Search Results for "cite" - Page 6
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Showing 206 open source projects for "cite"
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FUBI
Full Body Interaction Framework
...Combination of postures and movements: Combines sets of 1 and 2 in a sequence of states with specific time constraints. 4. Symbolic gestures: Gesture with complex shape that are defined by recorded sample data. If you use Fubi in a scientific project, please cite one of the related publications mentioned on the project website. -
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SampleSpecificDBGenerator
Generates custom UniProt-XML databases from RNA-Seq data
SampleSpecificDBGenerator is a program that takes RNA sequencing data analysis results and translates them into protein database entries that are appended to a UniProt-XML file. This XML is condensed, meaning that much of the extraneous author information in UniProt-XMLs is removed for faster search times in Morpheus. Please cite http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00817. -
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CT-Finder
A Web Service for CRISPR Optimal Target Prediction and Visualization
...A visualization of on-target and off-target matches against the chosen reference genome is provided in JBrowse. [1] Who are we? Please visit our website http://bioinfolab.miamioh.edu [2] How to cite CT-Finder? Zhu, H. et al. CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization. Sci. Rep. 6, 25516; doi: 10.1038/srep25516 (2016). http://www.nature.com/articles/srep25516 [3] CT-Finder Installation manual For user manual, please visit the Wiki page of this website. [4] CT-Finder Q&A For Q&A, please visit the Blog page of this website... -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
...Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. If you use the NGS TOOLBOX you for publication purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313. -
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RootGraph
A graphic optimization tool for automad image analysis of plant roots
...The performance of this approach was evaluated through comparisons with other automated and semi-automated software solutions as well as against results based on manual measurements. Please cite: Cai, Jinhai and Zeng, Zhanghui and Connor, Jason N. and Huang, Chun Yuan and Melino, Vanessa and Kumar, Pankaj and Miklavcic, Stanley J. (2015), "RootGraph: a graphic optimization tool for automated image analysis of plant roots" Journal of Experimental Botany, 66(21), pp.6551-6562. -
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RAMBO-K
Read Assignment Method Based On K-mers
RAMBO-K is a tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data. Please cite our publication (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137896) if you use RAMBO-K. We moved to GitLab, please visit our homepage for latest development. The latest stable versions of RAMBO-K will still be provided here. -
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tao-multishell
Shell to work with libgreattao applications
...Libgreattao applications won't run in normal mode, but network mode, so you can use it with tao-multishell. It allow to write script, which use many libgreattao applications. Due to ex. security reasons shell buildin in libgreattao disallow to cite command output or run another command. Tao-multishell fill this gap. -
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SeedBasedBicluster
Seed-based biclustering of Gene Expression Data
please cite: An J, Liew AW-C, Nelson CC (2012) Seed-Based Biclustering of Gene Expression Data. PLoS ONE 7(8): e42431. -
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SoftSV
Calling structural variations. The soft way.
...For more information about the algorithm and an evaluation, have a look at this publication: "Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms" (PMID 25998133) Please cite this artilce if you used SoftSV in your publication. -
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Cross-Language Computational Linguistics
cross-languages resources
...It is composed of 40K aligned articles, 91.3M English words, 57.8M French words, 22M Arabic words, 2.8M English unique words, 1.9M French unique words, and 1.5M Arabic unique words. Wikipedia text is available under Creative Commons Attribution-ShareAlike 3.0 License. https://en.wikipedia.org/wiki/Wikipedia:About To cite the corpora: M. Saad, D. Langlois, and K. Smaïli. Extracting Comparable Articles from Wikipedia and Measuring their Comparabilities. Procedia - Social and Behavioral Sciences, 95(0):40 – 47, 2013. ISSN 1877-0428. -
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CUDA-Quicksort
CUDA-Quicksort: A GPU-based implementation of the quicksort algorithm
CUDA-quicksort is a GPU-based implementation of the quicksort algorithm. CUDA-quicksort is designed to exploit the power computing of modern NVIDIA GPUs. "Two GPU-based implementations of the quicksort were presented in literature: the GPU-quicksort, a compute-unified device architecture (CUDA) iterative implementation, and the CUDA dynamic parallel (CDP) quicksort, a recursive implementation provided by NVIDIA Corporation."[*]. CUDA-quicksort is an iterative GPU-based implementation of the... -
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detectIR
Detection of Perfect and Imperfect Inverted Repeats
detectIR - a MATLAB-based tool for detecting perfect and imperfect inverted repeats in genomes. [1] Who are we? Please visit website: http://bioinfolab.miamioh.edu [2] How to cite detectIR? Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation. PLoS ONE 9(11): e113349. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349 [3] detectIR user manual Please visit the Wiki page of this website... -
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Preference Learning Toolbox
Open source toolbox to create preference models
...Information about how to use and modify the tool is available on the wiki: https://github.com/TAPeri/pl-toolbox/wiki The tool is free for scientific use. If you use PLT in your scientific work, please cite as: Farrugia, Vincent E., Héctor P. Martínez, and Georgios N. Yannakakis. "The Preference Learning Toolbox." arXiv preprint arXiv:1506.01709 (2015) -
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The GVAP is a reliable open access program for analysing different glycaemic variability parameters.
