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Performance Analysis Strategies for Software Variants and Versions [chapter]

Thomas Thüm, André van Hoorn, Sven Apel, Johannes Bürdek, Sinem Getir, Robert Heinrich, Reiner Jung, Matthias Kowal, Malte Lochau, Ina Schaefer, Jürgen Walter
2019 Managed Software Evolution  
Analysis Strategies for Software Versions Section 8.1 covered performance analysis strategies for software variants, focusing on the problem of how to efficiently analyse large configuration spaces.  ...  Analysis Strategies for Software Variants Numerous strategies are known to analyse software variants [Thü+14a] .  ... 
doi:10.1007/978-3-030-13499-0_8 fatcat:wr7xybqhpfg5vl4fd7xhx6s464

Lessons Learned [chapter]

Ralf Reussner, Michael Goedicke, Wilhelm Hasselbring, Birgit Vogel-Heuser, Jan Keim, Lukas Märtin
2019 Managed Software Evolution  
The lessons learned while investigating new methods and techniques for knowledgecarrying software in SPP 1593 are summarised below.  ...  Potentially wrong usage behaviour might transition into a pattern that is of interest and relevant for a new feature or functionality of an application.  ...  Strategies on how to efficiently address performance for variants and versions have been developed throughout the last years, and we have presented selected and complementary approaches based on the two  ... 
doi:10.1007/978-3-030-13499-0_13 fatcat:2hqg6g3qazdcblioqmn5gklv4i

Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery [article]

Ruslan Abasov, Varvara E. Tvorogova, Andrey S. Glotov, Alexander V. Predeus, Yury A. Barbitoff
2021 bioRxiv   pre-print
Our results suggest that Bowtie2 performs significantly worse than other aligners and should not be used for medical variant calling.  ...  calling software.  ...  Variant calling pipelines Variant discovery and filtering was performed using 24 different strategies, with 4 different read alignment software and 4 modern variant calling solutions used.  ... 
doi:10.1101/2021.04.13.439626 fatcat:2ggnl2qh55hjtih7fi6nu6wwyy

A biologically informed method for detecting rare variant associations

Carrie Colleen Buchanan Moore, Anna Okula Basile, John Robert Wallace, Alex Thomas Frase, Marylyn DeRiggi Ritchie
2016 BioData Mining  
BioBin is a bioinformatics software package developed to automate the process of binning rare variants into groups for statistical association analysis using a biological knowledge-driven framework.  ...  BioBin provides the infrastructure to create complex and interesting hypotheses in an automated fashion thereby circumventing the necessity for advanced and time consuming scripting.  ...  The BioBin software package has the capability to transform and streamline analysis pipelines for researchers analyzing rare variants in DNA sequencing data.  ... 
doi:10.1186/s13040-016-0107-3 pmid:27582876 pmcid:PMC5006419 fatcat:4vdiohz36bbpvoevnitxkqmbr4

A three-caller pipeline for variant analysis of cancer whole-exome sequencing data

Ze-Kun Liu, Yu-Kui Shang, Zhi-Nan Chen, Huijie Bian
2017 Molecular Medicine Reports  
An increasing number of software and methodological guidelines are being published for the analysis of sequencing data.  ...  by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis.  ...  The gene sets screened were used for functional annotation analysis by the Database for Annotation, Visualization and Integrate Discovery software (25) , which consists of the Kyoto Encyclopedia of Genes  ... 
doi:10.3892/mmr.2017.6336 pmid:28447726 pmcid:PMC5428716 fatcat:w74rzi6eyzgyvdw3jny4udnpye

Multi-Variant Execution Research of Software Diversity

Zhenwu Liu, Zheng Zhang, Jiexin Zhang, Hao Liu
2019 Journal of Physics, Conference Series  
As more and more software products are threatened by malicious reverse analysis, along with software products are pirated, tampered with and so on, it is of great significance to study software security  ...  The tradeoffs between performance and security are also analyzed. Finally, the work of the full text is summarized.  ...  Acknowledgments The authors thank Jiexin Zhang for his assistance and encouragement in this research.  ... 
doi:10.1088/1742-6596/1325/1/012107 fatcat:5xo7gqyy5zgl7otewo64wgstg4

Strategies for phasing and imputation in a population isolate

Anthony Francis Herzig, Teresa Nutile, Marie-Claude Babron, Marina Ciullo, Céline Bellenguez, Anne-Louise Leutenegger
2018 Genetic Epidemiology  
To identify an effective study-design, we compare by simulation a range of phasing and imputation software and strategies.  ...  For imputation we compared IMPUTE2, IMPUTE4, MINIMAC3, BEAGLE, and new software PBWT.  ...  SHAPEIT3 performed similarly to 202 SHAPEIT2 and for subsequent analysis we will only present results for SHAPEIT2+duohmm+1000G. for all phasing strategies considered are given inSupplementary Table 2.  ... 
doi:10.1002/gepi.22109 pmid:29319195 fatcat:7kx7ewx5c5abnam7e6uqblhat4

VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

Ramesh Menon, Namrata V. Patel, Amitbikram Mohapatra, Chaitanya G. Joshi
2016 3 Biotech  
It supports multiple NGS platforms and has four methodological choices for variant detection.  ...  Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which  ...  Acknowledgments The study was supported by Department of Biotechnology, Ministry of science and technology, India.  ... 
doi:10.1007/s13205-016-0382-1 pmid:28330138 pmcid:PMC4754298 fatcat:wsxqblo36bgcxbmmmzu7d5davm

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing [article]

Jordi Valls-Margarit, Iván Galván-Femenía, Daniel Matias, Natalia Blay, Montserrat Puiggròs, Anna Carreras, Cecilia Salvoro, Beatriz Cortés, Ramon Amela, Xavier Farre, Jon Lerga-Jaso, Marta Puig (+9 others)
2021 bioRxiv   pre-print
The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with mononeuritis of lower limb, a rare neuromuscular disease.  ...  However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels).  ...  The LRM was developed using R software (version 3.3.1) and the ISLR package.  ... 
doi:10.1101/2021.07.20.453041 fatcat:vjnauvqhezhebjcr2c3jlznsre

AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting

Christian Wünsch, Henrik Banck, Carsten Müller-Tidow, Martin Dugas
2020 BMC Medical Genomics  
Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants.  ...  The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists.  ...  Bo Peng, developed VariantTools, which is used for normalization and integration of the results of different caller tools, and gave a lot of support with usage.  ... 
doi:10.1186/s12920-020-0668-3 pmid:32019565 pmcid:PMC7001226 fatcat:sq2gebnr5jgvvhx4odpayzrqbu

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

Jordi Valls-Margarit, Iván Galván-Femenía, Daniel Matías-Sánchez, Natalia Blay, Montserrat Puiggròs, Anna Carreras, Cecilia Salvoro, Beatriz Cortés, Ramon Amela, Xavier Farre, Jon Lerga-Jaso, Marta Puig (+9 others)
2022 Nucleic Acids Research  
The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with Mononeuritis of lower limb, a rare neuromuscular disease.  ...  However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels).  ...  ACKNOWLEDGEMENTS We thank Dr Lluís Puig and Vanessa Plegezuelos on behalf of Blood and Tissue Bank from Catalonia (BST), who collaborated in GCAT recruitment, and all the GCAT volunteers that participated  ... 
doi:10.1093/nar/gkac076 pmid:35176773 pmcid:PMC8934637 fatcat:lo4xvqbimjfypm62kokt6acpja

Defining a strategy to introduce a software product line using existing embedded systems

Kentaro Yoshimura, Dharmalingam Ganesan, Dirk Muthig
2006 Proceedings of the 6th ACM & IEEE International conference on Embedded software - EMSOFT '06  
Engine Control Systems (ECS) for automobiles have numerous variants for many manufactures and different markets.  ...  We did a clone analysis to provide the basis for effort estimation for merge potential assessment of existing variants. We also report on a case study with ECS.  ...  Acknowledgement It is our pleasure to thank the Hitachi Research Laboratory and Engine Management Systems business unit for fruitful  ... 
doi:10.1145/1176887.1176897 dblp:conf/emsoft/YoshimuraGM06 fatcat:dryjzpa2ing5lko6z3i5ig26cy

Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform

Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara, Paul Scheet
2018 BMC Bioinformatics  
Visual validation of 434 called variants was performed, and performance of the methods assessed individually and in combination.  ...  This study suggests combined strategies to maximize sensitivity and positive predictive value in variant calling using IONT deep sequencing.  ...  Availability of data and materials The called variant dataframe and python script for relaxed variant filtering are available at http://scheet.org/pubs.html.  ... 
doi:10.1186/s12859-017-1991-3 pmid:29301485 pmcid:PMC5753459 fatcat:g7slyj3j6fhbhnmdas2343hyxi

Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery

Yury A. Barbitoff, Ruslan Abasov, Varvara E. Tvorogova, Andrey S. Glotov, Alexander V. Predeus
2022 BMC Genomics  
calling software.  ...  In our benchmark, Bowtie2 performed significantly worse than other aligners, suggesting it should not be used for medical variant calling.  ...  Acknowledgements We thank the financial assistance provided by the Systems Biology Fellowship to Y.A.B. and the Presidential Fellowship for Young Scientists (SP-4503.2021.4) to Y.A.B.  ... 
doi:10.1186/s12864-022-08365-3 pmid:35193511 pmcid:PMC8862519 fatcat:wu2tgd7w6jcnnd43dolf5glkgm

An Information Retrieval Approach for Regression Test Prioritization Based on Program Changes

Ripon K. Saha, Lingming Zhang, Sarfraz Khurshid, Dewayne E. Perry
2015 2015 IEEE/ACM 37th IEEE International Conference on Software Engineering  
An empirical evaluation using eight open-source Java projects shows that REPiR is computationally efficient and performs better than existing (dynamic or static) techniques for the majority of subject  ...  A vast majority of these techniques are based on dynamic analysis, which can be precise but can also have significant overhead (e.g., for program instrumentation and test-coverage collection).  ...  At test-method level the mean APFD achieved by REPiR are 0.73 using LDiff and REPiR performs better than all total strategies, and performs equally well or better than additional strategies.  ... 
doi:10.1109/icse.2015.47 dblp:conf/icse/SahaZKP15 fatcat:yxl4h7r2zbeepf46mjy35strv4
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