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Journal articles on the topic 'Executabel file formats'
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1
Křoustek, Jakub, and Dusan Kolář. "Context parsing (not only) of the object-file-format description language." Computer Science and Information Systems 10, no. 4 (2013): 1673–701. http://dx.doi.org/10.2298/csis130120071k.
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The very first step of each tool such as linker, disassembler, or debugger is parsing of an input executable or object file. These files are stored in one of the existing object file formats (OFF). Retargetable tools are not limited to any particular target platform and they have to deal with handling of several OFFs. Handling of these formats is similar to parsing of computer languages - both of them have a predefined structure and a list of allowed constructions. However, OFF constructions are heavily mutually interconnected and they create context-sensitive units. In present, there is no generic system, which can be used for OFF description and its effective parsing. In this paper, we propose a formal language that can be used for OFF description. Furthermore, we present a design of a context parser of this language that is based on the formal models. The major advance of this solution is an ability to describe context-sensitive properties on the level of the language itself. This concept is planned to be used in the existing retargetable decompiler developed within the Lissom project. In this project, the language and its parser will be used for an object file parsing and its automatic conversion into the internal uniform file format. It is important to say that the concept of this parser can be utilized within other programming languages.
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Li, Yang, Ye Liang, and Jing Zhang Liang. "Applied-Information Technology with Trojan Horse Detection Method Based on C5.0 Decision Tree." Applied Mechanics and Materials 540 (April 2014): 439–42. http://dx.doi.org/10.4028/www.scientific.net/amm.540.439.
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This paper discusses the Trojan horse detection methods by analysis on Portable Executable File Format through which we can get much useful information. In order to deal with the information extracted from Portable Executable file, our methods constructed a decision tree based on C5.0 decision tree algorithm. Our approach can be divided into two steps. Firstly, we extracted some features from Portable Executable file by a portable executable attribute filter. Secondly, we handled the features extracted and then construct a classifier to identify the Trojan horse. The original in this paper is the application of a more effective algorithm C5.0 to construct the decision tree.
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Голембиовская, Оксана, Oksana Golembiovskaya, Александр Козачок, Aleksandr Kozachok, Минь Лай, and Min Lay. "Prototype of access controlled differentiation system to files of documentation formats." Bulletin of Bryansk state technical university 2015, no. 4 (December 30, 2015): 127–34. http://dx.doi.org/10.12737/17148.
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The safety problem with information circulating in corporate informationcomputer nets is urgent under conditions of presentday information society. The authors have developed a generalized functional model of the process of controlled access differentiation. At the same time come forward users identified by accounts as access subjects in the model and files of documentation formats are objects. Rules for the differentiation of a subject access to objects are specified as a matrix of powers taking into account marks of confidentiality. A distinguishing feature consists in that a container storing data is protected on basis of the method of indistinguishable obfuscation. The model developed allows storing data in a uniformed kind and ensuring a single method for an access to them. For safe storing is used a format of the protected container where information is stored in an obfuscated form. A container represents an executable file having a number of preset properties and functions allowing unambiguously the user identification, differentiation of an access to data (rights: to read, write, and assignation), assurance of the security for a confidence of the document implemented. The container format ensures its safe storing and transmission through a network.
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Smith, Mike L., Andrzej K. Oleś, and Wolfgang Huber. "Authoring Bioconductor workflows with BiocWorkflowTools." F1000Research 7 (April 6, 2018): 431. http://dx.doi.org/10.12688/f1000research.14399.1.
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The Bioconductor Gateway on the F1000Research platform is a channel for peer-reviewed and citable publication of end-to-end data analysis workflows rooted in the Bioconductor ecosystem. In addition to the largely static journal publication, it is hoped that authors will also deposit their workflows as executable documents on Bioconductor, where the benefits of regular code testing and easy updating can be realized. Ideally these two endpoints would be met from a single source document. However, so far this has not been easy, due to lack of a technical solution that meets both the requirements of the F1000Research article submission format and the executable documents on Bioconductor. Submission to the platform requires a LaTeX file, which many authors traditionally have produced by writing an Rnw document for Sweave or knitr. On the other hand, to produce the HTML rendering of the document hosted by Bioconductor, the most straightforward starting point is the R Markdown format. Tools such as pandoc enable conversion between many formats, but typically a high degree of manual intervention used to be required to satisfactorily handle aspects such as floating figures, cross-references, literature references, and author affiliations. The BiocWorkflowTools package aims to solve this problem by enabling authors to work with R Markdown right up until the moment they wish to submit to the platform.
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Et. al., Balal Sohail. "Macro Based Malware Detection System." Turkish Journal of Computer and Mathematics Education (TURCOMAT) 12, no. 3 (April 10, 2021): 5776–87. http://dx.doi.org/10.17762/turcomat.v12i3.2254.
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Macro based Malware has taken a great rise is these recent years, Attackers are now using this malware for hacking purposes. This virus is embedded inside the macro of a word document and can be used to infect the victim’s machine. These infected files are usually sent through emails and all antivirus software are unable to detect the virus due to the format of the file. Due to the format being a rich text file and not an executable file, the infected file is able to bypass all security. Hence it is necessary to develop a detection system for such attacks to help reduce the threat.
