Search Results for "cite"
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Showing 252 open source projects for "cite"
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Alphafold
Open source code for AlphaFold
This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from using this source code or the model parameters should cite the AlphaFold paper. Please also refer to the Supplementary Information for a detailed description of the method. You can use... -
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adstex
Automated generation of NASA ADS bibtex entries directly from citation
adstex automatically identifies all citation keys (e.g., identifiers, author+year) in your TeX source files and uses NASA's Astrophysics Data System (ADS) to generate corresponding bibtex entries. Write your papers without worrying about the bibtex entries. Simply put down arXiv IDs, ADS bibcodes, DOIs, or first author & year citation keys in your \cite commands, and then use adstex to automatically generate the bibtex file for you. -
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BQSKit
Berkeley Quantum Synthesis Toolkit
The Berkeley Quantum Synthesis Toolkit (BQSKit) [bis • kit] is a powerful and portable quantum compiler framework. It can be used with ease to compile quantum programs to efficient physical circuits for any QPU. A standard workflow utilizing BQSKit consists of loading a program into the framework, modeling the target QPU, compiling the program, and exporting the resulting circuit. -
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Zettlr
A Markdown Editor for the 21st century
.... And the best is, unlike many competitors, Zettlr never locks you in. Zettlr supports almost every conceivable way to create links and identify your files. In other words: No matter where you come from — all Zettelkästen are beautiful and supported by Zettlr. Out of the box. Zettlr integrates well with reference managers such as Zotero, JabRef, or Juris-M. Simply load your library into Zettlr, and begin to cite. Zettlr strictly adheres to established standards and does not reinvent the wheel. -
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Krylov.jl
A Julia Basket of Hand-Picked Krylov Methods
If you use Krylov.jl in your work, please cite it using the metadata given in CITATION.cff. -
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Citar
Emacs package to quickly find and act on bibliographic references
Emacs package to quickly find and act on bibliographic references, and edit org, markdown, and latex academic documents. Citar provides a highly configurable completing-read front-end to browse and act on BibTeX, BibLaTeX, and CSL JSON bibliographic data, and LaTeX, markdown, and org-cite editing support. -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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MatCont
Numerical Bifurcation Analysis Toolbox in Matlab
MatCont is a Matlab software project for the numerical continuation and bifurcation study of continuous and discrete parameterized dynamical systems. Leaders of the project are Willy Govaerts (Gent,B) and Yuri A. Kuznetsov (Utrecht,NL) and Hil G.E. Meijer (UT, Enschede, NL). Matcont for ODEs and MatcontM for Maps Publishing a paper using our software? That's great. Please do us a favour and cite: New features of the software MatCont for bifurcation analysis of dynamical systems... -
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ToxTrac
Free Animal Tracking Software
ToxTrac is a free Windows program optimized for tracking animals. It uses an advanced tracking algorithm and includes Preprocessing, Background subtraction, Thresholding, Post-processing, and Filters. It is robust; very fast; and can handle one or several animals in one or several environments. The program provides useful statistics as output. ToxTrac can be used for fish, insects, rodents, etc. If used, please cite: Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., Andersson, P. L... -
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AnaSP
AnaSP, a MATLAB software suite to ANAlyse SPheroids' features
... modular architecture and graphical user interface make it attractive also for non-Computer Scientist people, and suitable for both high content screenings and occasional spheroid-based experiments. Please, when using AnaSP, cite: "F. Piccinini, AnaSP: a software suite for automatic image analysis of multicellular spheroids. Computer Methods and Programs in Biomedicine, 119(1):43-52, 2015." Requirements: MATLAB R2022a or later versions. -
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... appreciate that you could cite this work: FeAture Explorer (FAE): A tool for developing and comparing radiomics models. PLoS One. 2020. DOI: https://doi.org/10.1371/journal.pone.0237587 * The released Windows64 version depends on VC_redist.x64 and OpenSSL * The Video: https://www.bilibili.com/video/BV1J14y1i73p
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Weinberg-R2R
Faster creation of aesthetic RNA secondary structure diagrams
R2R is a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules. R2R is freely available under the GNU Public License, and runs as a command-line program under UNIX-like systems such as Linux, MacOS Darwin or Cygwin on Windows. R2R was written by Zasha Weinberg. If you use it, please cite this paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-3 -
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Artifact3-D
Artifact3-D: 3D Analysis and Documentation of Archaeological Artifacts
Artifact3-D offers a suite of functions for analysing 3D scans of archaeological artifacts. These functions are repeatable, objective, precise, and customizable. Functions are also available for the neat documentation of artifacts. Individual artifacts can be imported, analyzed and their documentation exported, or entire assemblages can be automatically analyzed. Please cite: Grosman L, et al. (2022) Artifact3-D: New software for accurate, objective and efficient 3D analysis... -
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Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families. Especially, it supports whole genome sequencing data even with low sequencing depth. If you use Lep-MAP3, please cite P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494. Please note Lep-Anchor...
