Search Results for "publication"
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Showing 66 open source projects for "publication"
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Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
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Apache Maven
Apache Maven core
Maven is a project development management and comprehension tool. Based on the concept of a project object model: builds, dependency management, documentation creation, site publication, and distribution publication are all controlled from the pom.xml declarative file. Maven can be extended by plugins to utilize a number of other development tools for reporting or the build process. -
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ORCID-Source
ORCID Open Source Project
The official source code for ORCID (Open Researcher and Contributor ID), an open-source platform that helps researchers maintain a unique identifier for their academic work. -
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Booklore
Digital library with smart shelves
Booklore is a comprehensive self-hosted digital library platform that helps readers organize, manage, track, and even read their personal collections of books and comics from a centralized web interface. It provides powerful metadata management that automatically fetches rich details like titles, authors, covers, and publication info so your library looks organized and beautiful without manual data entry. Users can create smart shelves with custom filters, build dynamic collections that update automatically, and search through thousands of entries instantly, turning chaotic folders of files into a curated reading experience. Booklore supports multi-user access with granular permission controls, making it suitable for families, book clubs, or shared collections, and its built-in reader can display PDFs, EPUBs, and comic formats directly in a browser. -
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Moshidon
Better modification of the official Mastodon for Android app
Moshidon is a modified version of the Mastodon official application for Android, which adds important features missing from the official application, such as a joint timeline, no Public publication, and an image description viewer. -
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GROBID
A machine learning software for extracting information
...References extraction and parsing from articles in PDF format, around .87 F1-score against on an independent PubMed Central set of 1943 PDF containing 90,125 references, and around .89 on a similar bioRxiv set of 2000 PDF (using the Deep Learning citation model). All the usual publication metadata are covered (including DOI, PMID, etc.). -
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HEALPix
Data Analysis, Simulations and Visualization on the Sphere
Software for pixelization, hierarchical indexation, synthesis, analysis, and visualization of data on the sphere. Please acknowledge HEALPix by quoting the web page http://healpix.sourceforge.net (or https://healpix.sourceforge.io) and publication: K.M. Gorski et al., 2005, Ap.J., 622, p.759 Full software documentation available at https://healpix.sourceforge.io/documentation.php Wiki Pages: https://sourceforge.net/p/healpix/wiki/Home Exchanging Data with HEALPix (in FITS files): https://sourceforge.net/p/healpix/wiki/Exchanging%20Data%20with%20HEALPix/ GDL and FL users should read https://sourceforge.net/p/healpix/wiki/HEALPix%20and%20GDL/ -
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multinotes
Text architecture for music theory.
...Furthermore, dynamic interactive documents can be useful for presenting complicated interdependencies to the reader more clearly, far beyond conventional paper publication. The mulitNotes text architecture and processing pipeline is based on d2d and standard technologies (XSLT, ECMAScript. LilyPond, PostScript, etc.) and addresses these issues. An overview about the software architecture and its operation is given in: Journal of the Text Encoding Initiative, Open Issue 18/2024: "Using d2d for Writing XML --- The multiNotes Text Architecture for Musical Analysis" https://doi.org/10.4000/132ex -
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Megalodon
Pink modification of the official Mastodon for Android app
Megalodon is a modified version of the Mastodon official application for Android with many features missing from the official app, such as the Timeline federation, posting unlisted posts and the ability to view image descriptions. -
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Mjograph is an XY (2D) graph editor that runs on Mac OSX and Java with the goal to provide researchers with a quick way to visualize numerical data and also create publication-quality plots.
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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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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....
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Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).