Technical research is carried out to identify the tools and techniques essential in the completion of this system. Research on methodology is done to finalise which development cycle will be used and how functions will be carried out at each phase of the development cycle. This paper outlines the problems that people face once they are attacked through macro malwares and the way it can be mitigated. Lastly, all information necessary to start the implementation has been gathered and analysed
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Na, Geonbae, Jongsu Lim, Sunjun Lee, and Jeong Hyun Yi. "Mobile Code Anti-Reversing Scheme Based on Bytecode Trapping in ART." Sensors 19, no. 11 (June 10, 2019): 2625. http://dx.doi.org/10.3390/s19112625.
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As interest in Internet of Things environments rapidly increases throughout the IT convergence field, compatibility with mobile devices must be provided to enable personalized services. The security of mobile platforms and applications is critical because security vulnerabilities of mobile devices can be spread to all things in these environments. Android, the leading open mobile platform, has long used the Dalvik virtual machine as its runtime system. However, it has recently been completely replaced by a new runtime system, namely Android Runtime (ART). The change from Android’s Dalvik to ART means that the existing Dalvik bytecode-based application execution structure has been changed to a machine code-based application execution structure. Consequently, a detailed understanding of ART, such as new file formats and execution switching methods between codes, is required from the viewpoint of application security. In this paper, we demonstrate that an existing Dalvik-based application vulnerability can be exploited as-is in ART. This is because existing Dalvik executable files coexist in the ART executable file, and these Dalvik bytecodes and compiled machine codes have one-to-one mapping relationships. We then propose an ART-based application protection scheme to secure this by dynamically eliminating the one-to-one mapping. In addition, the proposed scheme is implemented to evaluate its reverse engineering resistance and performance through experiments.
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Yehorov, Serhii, and Tetyana Shkvarnytska. "ADVANCED METHOD OF ANALYSIS OF MALICIOUS SOFTWARE FOR THE PURPOSE OF CREATING SIGNATURES." Visnyk Universytetu “Ukraina”, no. 1 (28) 2020 (2020): 161–70. http://dx.doi.org/10.36994/2707-4110-2020-1-28-14.
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The method of basic static analysis of harmful software is considered, which is based on searching and analyzing the term in files that are built using the PE (Portable Executable) format. The method of basic static analysis of malicious software is considered, which is based on the analysis of headers of executable files, and dynamic libraries, which are built using the PE format. An extended static analysis method is considered, which, in addition to analyzing the term and file headers, uses disassembly of executable files and dynamic libraries and further analysis of the resulting assembler text. In order to penetrate the operating system, cybercriminals use specialized software and network attacks. Moreover, a network attack does not have to be massive and widespread. To penetrate a particular operating system, for example, you can take advantage of vulnerabilities in both the operating system itself and the software that is installed on such an operating system. Moreover, successful attacks of this type are often made quiet and unobtrusive. To prevent hacker attacks that are accompanied by hidden software installation and to minimize harm from such attacks, it is necessary to apply adequate countermeasures in a timely manner. One of the most widespread and easy methods of fighting hackers is the timely updating of software, virus databases, installation and configuration of a firewall. Everything related to software updates is a reaction to threats that have already been identified. Therefore, the software update does not provide protection against the threats just identified. That is why the signatures of virus databases are created as a result of the analysis of the detected virus programs. Antivirus software also uses program behavior analysis to enhance the detection of malware. But even in this case, it is necessary to analyze the disassembled text of malicious software to identify new types of abnormal activity. Therefore, the analysis of malicious software is an urgent task and determines the direction of the study.
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Bukhanov, D. G., V. M. Polyakov, and M. A. Redkina. "Detection of malware using an artificial neural network based on adaptive resonant theory." Prikladnaya Diskretnaya Matematika, no. 52 (2021): 69–82. http://dx.doi.org/10.17223/20710410/52/4.
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The process of detecting malicious code by anti-virus systems is considered. The main part of this process is the procedure for analyzing a file or process. Artificial neural networks based on the adaptive-resonance theory are proposed to use as a method of analysis. The graph2vec vectorization algorithm is used to represent the analyzed program codes in numerical format. Despite the fact that the use of this vectorization method ignores the semantic relationships between the sequence of executable commands, it allows to reduce the analysis time without significant loss of accuracy. The use of an artificial neural network ART-2m with a hierarchical memory structure made it possible to reduce the classification time for a malicious file. Reducing the classification time allows to set more memory levels and increase the similarity parameter, which leads to an improved classification quality. Experiments show that with this approach to detecting malicious software, similar files can be recognized by both size and behavior.
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Bai, Jinrong, Junfeng Wang, and Guozhong Zou. "A Malware Detection Scheme Based on Mining Format Information." Scientific World Journal 2014 (2014): 1–11. http://dx.doi.org/10.1155/2014/260905.