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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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ArchCUT3-D
ArchCUT3-D: 3-D Analysis of Incised Archeological Surfaces
Software developed to precisely evaluate the 3-D micromorphological characteristics of archaeological surface incisions. Analysis is based on a continuous 3-D sliced sequence from a chosen range within the incision path. Measurements and shapes of individual slices can be extracted. ArchCUT3-D’s interface is designed to provide a computational and mathematical analysis of engravings approachable to a wide audience. Please cite Dubinsky, L., David, M., & Grosman, L. (2023). Recognizing... -
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OCTAVA is designed for quantitative characterization of microvascular archetecture based on OCTA images OCTAVA is available free for use under an MIT licence. If you use this software in your research, please cite the following papers: Untracht, G.R., Durkee, M.S., Zhao, M. et al. Towards standardising retinal OCT angiography image analysis with open-source toolbox OCTAVA. Sci Rep 14, 5979 (2024). https://doi.org/10.1038/s41598-024-53501-6 Untracht GR, Matos RS, Dikaios N, Bapir M...
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
..., 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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SecurePose
Automated Face Blurring, Kinematics Extraction and Leg dystonia Dx
... and blurring and outperformed human performance in leg dystonia identification. This validation establishes its effectiveness and usability in clinically recorded gait videos for face blurring and kinematics extraction. For installation, https://www.rishabh-bajpai.com/secureposeinstallation Tutorial Videos https://www.youtube.com/playlist?list=PLO4_jCYO5Ib23MoBpn-Wpj1_b6DAYlDwk Please cite the paper: https://arxiv.org/abs/2402.14143 -
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TRACK code
Code for finding the transport properties using Kubo formalism.
... using interacting (DFT+DMFT) and non-interacting (DFT) electronic structure methods. It is possible to use the relaxation time approximation in this code with the eigenvalues of DFT method. In present version, the code is interfaced with WIEN2k and eDMFTF codes. Please cite the paper mentioned below while using the TRACK code for your research. A. Sihi and S. K. Pandey, Comput. Phys. Commun. 285, 108640 (2023). Link of the paper: https://doi.org/10.1016/j.cpc.2022.108640 -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1. Vengadesan, K. & Gautham, N. Enhanced sampling...
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
...://plateeditor.sourceforge.io - The source code is also available on GitHub, visit: https://github.com/vindelorme/PlateEditor More information about the source code and the API are available there (the wiki is still under construction, thanks for your patience!) For a list of recent updates, visit: https://sourceforge.net/p/plateeditor/wiki/Updates/ Hoping PlateEditor will make your life easier in the lab! If yes, please cite us: https://doi.org/10.1371/journal.pone.0252488 -
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The proper way to cite TRAUPIXE is: L. Pichon, T. Calligaro, Q. Lemasson, B. Moignard, C. Pacheco, Programs for visualization, handling and quantification of PIXE maps at the AGLAE facility, Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. At. 363 (2015) 48–54. https://doi.org/10.1016/j.nimb.2015.08.086.
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. 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... -
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PH-NODE
Code for finding phonon nodes using first-principle approach.
PH-NODE is a Python 3 based code designed for finding topological phonon nodes (branch-degenerate points) in a material using first-principle approach. It is a density-functional perturbation theory and finite displacement supercell based software package for efficiently computing phonon nodes present in real material. The present version of the code is interfaced with the WIEN2k, Elk, and ABINIT packages. Please cite the paper mentioned below while using the PH-NODE code for your research...