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Selecting Software Phase Markers with Code Structure Analysis

J. Lau, E. Perelman, B. Calder
International Symposium on Code Generation and Optimization (CGO'06)  
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

Ofir Davidovich, Gad Kimmel, Ron Shamir
2007 BMC Bioinformatics  
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

S. Allen, H. S. Ginwal, S. Barthwal
2015 Silvae Genetica  
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

Alejandro A. Schäffer, Mathieu Lemire, Jürg Ott, G. Mark Lathrop, Daniel E. Weeks
2011 Human Heredity  
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

Archana Ravindar, Y.N. Srikant
2011 2011 15th Workshop on Interaction between Compilers and Computer Architectures  
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

J. Zhang
2002 Nucleic Acids Research  
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

Zhe Zhang, Xiujin Li, Xiangdong Ding, Jiaqi Li, Qin Zhang
2015 BMC Genetics  
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

Lucia HLAVACKOV�, Janka N��kov�, Elizaveta POROKHOVINOVA, Nina BRUTCH, Tatiana SHELENGA, Marie Bjelkov�, Katar�na RA�N�
2016 Journal of Central European Agriculture  
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]

Janusz Rygał, Jakub Romanowski, Rafał Scherer, Sohrab Ferdowsi
2014 Lecture Notes in Computer Science  
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]

Davide Brugali, Luca Gherardi, A. Biziak, Andrea Luzzana, Alexey Zakharov
2012 Lecture Notes in Computer Science  
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

Adalgisa Ribeiro Torres, Anna Karolina Grunvald, Talita Busulini Martins, Maria Aparecida dos Santos, Noélle Giacomini Lemos, Luis Antônio Stabile Silva, Mariangela Hungria
2015 Scientia Agricola  
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

Imran Majid, Martin P. Robillard
2005 Proceedings of the 2005 OOPSLA workshop on Eclipse technology eXchange - eclipse '05  
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

Alice Mantoan, Claudio Pizzolato, Massimo Sartori, Zimi Sawacha, Claudio Cobelli, Monica Reggiani
2015 Source Code for Biology and Medicine  
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

A Haghighatnia, S Vallian, J Mowla, Z Fazeli
2012 Iranian Journal of Public Health  
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

Xipeng Shen, Michael L. Scott, Chengliang Zhang, Sandhya Dwarkadas, Chen Ding, Mitsunori Ogihara
2007 Proceedings of the 2007 workshop on Experimental computer science - ExpCS '07  
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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