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Malware has become one of the most serious threats to computer information system and the current malware detection technology still has very significant limitations. In this paper, we proposed a malware detection approach by mining format information of PE (portable executable) files. Based on in-depth analysis of the static format information of the PE files, we extracted 197 features from format information of PE files and applied feature selection methods to reduce the dimensionality of the features and achieve acceptable high performance. When the selected features were trained using classification algorithms, the results of our experiments indicate that the accuracy of the top classification algorithm is 99.1% and the value of the AUC is 0.998. We designed three experiments to evaluate the performance of our detection scheme and the ability of detecting unknown and new malware. Although the experimental results of identifying new malware are not perfect, our method is still able to identify 97.6% of new malware with 1.3% false positive rates.
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Takefuji, Yoshiyasu. "Python Programming in PyPI for Translational Medicine." International Journal of Translational Medicine 1, no. 3 (November 24, 2021): 323–31. http://dx.doi.org/10.3390/ijtm1030019.
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This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers need to deal with big data. This paper describes how to build an executable Python Package Index (PyPI) code and package. PyPI is a repository of software for the Python programming language with 5,019,737 files and 544,359 users (programmers) as of 19 October 2021. First, programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package. This paper depicts a covidlag executable package as an example for calculating the accurate case fatality rate (CFR) and the lag time from infection to death. You can install the covidlag by pip terminal command and test it. This paper also introduces deathdaily and scorecovid packages on PyPI Stats, which can inform how many users have downloaded the specified PyPI package. The usefulness and applicability of a developed tool can be verified by PyPI Stats with the number of downloaded users.
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Rosenberg, David M., and Charles C. Horn. "Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks." Journal of Neurophysiology 116, no. 2 (August 1, 2016): 252–62. http://dx.doi.org/10.1152/jn.00137.2016.
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Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus—a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software—an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research.
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Shim, Jaewoo, Kyeonghwan Lim, Seong-je Cho, Sangchul Han, and Minkyu Park. "Static and Dynamic Analysis of Android Malware and Goodware Written with Unity Framework." Security and Communication Networks 2018 (June 20, 2018): 1–12. http://dx.doi.org/10.1155/2018/6280768.
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Unity is the most popular cross-platform development framework to develop games for multiple platforms such as Android, iOS, and Windows Mobile. While Unity developers can easily develop mobile apps for multiple platforms, adversaries can also easily build malicious apps based on the “write once, run anywhere” (WORA) feature. Even though malicious apps were discovered among Android apps written with Unity framework (Unity apps), little research has been done on analysing the malicious apps. We propose static and dynamic reverse engineering techniques for malicious Unity apps. We first inspect the executable file format of a Unity app and present an effective static analysis technique of the Unity app. Then, we also propose a systematic technique to analyse dynamically the Unity app. Using the proposed techniques, the malware analyst can statically and dynamically analyse Java code, native code in C or C ++, and the Mono runtime layer where the C# code is running.
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Krawczyk, Artur, and Paweł Owsianka. "Using the Bentley MicroStation environment to program calculations of predicted ground subsidence caused by underground mining exploitation." E3S Web of Conferences 106 (2019): 01003. http://dx.doi.org/10.1051/e3sconf/201910601003.
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The paper presents a new concept of creating a program for calculating ground subsidence caused by underground mining extraction, which is substantially different than previously used solutions. Instead of compiling the calculation algorithm to an executable file, the whole application algorithm has been written in the Bentley MicroStation graphic environment’s interpreted language. This graphic environment is used in mining for keeping mining maps and the format is used for storing finished and designed mining exploitation data sets. The paper describes S. Knothe’s theory of the influence of mining exploitation on the terrain surface in the context of the calculation methodology used for terrain subsidence computation. Based on the theory of influence, the structure of the created MVBA (MicroStation Visual Basic for Applications) algorithm for interpolating subsidence contours is described. The new application is called uDEFO. Calculation results from the program are compared with calculation results from software currently used in coal mines.
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Handoko, Budhi, Yeny Krista Franty, and Gumgum Darmawan. "PEMBUATAN APLIKASI PRAKTIS DESAIN BLOK ACAK LENGKAP MENGGUNAKAN BAHASA PEMROGRAMAN LAZARUS." Jurnal Ilmiah Matematika dan Pendidikan Matematika 9, no. 1 (June 23, 2017): 23. http://dx.doi.org/10.20884/1.jmp.2017.9.1.2852.
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Completely Randomized Block Design is one type of design experiments in Statistics which is used to conduct experiment involving treatments and blocks. Blocking is used to make experimental unit become homogen in each blok. Analysis to the reults of the experiment using the design usually perform using licensed software such as SPSS or Minitab. In order to use those softwares, we have to buy the license. In addition, if use them, we have to arrange the data into column form which require knowledge about orthogonality principle. This research will develop an application to analyze the experimental data easily, because the input in the form of table that suitable with experimental data format. In this research we used Lazarus Visual Programming which is one of open source software. The result of this research is a practical application that can be used to analyze experimental result produced using completely randomized block design which is bery easy to use. Experimental data from table of experimental result can be directly copied into the cells of the program thus data entry can be fastened. This program is an executable file (*.exe) so it is not necessary to be installed and the size of file is small enough which is 19 megabyte.
