Search Results for "cite" - Page 3
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Showing 206 open source projects for "cite"
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DEPRECATED - KVFinder
Cavity Detection PyMOL plugin
...[parKVFinder] A Linux/macOS version is available in this GitHub repository, https://github.com/LBC-LNBio/parKVFinder, while a Windows version is in this GitHub repository, https://github.com/LBC-LNBio/parKVFinder-win. Please read and cite the original paper ParKVFinder: A thread-level parallel approach in biomolecular cavity detection (10.1016/j.softx.2020.100606). [pyKVFinder] pyKVFinder is available in this Python Package Index (PyPI) repository, https://pypi.org/project/pyKVFinder and this GitHub repository, https://github.com/LBC-LNBio/pyKVFinder. Please read and cite the original paper pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science (10.1186/s12859-021-04519-4). -
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...If you have any questions, please contact Shengmin Zhou(email: 2495077522@qq.com or 220180304@seu.edu.cn). If you want to download this project and use it, please cite the paper: Zhou, S., Li, B. & Nie, H. Parametric fitting and morphometric analysis of 3D open curves based on discrete cosine transform. Zoomorphology (2021). https://doi.org/10.1007/s00435-021-00520-w
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DeepMind Lab
A customizable 3D platform for agent-based AI research
...Its primary purpose is to act as a testbed for research in artificial intelligence, especially deep reinforcement learning. If you use DeepMind Lab in your research and would like to cite the DeepMind Lab environment, we suggest you cite the DeepMind Lab paper. To enable compiler optimizations, pass the flag --compilation_mode=opt, or -c opt for short, to each bazel build, bazel test and bazel run command. The flag is omitted from the examples here for brevity, but it should be used for real training and evaluation where performance matters. ... -
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IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Please cite: Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. LNBI. 4463:394-405.
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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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vipie
http://vipie.rd.tuni.fi/vipie/index.html
Open access and web based virome population profiling for multi-sample metagenomics NGS, please note that the web server has been updated to: http://vipie.rd.tuni.fi/vipie/index.html Now supporting COVID-19 User guide: http://vipie.rd.tuni.fi/vipie/doc/vipie_user_guide.pdf Open access: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3721-7 Please cite: Lin, J., Kramna, L., Autio, R. et al. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples. BMC Genomics 18, 378 (2017). https://doi.org/10.1186/s12864-017-3721-7 -
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APAtrap
Identification of APA sites from RNA-seq data
... [2] APAtrap Q&A For Q&A, please visit the Blog page of this website. [3] APAtrap bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite APAtrap? Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 34(11): 1841–1849. https://academic.oup.com/bioinformatics/article/34/11/1841/4816794 -
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MetaPhat -meta-pheno-association-tracker
Multivariate traits genome-wide association analysis and decomposition
...released with LD function https://sourceforge.net/projects/meta-pheno-association-tracer/files/Dist/meta_phat.tar.gz/download Quick start https://sourceforge.net/p/meta-pheno-association-tracer/wiki/Quick%20Start Inputs https://sourceforge.net/p/meta-pheno-association-tracer/wiki/Inputs Global Lipids example https://sourceforge.net/p/meta-pheno-association-tracer/wiki/Installation_global_lipids Cite: Lin et al. (2020) MetaPhat: Detecting and decomposing multivariate associations from univariate genome-wide association statistics. Front. Genet. doi: 10. -
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MaxBin
An automatic tool for binning metagenomics sequences
...Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.7. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. -
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TauFactor
MatLab App for calculating the tortuosity factor of microstructure
Please contact the author at sjc08@ic.ac.uk for any questions or if you wish to cite this application in a academic study. Journal paper available here: http://www.sciencedirect.com/science/article/pii/S2352711016300280 TauFactor is a MatLab application for efficiently calculating the tortuosity factor, as well as volume fractions, surface areas and triple phase boundary densities, from image based microstructural data. -
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Phenalysis
Analyze agronomic plant research plots in aerial orthomosaic images.