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Golden Retriever-Image Retrieval Engine
Library and frontend engine for performing Image Retrieval tasks.
...The purpose of the project is to help developers create and distribute their methods and test the performance of their BOVW systems in actual databases with minimum effort and without having to deal with every aspect of the model. Please cite: Lazaros T. Tsochatzidis, Chryssanthi Iakovidou, Savvas A. Chatzichristofis, and Yiannis S. Boutalis. 2013. Golden retriever: a Java based open source image retrieval engine. In Proceedings of the 21st ACM International Conference on Multimedia (MM ’13). -
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Gen3D
A tool for 3D genome and chromosome structural model construction
...Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use Gen3D in your research, please cite: Nowotny, Jackson, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao, and Jianlin Cheng. "Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data." BMC bioinformatics 16, no. 1 (2015): 338. -
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Concept Extractor
Concept Extractor
...The cancer (C0027651, Neoplasms) cells (C0007634, Cells) produce and release a male (C0024554, Male) sex hormone (C0036884, Gonadal Steroid Hormones)... If you use the cxtractor, please cite the following work: https://sites.google.com/site/dinhbaduy/bibtex#Dinh-Phdthesis-2012 -
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...ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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SOAPdenovo2
Large-size genome de-novo assembler
...It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. Cite the paper published in GigaScience (see website below) if you want to cite SOAPdenovo2. -
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STELLA Data Reduction Pipeline
The STELLA Data-Reduction Pipeline for all kinds of Spectra
The STELLA pipeline and all sources are now available for download. If you encounter any problems, please send an email to azuri.ritter@gmail.com. If you use any of these programs to reduce data for a publication you must cite the paper "A Fast and Portable Reimplementation of Piskunov and Valenti's Optimal Extraction Algorithm with improved Cosmic Ray Removal and Optimal Sky Subtraction" by A. Ritter, E. A. Hyde, and Q. A. Parker, published in PASP 126, February 2014. -
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Automatic cell lineage reconstruction
Automatic segmentation and tracking for 3D time-lapse microscopy
...We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities." *Please cite this paper if you use this code for your research -
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MASS KIR Analyzer provides a Graphical User Interface to analyze the KIR genotyping data taking into consideration the KIR gene content diversity among intra and inter population(s). This is a quite useful software as it may increase the accuracy of KIR data which otherwise may reveal many errors while doing the manual calculations. How to cite: Pandey M, Sarangi AN, Prakash S, Agrawal S.MASS KIR Analyzer: An In Silico Approach for Analyzing the Killer Immunoglobulin Receptor Gene Content and its Diversity. Current Bioinformatics. 2015 July; Vol 10 (3): 292-298(7). DOI: 10.2174/1574893609999140918200855 To obtain the software MASSKIRanalyzer, download the registration form (http://sourceforge.net/projects/masskiranalyzer/files/MASSKIRAnalyzer%20Registration%20Form.pdf/download) fill it and please email to masskiranalyzer@gmail.com
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CCH
A genetics tool that identifies genomic regions of shared ancestry
...CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry. The associated publication regarding CCH may be accessed here: http://www.biomedcentral.com/1471-2164/16/163 If you use CCH please cite: Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP. Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies. BMC Genomics. 2015 Dec;16(1):1360. doi: 10.1186/s12864-015-1360-4. Epub 2015 Mar 10. -
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Soft-DeCO
Software-Defined Cloud Orchestration
Software-Defined Cloud Orchestration: An Integrated Architecture and Deployment Process This is an expansion of the project xSDN, an Expressive Simulator for Dynamic Network Flows. Please cite the below papers, if you used this project or referred to this in your work. Kathiravelu, Pradeeban; Veiga, Luis, "An Expressive Simulator for Dynamic Network Flows," Cloud Engineering (IC2E), 2015 IEEE International Conference on , vol., no., pp.311,316, 9-13 March 2015 doi: 10.1109/IC2E.2015.43 -
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SDNSim
A Compact Simulator for Software-Defined Networking and Systems
SDNSim, A Compact Simulator for Software-Defined Networking This is an expansion of the project xSDN, an Expressive Simulator for Dynamic Network Flows. Please cite the below papers, if you used this project or referred to this in your work. Kathiravelu, Pradeeban; Veiga, Luis, "An Expressive Simulator for Dynamic Network Flows," Cloud Engineering (IC2E), 2015 IEEE International Conference on , vol., no., pp.311,316, 9-13 March 2015 doi: 10.1109/IC2E.2015.43