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Finney, Richard P., Qing-Rong Chen, Cu V. Nguyen, Chih Hao Hsu, Chunhua Yan, Ying Hu, Massih Abawi, Xiaopeng Bian, and Daoud M. Meerzaman. "Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files." Cancer Informatics 14 (January 2015): CIN.S26470. http://dx.doi.org/10.4137/cin.s26470.
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The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .
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Hwang, Chanwoong, Junho Hwang, Jin Kwak, and Taejin Lee. "Platform-Independent Malware Analysis Applicable to Windows and Linux Environments." Electronics 9, no. 5 (May 12, 2020): 793. http://dx.doi.org/10.3390/electronics9050793.
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Most cyberattacks use malicious codes, and according to AV-TEST, more than 1 billion malicious codes are expected to emerge in 2020. Although such malicious codes have been widely seen around the PC environment, they have been on the rise recently, focusing on IoT devices such as smartphones, refrigerators, irons, and various sensors. As is known, Linux/embedded environments support various architectures, so it is difficult to identify the architecture in which malware operates when analyzing malware. This paper proposes an AI-based malware analysis technology that is not affected by the operating system or architecture platform. The proposed technology works intuitively. It uses platform-independent binary data rather than features based on the structured format of the executable files. We analyzed the strings from binary data to classify malware. The experimental results achieved 94% accuracy on Windows and Linux datasets. Based on this, we expect the proposed technology to work effectively on other platforms and improve through continuous operation/verification.
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Demetrio, Luca, Scott E. Coull, Battista Biggio, Giovanni Lagorio, Alessandro Armando, and Fabio Roli. "Adversarial EXEmples." ACM Transactions on Privacy and Security 24, no. 4 (November 30, 2021): 1–31. http://dx.doi.org/10.1145/3473039.
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Recent work has shown that adversarial Windows malware samples—referred to as adversarial EXE mples in this article—can bypass machine learning-based detection relying on static code analysis by perturbing relatively few input bytes. To preserve malicious functionality, previous attacks either add bytes to existing non-functional areas of the file, potentially limiting their effectiveness, or require running computationally demanding validation steps to discard malware variants that do not correctly execute in sandbox environments. In this work, we overcome these limitations by developing a unifying framework that does not only encompass and generalize previous attacks against machine-learning models, but also includes three novel attacks based on practical, functionality-preserving manipulations to the Windows Portable Executable file format. These attacks, named Full DOS , Extend , and Shift , inject the adversarial payload by respectively manipulating the DOS header, extending it, and shifting the content of the first section. Our experimental results show that these attacks outperform existing ones in both white-box and black-box scenarios, achieving a better tradeoff in terms of evasion rate and size of the injected payload, while also enabling evasion of models that have been shown to be robust to previous attacks. To facilitate reproducibility of our findings, we open source our framework and all the corresponding attack implementations as part of the secml-malware Python library. We conclude this work by discussing the limitations of current machine learning-based malware detectors, along with potential mitigation strategies based on embedding domain knowledge coming from subject-matter experts directly into the learning process.
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Wang, Hang, Yunfeng Chen, Omar M. Saad, Wei Chen, Yapo Abolé Serge Innocent Oboué, Liuqing Yang, Sergey Fomel, and Yangkang Chen. "A MATLAB code package for 2D/3D local slope estimation and structural filtering." GEOPHYSICS 87, no. 3 (March 3, 2022): F1—F14. http://dx.doi.org/10.1190/geo2021-0266.1.
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Local slope is an important attribute that can help distinguish seismic signals from noise. Based on optimal slope estimation, many filtering methods can be designed to enhance the signal-to-noise ratio of noisy seismic data. We present an open-source MATLAB code package for local slope estimation and corresponding structural filtering. This package includes 2D and 3D examples with two main executable scripts and related subfunctions. All code files are in the MATLAB format. In each main script, local slope is estimated based on the well-known plane-wave destruction algorithm. Then, the seismic data are transformed to the flattened domain by utilizing this slope information. Furthermore, the smoothing operator can be effectively applied in the flattened domain. We introduce the theory and mathematics related to these programs and present the synthetic and field data examples to show the usefulness of this open-source package. The results of local slope estimation and structural filtering demonstrate that this package can be conveniently and effectively applied to the seismic signal analysis and denoising.
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ARDELEAN, ADORIAN, KARINA KERVIN, SUMAN KANSAKAR, and DAPHNE GAIL FAUTIN. "Syngraph: An application for graphic display and interactive use of synonym lists." Zootaxa 2283, no. 1 (November 6, 2009): 29–39. http://dx.doi.org/10.11646/zootaxa.2283.1.3.