A graphical user interface to import, analyze and export plots from orthomosaic images of agronomic trials. Please cite the following reference in your work if you use Phenalysis: Khan Z and Miklavcic SJ (2019) An Automatic Field Plot Extraction Method From Aerial Orthomosaic Images. Front. Plant Sci. 10:683. doi: https://doi.org/10.3389/fpls.2019.00683 This tool is being developed through the sponsorship of the Australian Research Council's Industrial Transformation Research Hub on Wheat in a Hot and Dry Climate. ... -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub repository: https://github.com/xiaoli-dong/metaerg -
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artext
Probabilistic Noising of Natural Language
...This kind of data can be useful for many NLP tasks, particulary to make models robust to erroneous text. This is a work in progress, and we will publish the results of our experiments soon. Meanwhile, if you use artext in your research please cite this repository. Github: https://github.com/nlpcl-lab/artext -
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI: 10.1007/s13127-011-0056-0
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
...To install in Linux, follow in-package instructions or visit the VirtualGlycome.org FAQ page. The source code can be edited and run using MATLAB2014b or later. How to Cite: DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information Kai Cheng; Yusen Zhou; Sriram Neelamegham Glycobiology (2017) 27 (3): 200-205 Source code also available at: https://github.com/neel-lab/DrawGlycan-SNFGv2 Abstract & Full Text: https://doi.org/10.1093/glycob/cww115 -
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...PTCLab 支持相变晶体学计算（包括马氏体相变晶体学，扩散型相变的相变晶体学），衍射斑模拟与标定，变体分析，极射投影图，Wulff网。支持主流操作系统。 Researchgate ID: https://www.researchgate.net/profile/Xinfu_Gu2 If you used PTCLab in your work, please cite: Gu, X.-F., Furuhara, T. & Zhang, W.-Z., (2016). J. Appl. Cryst. 49, 1099 –1106.
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FHiTINGS
Fungal High-throughput Taxonomic Identification tool for use with NGS
...This software is useful for fungal ecology studies using next generation sequencing (NGS). See our paper in the Journal of Basic Microbiology (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201200507/pdf) for more information and please cite that paper if you use our program. Thank you for using FHiTINGS! Note: FHiTINGS version 1-4 has been released. This uses an update to the BLAST database used by FHiTINGS. Also note that FHiTINGS must run on Python 2.4-2.7.1 (it will NOT run on Python 3.0 or higher). © 2012 by Karen Dannemiller. FHiTINGS is made available under the terms of the Creative Commons Attribution-ShareAlike 3.0 license, http://creativecommons.org/licenses/by-sa/3.0/. ... -
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ImproveAssembly
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206
The availability of biological information in public databases has increased exponentially. To ensure the accuracy of this information, researchers have adopted several methods and refinements to avoid the dissemination of incorrect information. However, manual curation ensures and enriches biological information. Additionally, the genomic finishing process is complex, resulting in increased deposition of drafts genomes. This introduces bias in other omics analyses because incomplete... -
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Hammurabi Code
Astrophysical magnetic fields simulator
...It is a modular C++ framework into which you can add your own models easily and then use it to perform the line-of-sight integration to compute the observables. See the wiki for installation and usage information. Please cite the original Waelkens et al. (2009) paper if you use hammurabi. This version of Hammurabi is deprecated and is no longer being supported. A new and improved version of Hammurabi (dubbed 'X') is available at : https://bitbucket.org/hammurabicode/hamx -
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VividSTORM
Correlated confocal and SMLM data visualization and analysis
...NOTE: If you encounter issues not addressed by the user guide, please contact by message on this site or via e-mail for additional support: vividstorm[at]koki.mta.hu If you find our software useful in your project, please cite: Correlated confocal and super-resolution imaging by VividSTORM Nature Protocols 11, 163–183 (2016) doi:10.1038/nprot.2016.002 -
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
Please cite: ForceGen: atomic covalent bond constant derivation for Gromacs. Nash A, Collier T, Birch HL, de Leeuw NH. Journal of Molecular Modeling (2018), (24)5. DOI: 10.1007/s00894-017-3530-6 Instruction video: https://youtu.be/fQVXv8Ge_tg This Java executable jar derives second order bond force constants for bond stretch and bond angle from quantum mechanical Gaussian calculations. -
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hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
...The first version handles protein-coding genes, lncRNAs and circRNAs and includes six core-workflows such as (1) Tophat - Cufflink - Cuffdiff; (2) Subread - featureCounts - DESeq2; (3) STAR - RSEM - EBSeq; (4) Bowtie - eXpress - edgeR; (5) kallisto - sleuth; (6) HISAT - StringTie - Ballgown. Please cite the following paper when using this package: Dapeng Wang. hppRNA—a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. Briefings in Bioinformatics, Volume 19, Issue 4, 20 July 2018, Pages 622–626. -
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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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ODFR
Software for simulation of slow motional EPR spectra in aligned media
...The detailed description of all models and approximations used in the program is contained in the following reference: A.Kh.Vorobiev, A.V.Bogdanov, T.S.Yankova, N.A.Chumakova, “Spin probe determination of molecular orientation distribution and rotational mobility in liquid crystals. Model-free approach.”, submitted to Phys. Chem. Chem. Phys., 2018. Please, cite this reference whenever you intend to publish results obtained with the software ODFR. ODFR was created in 2018 in Moscow State University by Prof. Andrey Kh. Vorobiev, mailto: a.kh.vorobiev[[at]]gmail.com -
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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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CIF2Cell
Generating cells for electronic structure calculations from CIF files
...The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files. The program has been published in Computer Physics Communications 182 (2011) 1183–1186. Please cite generously.