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PPIXpress
specific protein interaction networks from transcript expression
...Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 . -
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CompleXChange
differential analysis of combinatorial protein complexes
...With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
...The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. The original publication can be found on http://bioinformatics.oxfordjournals.org/content/30/17/i415 . -
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ProMoVis
A Tool for Control Structure Selection in Interconnected Processes
...ProMoVis is not limited to the control structure selection problem as additional analysis methods can be added easily. For the re-use of existing models a Modelica interface is under development. If you want to refer to ProMoVis in a publication, please use the following: "Wolfgang Birk, Miguel Castaño, Andreas Johansson, An application software for visualization and control configuration selection of interconnected processes, Control Engineering Practice, Volume 26, May 2014, Pages 188-200." -
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Docmenta
Single Source Publishing Web-Application
Docmenta is a Java web-application for single source publishing and help authoring. The application allows collaborative creation of documentation, e-books and online-help. Supported output formats are PDF, HTML, WebHelp, EPUB (eBook) and DocBook. For more information, visit: http://www.docmenta.org -
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PPICompare
detection of rewiring events in protein interaction networks
PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x. -
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JPIV
Particle Image Velocimetry
JPIV is a platform independent, graphical stand-alone application for Particle Image Velocimetry (PIV) written in Java. PIV is an optical technique for measuring fluid flow velocities. JPIV moved to GitHub. Please visit us at: https://eguvep.github.io/jpiv/ -
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Point Symmetry Clustering
Point Symmetry Clustering Approach Using Differential Evolution
...(It is also modified to search for multiple nearest points instead only for one.) Used those academic works for algorithm implementation: http://cs.cug.edu.cn/teacherweb/gwy/Publication/ISICA-09.pdf http://www.isical.ac.in/~sanghami/ieeetkde_cameraready.pdf http://www.softcomputing.net/smca-paper1.pdf 1. You may download code: git clone git://git.code.sf.net/p/pointsymmetryclustering/code pointsymmetryclustering-code 2. Build: mvn clean install assembly:assembly -DskipTests -Dmaven.test.skip=true -DdownloadSources=true -Dcheckstyle.skip=true 3. ... -
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Format-Preserving Encryption
Format-Preserving Encryption Library for Java
This package implements the FF1, FF3, and FFX algorithms and the A2 and A10 parameter sets for format-preserving encryption. The FF1 and FF3 methods for format-preserving encryption are implementations of NIST Special Publication 800-38G, Recommendation for Block Cipher Modes of Operation: Methods for Format-Preserving Encryption. The FFX algorithm and A2 and A10 parameter sets are implementations of "The FFX Mode of Operation for Format-Preserving Encryption," by Mihir Bellare, Phillip Rogaway, and Terence Spies. For more information see the README.txt and package-info.java files in the source. -
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DORY
For mining KASH proteins (SUN domain-interacting proteins)
DORY is a java program developed for searching KASH protein in large protein databases (in FASTA format). DORY is upgraded to DORY2. DORY2 required BLAST+ to run. ***Please make sure BLAST+ is installed on your computer.*** Please see the following publication for detail: Zhou X, Graumann K, Wirthmueller L, Jones JDG, Meier I (2014) Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants. The Journal of Cell Biology 205(5):677-692. http://jcb.rupress.org/content/205/5/677.full Please see other useful tools for biology research: https://sourceforge.net/projects/cloversystem/?... -
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Cambridge Rocketry Simulator
Simulate high power rocket flights with splash down plots
...Running in Monte Carlo mode allows generates multiple possible flight paths and splash down plots, indicating the probability of landing in an area. Peer-reviewed publication in the Journal of Open Research Software (JORS) http://doi.org/10.5334/jors.137 "Cambridge Rocketry Simulator – A Stochastic Six-Degrees-of-Freedom Rocket Flight Simulator" -
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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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GUITAR - A GUI Testing Framework
A model-based test automation framework for GUI applications
...Software developers and quality assurance engineers may use this architecture to create new toolchains, new workflows based on the toolchains, and plug in a variety of measurement tools to conduct GUI testing. More detail is presented in this publication: GUITAR: An Innovative Tool for Automated Testing of GUI-driven Software. Bao N. Nguyen, Bryan Robbins, Ishan Banerjee, and Atif Memon. Automated Software Engineering Journal. p.21, 1. 2014 -
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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.