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Multiple names that refer to a single species (synonyms) and more than one species being referred to by the same name (homonyms) bedevil taxonomy. They produce ambiguity about the entity under discussion. Syngraph is a computer application that organizes information about synonyms and homonyms. It can track different names that potentially have been applied to the same species, or identical names that have been applied to different species. It can create a list of synonyms in conventional format for use in publication, as for a taxonomic monograph. It can also display and print names so they are linked, thereby providing information on the conceptual basis of a name and the action taken in a publication. In the display, each name is imposed on a color-coded rectangle; all names on rectangles of the same color refer to records that stem from a single description. This allows quick visualization of the taxonomic history. When linked to a geographical information system application, the color can be used for points plotted on a map that displays the geographical locality of specimens referred to in each record. This visualization of the geographic distribution of the nominal species can provide tests of the hypothesis that the names are, indeed, synonyms. Syngraph is available for download; help files accompany the executable files.
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WARD, MONICA. "Reusable XML technologies and the development of language learning materials." ReCALL 14, no. 2 (November 2002): 285–94. http://dx.doi.org/10.1017/s0958344002000629.
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There are many CALL resources available today but often they need to be adapted for level or culture. CALL practitioners would like to reuse currently existing material rather than reinvent the wheel, but often this is not possible. Thus, they end up building CALL material, both language content and software, from scratch. This is inefficient in terms of CALL practitioners’ time and as Felix (1999) points out, there is no point ‘doing badly’ what has already been done well. Why can’t we reuse what already exists? Often the language content is hard-wired in the software and cannot be modified or the CALL material comes as an executable which is hard or impossible to change. Authoring tools can provide a degree of flexibility, but often focus on particular parts of the language learning process (e.g. interactive exercises) and the associated language content cannot, in general, easily be exported into other formats and presentation software. One solution to this problem is provided by XML technologies. They provide a strict separation between data and processing. Thus, three types of reuse are possible: reuse of the data processing engine (i.e. the XSL processing files), reuse of the language content structure (i.e. the XML data files) and reuse the linguistic resources (i.e. the language content). In this paper, an example is given of a CALL template that has been developed using XML technologies. The template provides a structure into which the language content can be slotted and a processing engine to act upon the data to create CALL material. The template was developed for the production of CALL materials for Endangered Languages (ELs), but could be used for MCTLs (Most Commonly Taught Languages) and LCTLs (Less Commonly Taught Languages) also. It has been used to develop a language learning course for Nawat (a language of El Salvador), Akan (a Ghanaian language) and Irish, demonstrating the reusability of the language content structure as well as proving the reusability of the processing engine provided by the template. A further reusable feature is the ability to create courseware in different media (Internet, CD and print) from the same source language content.
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Aghamiri, Sara Sadat, Vidisha Singh, Aurélien Naldi, Tomáš Helikar, Sylvain Soliman, and Anna Niarakis. "Automated inference of Boolean models from molecular interaction maps using CaSQ." Bioinformatics 36, no. 16 (May 13, 2020): 4473–82. http://dx.doi.org/10.1093/bioinformatics/btaa484.
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Abstract Motivation Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap between static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner. Results We developed CaSQ by defining conversion rules and logical formulas for inferred Boolean models according to the topology and the annotations of the starting molecular interaction maps. We used CaSQ to produce executable files of existing molecular maps that differ in size, complexity and the use of Systems Biology Graphical Notation (SBGN) standards. We also compared, where possible, the manually built logical models corresponding to a molecular map to the ones inferred by CaSQ. The tool is able to process large and complex maps built with CellDesigner (either following SBGN standards or not) and produce Boolean models in a standard output format, Systems Biology Marked Up Language-qualitative (SBML-qual), that can be further analyzed using popular modelling tools. References, annotations and layout of the CellDesigner molecular map are retained in the obtained model, facilitating interoperability and model reusability. Availability and implementation The present tool is available online: https://lifeware.inria.fr/∼soliman/post/casq/ and distributed as a Python package under the GNU GPLv3 license. The code can be accessed here: https://gitlab.inria.fr/soliman/casq. Supplementary information Supplementary data are available at Bioinformatics online.
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Colleter, Rozenn, Jean-Baptiste Romain, and Jean-Baptiste Barreau. "HumanOS: an open source nomadic software database for physical anthropology and archaeology." Virtual Archaeology Review 11, no. 23 (July 8, 2020): 94. http://dx.doi.org/10.4995/var.2020.13422.
