Search Results for "cite"
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Showing 35 open source projects for "cite"
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
...Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ, please cite this preprint: 123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads https://www.biorxiv.org/content/10.1101/2024.03.08.584032v1 ########################################################## Take care of the details and ensure you use the latest version. We hope this helps... -
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
...It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
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BD-Func
Bidirectional Functional Enrichment of Gene Expression Data
BD-Func is an algorithm to predict activation or inhibition of pathways based upon gene expression patterns. If you use BD-Func, please cite: Warden C, Kanaya N, Chen S, and Yuan Y-C. (2013) BD-Func: A Streamlined Algorithm for Predicting Activation and Inhibition of Pathways. peerJ, 1:e159 -
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MolMarker
Java software to evaluate the results obtained by molecular markers
Journal article to cite: Jahnke, G.; Smidla, J.; Poczai, P. MolMarker: A Simple Tool for DNA Fingerprinting Studies and Polymorphic Information Content Calculation. Diversity 2022, 14, 497. https://doi.org/10.3390/d14060497 Leave a review, please! Your opinion matters! :-) MolMarker is user-friendly software to help evaluate the research results obtained by molecular markers. -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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GMOL
A tool for 3D genome structure visualization
...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 GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. "GMOL: an interactive tool for 3D genome structure visualization." Scientific reports 6 (2016): 20802. -
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Bibreducer
Filter out not cited bibliographic entries
Use this to remove all unused entries in bibliographic files (.bib). Keys used with cite, citep and citet commands in the manuscript will be kept by default. More commands may be added. -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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ApkFor 1.0
ApkFor helps to transfer forest growth and yield models using Android
...ApkFor was developed by Fernando PÉREZ-RODRÍGUEZ (fernando.perez@fora.es) and Maria MENÉNDEZ-MIGUÉLEZ. The project and Code are Beta and could be improved and re-used by anyone. In this case cite font as follows: "PÉREZ-RODRÍGUEZ F., MENÉNDEZ-MIGUÉLEZ M. 2017. ApkFor: Project and Code. https://sourceforge.net/projects/apkfor/" This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 613762 -
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Service Grid - Language Grid Base System
SOA infrastracture initially developed by NICT Language Grid Project
...[SOFTWARE] is one of: * Service Grid Server Software (http://langrid.org/oss-project/en/service_grid.html) * Language Service Development Libraries (http://langrid.org/oss-project/en/language_service.html) * Language Grid Toolbox (http://langrid.org/oss-project/en/toolbox.html) If you publish a paper by using the software of this project, please cite the following book. * Toru Ishida Ed. The Language Grid: Service-Oriented Collective Intelligence for Laguage Resource Interoperability. Springer, 2011. ISBN 978-3-642-21177-5. -
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EntOpt Layout
Relative entropy optimization network layout plugin
The goal of this project is to implement a graph layout / network visualization algorithm as a Java plugin for Cytoscape (http://cytoscape.org/), using a recently published relative entropy optimization based method, called Unified Data Representation (Kovács IA et al. Sci Rep. 2015). If you are using the plugin, please cite: Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks, Bioinformatics 35(21):4490-4492 https://academic.oup.com/bioinformatics/article/35/21/4490/5475596 Our detailed Tutorial on the use of the plugin: https://suopte.com/entopt_2_1_tutorial_20200518.pdf A video about the version 2.1: http://suopte.com/entopt_2_1_tutorial_video.mp4 Don't hesitate to send any questions, comments or bug reports also to agg.bence {at} med.semmelweis-univ.hu. -
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SmartRoot
Semi-automated root image analysis software
...SmartRoot is an operating system independent freeware based on ImageJ and uses cross-platform standards (XML, SQL, Java) for communication with data analysis softwares. To cite us: Guillaume Lobet, Loïc Pagès and Xavier Draye. A Novel Image Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture. 2011 Plant Physiology, Vol. 157 -
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Priority Estimation Tool (AHP)
PriEsT is a decision making tool for Analytic Hierarchy Process (AHP).
...After defining criteria, PriEsT allows you to enter your judgements against each criterion, which are then used to calculate the final ranking (or weights). Please cite this if you find it useful:- Siraj, S., Mikhailov, L. and Keane, J. A. (2015), "PriEsT: an interactive decision support tool to estimate priorities from pairwise comparison judgments". International Transactions in Operational Research. 22: 217–235. doi:10.1111/itor.12054 -
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JCLAL
A Java Class Library for Active Learning
...It is constructed with a high-level software environment, with a strong object oriented design and use of design patterns, which allow to the developers reuse, modify and extend the framework. If you want to refer to JCLAL in a publication, please cite the following JMLR paper. The full citation is: Oscar Reyes, Eduardo Pérez, María del Carmen Rodríguez-Hernández, Habib M. Fardoun, Sebastián Ventura. JCLAL: A Java Framework for Active Learning. Journal of Machine Learning Research, 17(95):1-5, 2016. -
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RoWordNetLib
Java API for the Romanian WordNet
...Please note that the actual WordNet for Romanian (the XML file containing the network) is not included, it can be obtained (due to its license restrictions) from: http://ws.racai.ro:9191/repository/browse/romanian-wordnet-30/4611a43efb6811e2a8ad00237df3e3580b6b50d1111c4a6292694bded91d5c14/ **** If you would like a direct download of the API containing the RoWordNet xml file, please download them both from : http://www.racai.ro/tools/text/rowordnet/ **** Please cite: Dumitrescu, Ștefan Daniel. RoWordNetLib - The first API for the Romanian WordNet. In Proceedings of the Romanian Academy, Series A (The Publishing House of the Romanian Academy). vol. 16, no. 1, pp. 87--94, 2015 Article PDF at: http://www.acad.ro/sectii2002/proceedings/doc2015-1/12-Dumitrescu.pdf It's free for research use. ... -
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.... _______________________________________ Please have also a look on our info page about other NetLogo extensions at http://www.uni-goettingen.de/en/315075.html. _______________________________________ Please cite this software in scientific publications as: Thiele, JC; Grimm, V (2010). NetLogo meets R: Linking agent-based models with a toolbox for their analysis. Environmental Modelling and Software, Volume 25, Issue 8: 972 - 974
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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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SENDIM
Simulation, Emulation and Deployment Integration Middleware
SENDIM for Incremental Development of Cloud Networks An Orchestration Middleware for Incremental Development of Software-Defined Cloud Networks. This projects forks and builds on top 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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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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GESPA
Accurately predicts disease association of single nucleotide mutations
...GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a -
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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 -
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IRToolkit
IRToolkit
...Furthermore, it offers a capability to compare the performance (in terms of precision, recall, index size, search response time and so on) between several open source IR applications. If you use the IRToolkit please cite the following work: https://sites.google.com/site/dinhbaduy/bibtex#Dinh-Phdthesis-2012 -
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gannu
Java API and tools for performing NLP and other AI tasks
...Gannu uses the following projects: Weka, JExcel API, Stanford POS Tagger and WordNet. Please cite them when using Gannu.