PRITCHARD et al., 2000) using the software ...
doi:10.1515/sg-2015-0020
fatcat:k6m6mclgozhvjdfjnfrdy4r5mq
Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees
2011
Human Heredity
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to simulate a much larger number of markers on the same chromosome, linked and possibly associated with a trait locus. ...
We review the history of SLINK and describe how SLINK and SUP are now coordinated to permit the simulation of large numbers of markers linked and possibly associated with a trait in large pedigrees. ...
Recent improvements focused on software engineering for both better speed and integration with SUP. ...
doi:10.1159/000324177
pmid:21734403
pmcid:PMC3136384
fatcat:iql62ds73ze4vjye53cbiyr5jy
Implications of Program Phase Behavior on Timing Analysis
2011
2011 15th Workshop on Interaction between Compilers and Computer Architectures
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In this paper, we show that phase behavior has important implications on timing analysis. ...
Each phase being distinct from the other, exhibit homogeneous behavior with respect to cycles per instruction(CPI), data cache misses etc. ...
Phases are identified by code structural analysis [14] . ...
doi:10.1109/interact.2011.12
dblp:conf/IEEEinteract/RavindarS11
fatcat:jnkqo7shgvdnnjvs2r7gpgxjfa
HapScope: a software system for automated and visual analysis of functionally annotated haplotypes
2002
Nucleic Acids Research
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It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined ...
The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classi®cation by protein coding change, homology ...
We thank Mr Richard Finney for implementing the SNPHAP parser code. ...
doi:10.1093/nar/gkf654
pmid:12466546
pmcid:PMC137968
fatcat:tur3u7wmejdobcncnmtwu5cdem
GPOPSIM: a simulation tool for whole-genome genetic data
2015
BMC Genetics
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GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. ...
Results: The model implemented in GPOPSIM is presented, and the code has been made freely available to the community. ...
The software can run on multiple platforms and the code has been made freely available to the community. ...
doi:10.1186/s12863-015-0173-4
pmid:25652552
pmcid:PMC4328615
fatcat:hbjdkkhxsze2vjutps5qoznbl4
Analysis of miRNA polymorphism during the selected developmental processes of flax
Anal�za polymorfizmu miRNA vo vybran�ch v�vojov�ch �t�di�ch lanu siateho
2016
Journal of Central European Agriculture
Anal�za polymorfizmu miRNA vo vybran�ch v�vojov�ch �t�di�ch lanu siateho
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The research was focused on the potential of selected miRNA-based molecular markers (miR156 and miR168) to map the polymorphism level of flax genome in the selected developmental stages (flower bud -floweringboll ...
Taking into account the genetic background of genotypes, based on the peak analysis profile of amplified miRNA loci, implemented by GeneTools software, was possible to identified unique loci in linseed ...
Results and discussion Polymorphism analysis by miR168a-based molecular marker miRNA-based primers combining with different places of the same stem-loop structure of miRNA can produce fragments of useful ...
doi:10.5513/jcea01/17.3.1767
fatcat:xkpe2wscivfmfjaxwmtprqgiji
Novel Algorithm for Translation from Image Content to Semantic Form
[chapter]
2014
Lecture Notes in Computer Science
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We will also concisely demonstrate the structure of the whole SIA (Semantic Image Analysis) project. ...
That is why in the next planed phase of our project we can combine diverse markers to achieve the best selectivity of similar images. ...
Each array of markers, which represents the single SWM is converted by the SHA-1 algorithm into a hash code. ...
doi:10.1007/978-3-319-07173-2_67
fatcat:ouy6xttat5bzpiw3e66qlp6syy
A Reuse-Oriented Development Process for Component-Based Robotic Systems
[chapter]
2012
Lecture Notes in Computer Science
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The aim of this paper is to illustrate the whole software development process that we have defined for developing flexible and reusable component-based robotics libraries, to exemplify it with the case ...
In the BRICS project we have defined a software development process that is based on the two most recent and promising approaches to software reuse, i.e. ...
This phase is typically called software development with reuse. Figure 1 illustrates the phases of the reuse-oriented development process described in this paper. ...
doi:10.1007/978-3-642-34327-8_33
fatcat:zdx5mo5fcvb37jkji5xv3ohk4y
Genetic structure and diversity of a soybean germplasm considering biological nitrogen fixation and protein content
2015
Scientia Agricola
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Population structure was inferred by principal component analysis and by the STRUCTURE software. ...
Soybeans were genotyped with 22 SSR markers, previously described as associated with BNF and protein content. Genetic diversity was evaluated using the DARwin 5.0 software. ...
Polymorphism index content; 3 The underlined markers were not selected for analysis of population structure by STRUCTURE software. ...
doi:10.1590/0103-9016-2014-0039
fatcat:smn3u6basrfz7brjgqhmz7xn2y
NaCIN
2005
Proceedings of the 2005 OOPSLA workshop on Eclipse technology eXchange - eclipse '05
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It performs an analysis of the navigation paths and structural dependencies of the recorded elements and clusters the results in groups potentially associated with high level concepts. ...
NaCIN partially automates the process of relating source code with high-level abstractions and enables knowledge about the implementation of different concerns to be reused in future investigations. ...
During the investigation of the source code, the probability that a certain element is associated with a given task can be determined by program investigation patterns, structural dependencies between ...
doi:10.1145/1117696.1117711
dblp:conf/eclipse/MajidR05
fatcat:iy4fbhagsjdqpjogtzecpuz7jq
MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation
2015
Source Code for Biology and Medicine
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MOtoNMS processes experimental data from different motion analysis devices and generates input data for neuromusculoskeletal modeling and simulation software, such as OpenSim and CEINMS (Calibrated EMG-Informed ...
Conclusions: MOtoNMS fills the gap between motion analysis and neuromusculoskeletal modeling and simulation. ...
Acknowledgements The authors would like to thank Michele Vivian for his contributions to the initial idea of this project, and Peter Staab for testing MOtoNMS with FP of type 3. ...
doi:10.1186/s13029-015-0044-4
pmid:26579208
pmcid:PMC4647340
fatcat:2m5fr5eg75ghlonf7bf57cna2e
Genetic Diversity and Balancing Selection within the Human Phenylalanine Hydroxylase (PAH) Gene Region in Iranian Population
2012
Iranian Journal of Public Health
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The haplotype estimation analysis of the markers resulted in nine informative haplotypes with frequencies ≥5%. ...
The allele frequency and population status of the alleles were estimated using PHASE, FBAT and GENEPOP software. ...
Therefore, these two markers of the PAH gene were not neutral and may be linked with some selection traits or genes. ...
pmid:23113183
pmcid:PMC3468980
fatcat:f7zq4jxhsvderhiinlwkhczcgy
Analysis of input-dependent program behavior using active profiling
2007
Proceedings of the 2007 workshop on Experimental computer science - ExpCS '07
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We demonstrate the effectiveness and programmability of active profiling via experiments with six utility programs from the SPEC benchmark suite; compare to code and interval phases; and describe applications ...
us to exploit phase transitions in production runs with arbitrary inputs. ...
Comparison with procedure and interval phases Program phase analysis takes a loop, subroutine, or other code structure as a phase [3, 17, 20, 23, 24, 25] . ...
doi:10.1145/1281700.1281705
dblp:conf/expcs/ShenSZDDO07
fatcat:o4dykadow5aghctxp5bpcqgp44
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