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<p class="VARAbstract">With the democratization of computers, tablets and smartphones, the data acquisition and exploration on archaeological sites are changing significantly. The digitization of information allows a faster, more efficient and more standardized data recording that facilitates the synthesis work required by the discipline. Numerous database programmes are being developed in archaeology and physical anthropology, notably with targeted tools developed to meet specific needs. However, to the authors’ knowledge, no efficient, free and open-source program for the recording of human bones in an archaeological context exists yet. In this paper, a mobile application for the intuitive recording of human bones from archaeological sites is described; this app, defined for the field and biological anthropologists, allows making an inventory of the burials from site to the laboratory from archaeological digs in an intuitive style. In addition to the recording of the skeleton, the application permits the recording of the discovery context. The application also gives significant freedom to the user, who can easily create research fields to their own research objectives. Finally, it permits exporting the information, either as text (automatic report) and/or as tables for statistical use. It is a modular, ergonomic and portable tool which meets researchers' requirements without needing an internet connection; it stores the recorded information in several formats (CSV, SVG, HTML and/or JSON), in a sustainable computer language, permitting complementary modules development. The system is implemented in the form of a free and open-source web application, programmed in JavaScript (available from http://www.humanos.cnrs.fr/) and supplied in the form of a simple ZIP file to decompress. The application does not require any special installation, as it opens by clicking on the executable "<em>HumanOS.html</em>" with any web browser, even without an Internet connection.</p><p>Highlights:</p><ul><li><p>We have developed a mobile application which allows "field anthropologists" to record burials inventories from archaeological excavations on site and in the laboratory, in an intuitive way.</p></li><li><p>In addition to recording the skeleton, the application makes it possible to note the context of the discovery and to create fields of investigation according to its own research objectives.</p></li><li><p>It allows data export in the form of text (automatic report) and/or tables for statistical uses.</p></li></ul>
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Madhusanka, Sajith, Anusha Walisadeera, Gilmini Dantanarayana, Jeevani Goonetillake, and Athula Ginige. "An Ontological Clinical Decision Support System Based on Clinical Guidelines for Diabetes Patients in Sri Lanka." Healthcare 8, no. 4 (December 18, 2020): 573. http://dx.doi.org/10.3390/healthcare8040573.
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Health professionals should follow the clinical guidelines to decrease healthcare costs to avoid unnecessary testing and to minimize the variations among healthcare providers. In addition, this will minimize the mistakes in diagnosis and treatment processes. To this end, it is possible to use Clinical Decision Support Systems that implement the clinical guidelines. Clinical guidelines published by international associations are not suitable for developing countries such as Sri Lanka, due to the economic background, lack of resources, and unavailability of some laboratory tests. Hence, a set of clinical guidelines has been formulated based on the various published international professional organizations from a Sri Lankan context. Furthermore, these guidelines are usually presented in non-computer-interpretable narrative text or non-executable flow chart formats. In order to fill this gap, this research study finds a suitable approach to represent/organize the clinical guidelines in a Sri Lankan context that is suitable to be used in a clinical decision support system. To this end, we introduced a novel approach which is an ontological model based on the clinical guidelines. As it is revealed that there are 4 million diabetes patients in Sri Lanka, which is approximately twenty percent of the total population, we used diabetes-related guidelines in this research. Firstly, conceptual models were designed to map the acquired diabetes-related clinical guidelines using Business Process Model and Notation 2.0. Two models were designed in mapping the diagnosis process of Type 1 and Type 2 Diabetes, and Gestational diabetes. Furthermore, several conceptual models were designed to map the treatment plans in guidelines by using flowcharting. These designs were validated by domain experts by using questionnaires. Grüninger and Fox’s method was used to design and evaluate the ontology based on the designed conceptual models. Domain experts’ feedback and several real-life diabetic scenarios were used to validate and evaluate the developed ontology. The evaluation results show that all suggested answers based on the proposed ontological model are accurate and well addressed with respect to the real-world scenarios. A clinical decision support system was implemented based on the ontological knowledge base using the Jena Framework, and this system can be used to access the diabetic information and knowledge in the Sri Lankan context. However, this contribution is not limited to diabetes or a local context, and can be applied to any disease or any context.
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Shah, Syed Shakir Hameed, Abd Rahim Ahmad, Norziana Jamil, and Atta ur Rehman Khan. "Memory Forensics-Based Malware Detection Using Computer Vision and Machine Learning." Electronics 11, no. 16 (August 18, 2022): 2579. http://dx.doi.org/10.3390/electronics11162579.
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Malware has recently grown exponentially in recent years and poses a serious threat to individual users, corporations, banks, and government agencies. This can be seen from the growth of Advanced Persistent Threats (APTs) that make use of advance and sophisticated malware. With the wide availability of computer-automated tools such as constructors, email flooders, and spoofers. Thus, it is now easy for users who are not technically inclined to create variations in existing malware. Researchers have developed various defense techniques in response to these threats, such as static and dynamic malware analyses. These techniques are ineffective at detecting new malware in the main memory of the computer and otherwise require considerable effort and domain-specific expertise. Moreover, recent techniques of malware detection require a long time for training and occupy a large amount of memory due to their reliance on multiple factors. In this paper, we propose a computer vision-based technique for detecting malware that resides in the main computer memory in which our technique is faster or memory efficient. It works by taking portable executables in a virtual environment to extract memory dump files from the volatile memory and transform them into a particular image format. The computer vision-based contrast-limited adaptive histogram equalization and the wavelet transform are used to improve the contrast of neighboring pixel and to reduce the entropy. We then use the support vector machine, random forest, decision tree, and XGBOOST machine learning classifiers to train the model on the transformed images with dimensions of 112 × 112 and 56 × 56. The proposed technique was able to detect and classify malware with an accuracy rate of 97.01%. Its precision, recall, and F1-score were 97.36%, 95.65%, and 96.36%, respectively. Our finding shows that our technique in preparing dataset with more efficient features to be trained by the Machine Learning classifiers has resulted in significant performance in terms of accuracy, precision, recall, F1-score, speed and memory consumption. The performance has superseded most of the existing techniques in its unique approach.
