A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification. by Loïc Omnes, Eric Angel, Pierre Bartet, François Radvanyi, Fariza Tahi

“…We show that our approach exhibits superior performance compared to state-of-the-art methods for pseudoknot prediction and secondary structure prediction including pseudoknots for long RNAs. The source code of DivideFold, along with all the datasets used in this study, is accessible at https://evryrna.ibisc.univ-evry.fr/evryrna/dividefold/home.…”
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GELSTATS: A Computer Program for Population Genetics Analyses Using VNTR Multilocus Probe Data by Steven H. Rogstad, Stephan Pelikan

“…GELSTATS, a computer program for population genetics analyses utilizing genetic markers revealed with variable number tandem repeat (VNTR) multilocus probes, is described and made available (both as C++ source code and as an executable DOS program). The program calculates several population genetics parameters, including: (i) individual and population band numbers; (ii) population bands exhibiting complete linkage (redundant examples of such bands can be removed in subsequent analyses); (iii) similarity (fraction of bands shared) between individuals and average similarity within and between designated groups; (iv) estimated probability that two individuals chosen at random will have identical band profiles; (v) heterozygosity estimates for designated groups; and (vi) Fst estimates. …”
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PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. by Robert Kofler, Pablo Orozco-terWengel, Nicola De Maio, Ram Vinay Pandey, Viola Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer

“…PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. …”
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Automatic Documentation of Java Programs by Dujan Taha, Asmaa Thanoon

“…The work concerns with constructing an automated tool ADT(Auto Documentation Tool) used for documenting source code for programs written in java programming languages in legacy systems particularly and for programs in general which does not have any documentation at all or it were documented poorly in order to make them, and producing as a result of the document process either the class diagrams using UML (Unified Modeling Language( or producing easy understandable textual output using XML (Extensible Markup Language).…”
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RNAtango: Analysing and comparing RNA 3D structures via torsional angles. by Marta Mackowiak, Bartosz Adamczyk, Marta Szachniuk, Tomasz Zok

“…Compatible with all modern web browsers, RNAtango is accessible freely along with the source code. It supports researchers in accurately assessing structural similarities, which contributes to the precision and efficiency of RNA modeling.…”
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High-Density Surface EMG Decomposition: Achievements, Challenges, and Concerns by Maoqi Chen, Ping Zhou

“…As varying high-density surface EMG decomposition programs are increasingly developed, we call for open access or sharing of source code and testing data developed by different groups. …”
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Understanding Open Source Software Evolution Using Fuzzy Data Mining Algorithm for Time Series Data by Munish Saini, Sandeep Mehmi, Kuljit Kaur Chahal

“…Source code management systems (such as Concurrent Versions System (CVS), Subversion, and git) record changes to code repositories of open source software projects. …”
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Jolie Static Type Checker: a Prototype by Daniel de Carvalho, Manuel Mazzara, Bogdan Mingela, Larisa Safina, Alexander Tchitchigin, Nikolay Troshkov

“…Static verification of a program source code correctness is an important element of software reliability. …”
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MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm. by Chao Wang, Quan Zou

“…We anticipate MFPSP to serve as a valuable bioinformatics tool and benefiting practical experiments by pre-screening potential phosphorylation sites and enhancing our functional understanding of phosphorylation modifications in fungi. The source code and datasets are accessible at https://github.com/AI4HKB/MFPSP/.…”
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From spots to cells: Cell segmentation in spatial transcriptomics with BOMS. by Ocima Kamboj, Jeongbin Park, Oliver Stegle, Fred A Hamprecht

“…We evaluate the performance of BOMS across various publicly available datasets and demonstrate that it achieves comparable results to the best existing method while being simple to implement and significantly faster in execution. Open-source code is available at https://github.com/sciai-lab/boms.…”
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Exploring Solar Granulation: from IMaX/SUNRISE to DKIST by Reza Mansouri, Rafal Angryk, Kevin Reardon

“…Inouye Solar Telescope (DKIST) telescope, generating preliminary annotations to facilitate future analysis, making this the first application of these techniques to data from DKIST. The source code is publicly available at github.com/rezmansouri/imax-to-dkist. …”
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EyeMMV toolbox: An eye movement post-analysis tool based on a two-step spatial dispersion threshold for fixation identification by Vassilios Krassanakis, Vassiliki Filippakopoulou, Byron Nakos

“…The EyeMMV software is developed using the scripting language of MATLAB and the source code is distributed through GitHub under the third version of GNU General Public License (link: https://github.com/krasvas/EyeMMV).…”
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Testing Deep Learning Recommender Systems Models on Synthetic GAN-Generated Datasets by Jesús Bobadilla, Abraham Gutiérrez

“…The published method Generative Adversarial Networks for Recommender Systems (GANRS) allows generating data sets for collaborative filtering recommendation systems. The GANRS source code is available along with a representative set of generated datasets. …”
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Attitude Analysis of Small Satellites Using Model-Based Simulation by Samir A. Rawashdeh

“…The simulation tool named the Smart Nanosatellite Attitude Propagator (SNAP) has been public in precompiled form and widely used since 2010; this paper accompanies the release of SNAP’s source code with the inclusion of new models for aerodynamic torque and other new features. …”
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Modelling of the Production of Source Neutrons from Low-Voltage Accelerated Deuterons on Titanium-Tritium Targets by A. Milocco, A. Trkov

“…The physics for the D-T neutron production was modelled at ENEA (Italy) in the SOURCE and SRCDX subroutines to compile with the MCNP source code. Some improvements to the original subroutines were introduced. …”
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STEME: a robust, accurate motif finder for large data sets. by John E Reid, Lorenz Wernisch

“…As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface.…”
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A GCC-based checker for compliance with MISRA-C's single-translation-unit rules by Chih-Yuan Chen, Yung-An Fang, Guan-Ren Wang, Peng-Sheng Chen

“…It can also obtain more accurate and more complete results than Cppcheck, a popular open-source checker. The source code can be downloaded from https://github.com/CCU-HPCLAB/GCC-MISRAC-Checker.…”
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A lightweight vulnerability detection method for long smart contracts based on bimodal feature fusion by Chen Yang Lin, Hui Zhao, Jing Han Liu

“…This method can combine the source code and opcode of smart contracts for analysis, and use a hierarchical attention network composed of bidirectional GRU and attention mechanism for vulnerability feature extraction. …”
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PENGEMBANGAN APLIKASIKONVERSI MATA KULIAH MENGGUNAKAN FRAMEWORKCODEIGNITER DAN BOOTSTRAP (Studi Kasus : Sekolah Tinggi Ilmu Komunikasi Profesi Indonesia) by Abu Sopian

“…Based on the analysis of the system design above, it can be concluded that the Model View Controller (MVC) architecture can be applied to the codeigniter framework and MVC architecturemaking it easier to repair changes to the source code without changing the entire logic and fungtion properly and meet the objectives the beginning of the development of this subject conversion application.…”
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Plagiarism types and detection methods: a systematic survey of algorithms in text analysis by Altynbek Amirzhanov, Cemil Turan, Alfira Makhmutova

“…We highlight notable works focusing on cross-language plagiarism detection, source code plagiarism, and intrinsic detection techniques, identifying their contributions and limitations. …”
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