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Friedenberg, Nicholas A. "EcologyEcological Models and Dynamics: An Interactive Textbook. By RogerSchmitz. New York: Garland Science. Taylor & Francis Group. $50.00 (CDROM and Booklet). CDROM Contents: Chapters 110 of Ecological Models and Dynamics in PowerPoint and PDF; Interactive PowerPoint, Mathcad, Acrobat, and Excel files and LabVIEW executables; LabVIEW runtime engine installer. Opens in PowerPoint and PDF format. 9780815344261. 2009." Quarterly Review of Biology 85, no. 3 (September 2010): 350. http://dx.doi.org/10.1086/655045.
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Bender, Julian, and Carla Schmidt. "The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments." Bioinformatics, September 28, 2019. http://dx.doi.org/10.1093/bioinformatics/btz732.
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Abstract Motivation A variety of search engines exists for the identification of peptide spectrum matches after cross-linking mass spectrometry experiments. The resulting diversity in output formats complicates data validation and visualization as well as exchange with collaborators, particularly from other research areas. Results Here, we present CroCo, a user-friendly standalone executable to convert cross-linking results to a comprehensive spreadsheet format. Using this format, CroCo can be employed to generate input files for a selection of the commonly utilized validation and visualization tools. Availability and implementation The source-code is freely available under a GNU general public license at https://github.com/cschmidtlab/croco. The standalone executable is available and documented at https://cschmidtlab.github.io/CroCo. Supplementary information Supplementary data are available at Bioinformatics online.
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Tian, Zuwei, and Hengfu Yang. "Code fusion information-hiding algorithm based on PE file function migration." EURASIP Journal on Image and Video Processing 2021, no. 1 (January 6, 2021). http://dx.doi.org/10.1186/s13640-020-00541-3.
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AbstractPE (portable executable) file has the characteristics of diversity, uncertainty of file size, complexity of file structure, and singleness of file format, which make it easy to be a carrier of information hiding, especially for that of large hiding capacity. This paper proposes an information-hiding algorithm based on PE file function migration, which utilizes disassembly engine to disassemble code section of PE file, processes function recognition, and shifts the whole codes of system or user-defined functions to the last section of PE file. Then it hides information in the original code space. The hidden information is combined with the main functions of the PE file, and the hidden information is coupled with the key codes of the program, which further enhances the concealment performance and anti-attack capability of the system.
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Vences, Miguel, Patmanidis Stefanos, Vladimir Kharchev, and Susanne S. Renner. "Concatenator, a user-friendly program to concatenate DNA sequences, implementing graphical user interfaces for MAFFT and FastTree." Bioinformatics Advances, July 21, 2022. http://dx.doi.org/10.1093/bioadv/vbac050.
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Abstract Motivation Phylogenetic and phylogenomic analyses require multi-gene input files in different formats, but there are few user-friendly programs facilitating the workflow of combining, concatenating or separating, aligning and exploring multi-gene data sets. Results We present Concatenator, a user-friendly GUI-driven program that accepts single-marker and multi-marker DNA sequences in different input formats, including Fasta, Phylip, and Nexus, and that outputs concatenated sequences as single-marker or multi-marker Fasta, interleaved nexus, or Phylip files, including command files for downstream model selection in IQ-TREE. It includes the option to (re)align markers with MAFFT and produces exploratory trees with FastTree. Although tailored for medium-sized phylogenetic projects, Concatenator is able to process phylogenomic data sets of up to 30,000 markers. Availability and implementation Concatenator is written in Python, with C extensions for MAFFT and FastTree. Compiled stand-alone executables of Concatenator for MS Windows and Mac OS along with a detailed manual can be downloaded from www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/ConcatenatorGui). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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"Predicting the Dynamic Behaviour of Malware using RNN." International Journal of Engineering and Advanced Technology 9, no. 3 (February 29, 2020): 3557–59. http://dx.doi.org/10.35940/ijeat.c6291.029320.
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Malware analysis can be classified as static and dynamic analysis. Static analysis involves the inspection of the malicious code by observing the features such as file signatures, strings etc. The code obfuscation techniques such as string encryption, class encryption etc can be easily applied on static code analysis. Dynamic or behavioural data is more difficult to obfuscate as the malicious payload may have already been executed before it is detected. In this paper, the dataset is obtained from repositories such as VirusShare and is run in Cuckoo Sandbox with the help of the agent.py. The dynamic features are extracted from the generated Cuckoo logs in the html and JSON format and it has to be determined whether it is malicious or not using recurrent neural networks. Recurrent Neural Networks are capable of predicting whether an executable is malicious and have the ability to capture time-series data.
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VENCES, MIGUEL, AURÉLIEN MIRALLES, SOPHIE BROUILLET, JACQUES DUCASSE, ALEXANDER FEDOSOV, VLADIMIR KHARCHEV, IVAYLO KOSTADINOV, et al. "iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists." Megataxa 6, no. 2 (July 23, 2021). http://dx.doi.org/10.11646/megataxa.6.2.1.
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While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org)
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"Overview of static methods of analysis malicious software." Computer Science and Cybersecurity, no. 2 (2020). http://dx.doi.org/10.26565/2519-2310-2020-2-02.
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In today's world, the problem of losses from the actions of malicious software (or ordinary software, which has the characteristics of undeclared functions) continues to be extremely relevant. Therefore, the creation and modification of anti-virus solutions for protection and analysis of malware (software) is a relevant and promising area of research. This is due to the lack of a single, universal method that provides 100% finding malicious code. The paper considers the composition and main components of static analysis. The main methods of static analysis is identified, and relevant examples of almost all of them are given. Got concluded that the main advantages of static analysis are that by using a relatively simple set of commands and tools, it is possible to perform malware analysis and partially understand how it works. Attention is drawn to the fact that static analysis does not give 100% certainty that the investigated software is malicious. With this in mind, to provide a more meaningful analysis, you need to collect as much data as possible about the structure of the file, its possible functions, etc. Analysis of files for the possible presence of malicious code is provided through the use of appropriate programs to view their structure and composition. A more informative way is to analyze the Portable Executable format. It consists of the analysis of various sections of the code of fields and resources. Since static analysis does not always provide the required level of guarantees, it is better to use machine learning algorithms at the stage of making the final classification decision (malicious or not). This approach will make it possible to process large data sets with greater accuracy in determining the nature of the software is analyzed. The main purpose of this work is to analyze the existing methods of static malware analysis, and review the features of their further development.
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Bolshakova, Natalia. "Electronic Library “Pskoviana” (structure, content, prospects of development)." Arts and Music in Cultural Discourse. Proceedings of the International Scientific and Practical Conference, September 28, 2013, 9. http://dx.doi.org/10.17770/amcd2013.1266.
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The aim of work is generalization of experience of introduction of innovative forms of storage, scientific treatment and publication of expeditionary materials of the Pskov dialectal and folklore- ethnographic archive that is a resource base for many research and educational projects. Formed during the field inspection for many decades and constantly executable archive contains a rich both language and culturological information generator about folk traditions, about the features of way of life, management, perception of the world, traditional and new values of carriers of folk culture of the Pskov region. The funds indicated till recently were unevenly used in scientifically-educational aims. If a dialectal archive during a few decades is a source lexicographic and areal researches, on his base ten of research works is written, including dissertations, then rich potential of folklore part of archive on a row of objective reasons was not exposed. Meantime an audiofund contains the records of works of verbal folk work of different genres: songs (ceremonial and calendar), fairy-tales, fables, legends, descriptions of ceremonies (wedding, baptismal, funeral- mention) etc. In addition, present records also are a base for a study and Pskov folk colloquial speech, as traditional folklore, especially in the verbal genres, is created and exists on dialectal basis. The artistic, historical and cultural value of various in a genre, stylish relation works of folklore does not cause doubts, but also their dialectal independence was not once marked by researchers and collectors. The search of NT used on archived business resulted in creation of e-library of texts of "Pskoviana", the source of that is not published before the archived exclusive. Unlike a traditional e-library, that, as a rule, is a mediator between a user and informative resource, the e-library of texts formed by us is such resource. Structural basis of library is made by the electronic databases created on the genre-thematic founding. Created and in 2012 got testifying to state registration electronic databases on themes: the "Verbal recitals of Great Patriotic war", "Traditional child's folklore", "Fairy-tales of the Pskov area". All three bases are placed on the specialized web-site (http://nocpskoviana.pskgu.ru/index.php). The prospects of development of e-library of texts of regional character of "Pskoviana" are set in next directions. Addition and correction of the formed fragments of library. So, for example, the base sanctified to the military theme, where verbal stories are while presented only, is complemented due to genre expansion: a selection is already executed from the archive of texts of songs and chastushkas on a military theme. Introduction of voice files (wherein they are while absent) supporting the "deciphered" texts. Presently in a state of preparation there is forming of collection of fairy-tales in the format of CD, after the publication of that all voice files containing the Pskov fairy-tales will be placed on a web-site. Thematic expansion enclosures databases, primarily in the development of the themes. Creation of databases, based on areal principle. Presently in the stage of forming there is a local base on one of south districts of the Pskov area – Sebeže, located on a border with Latvia and Belorussia. Decision of complex of the research and practice tasks related to informatization of the archived work, the row of the theoretical questions, related to the area of textual criticism, communicative dialectology, folklore, philological regional science, requires working. Thus, experience showed that for positioning of regional specific of traditional folk culture in her speech forms an e-library of texts is most representative. The form of library, structured and at the same time allowing a high degree of variability, allows you to optimally organize archival data. The applied methodologies showed perspective of select direction in-process with the archived material of high-cube. The complex of works carried out during the row of years in final analysis must result in creation of single accessible electronic archive to the users. But already the e-library of "Pskoviana" formed and now on the basis of the Pskov dialectal and folklore-ethnographic archive executes the functions of reliable storage and presentation of folk speech culture and language of Pskov earth.