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Gagniuc/README.md
Algorithms for Cyber Defense: From Cryptography to Behavioral Analysis! A repository for resources and updates related to the Algorithms special issue. Focused on secure algorithmic solutions for cyber defense, including encryption, authentication, anomaly detection, reverse engineering, and security-aware AI. Submission deadline: July 31, 2026. |
Statement [+] Special Issue | Algorithms for Cyber Defense
Python Coding Examples from Simple to Complex JavaScript Coding Examples from Simple to Complex MATLAB Coding Examples from Simple to Complex
Bioinformatics Algorithms in JavaScript Visual Basic (VBA; VB 6.0) - Markov-Chains An Introduction to Programming Languages: Simultaneous Learning in Multiple Coding Environments

Note: all applications presented here are designed natively in their respective programming or scripting languages, without libraries or external files. Thus, the applications have no dependencies and can be used offline. There are about 100 posts uploaded here, however, below are some useful projects that I have chosen to show as a preview:

Jupiter Bioinformatics (V1) Jupiter Bioinformatics V2 (normal) Jupiter Bioinformatics V2 (dark) Jupiter Bioinformatics V2 experiments Sequence Logo (relative style) Sequence Logo (block style)

More [+]

Discrete Probability Detector (DPD) Predictions with Markov Chains Objective Digital Stains Markov Chains scanner Linear congruential generator Information content vs percentage A high discrimination motif scanner A high discrimination motif scanner (variable sensitivity) Information content vs Information entropy Sequence Logo (relative style with axes) Sequence Logo (block style with axes) Spectral Forecast model for signals Chaos & noise Spectral Forecast equation for signals Spectral Forecast equation for matrices

Waveform-mixing-with-Spectral-Forecast-in-JS Waveform-mixing-with-Spectral-Forecast-in-JS Waveform-mixing-with-Spectral-Forecast-in-JS

Waveform-mixing-with-Spectral-Forecast-in-JS Waveform-mixing-with-Spectral-Forecast-in-JS Waveform-mixing-with-Spectral-Forecast-in-JS

native - Java Script Charts native - Java Script Charts native - Java Script Charts

Diabetes prediction prototype Prototype software for Photon-pixel coupling method PI laboratory in VB6 Motif detection VB6 Visual Sequence Alignment in VB6 Markov Chains detector in VB6Dynamic Block Allocation algorithm PromKappa 3.0 Objective Digital Stains in VB6 Markov Chains Simulation framework

Markov Chains Prediction framework Spectral-Forecast-equation-VB6-app-2.0 Markov Chains The weather

Bioinformatics Algorithms in JavaScript Bioinformatics Algorithms in JavaScript PromKappa 3.0 Objective Digital Stains in VB6

RNA complementarity DNA complementarity Entropy of text

Historical Software Archive

Original software projects developed during the early years of Windows programming and preserved together with their source code, executables, interfaces, documentation and distribution materials. These repositories document both the applications themselves and the programming techniques, visual styles and software-distribution practices of their period.

RAM & CPU RAM Limits
Delta Memory Force 2.0 is a real-time Windows system utility for RAM optimization, CPU monitoring, process inspection and control, disk-space analysis, and automated memory recovery. Designed for Windows 95, 98, ME, NT, and 2000, it features dynamically generated charts, LEDs, VU-style indicators, System Tray monitoring, configurable optimization rules, and a proprietary trial-key licensing system. This repository preserves the complete software archive, including all versions, source code, installation kits, licensing tools, original interface assets, documentation, CD images.
Mini AVI CD is a multimedia application developed in the early 2000s for the simple playback of AVI files distributed on CDs. It features a compact interface typical of Windows software from that period and was designed to start quickly without installation or complex configuration. Today, the project is preserved as historical software and has been adapted to run on modern versions of Windows while retaining its original appearance and behavior. Mini AVI 2.1 player interface

Delta Memory Force 2.0 on Windows 11

Delta Memory Force 2.0 (1999-2002)

Delta Memory Force 2.0 is a real-time Windows system utility for RAM optimization, CPU monitoring, process inspection and control, disk-space analysis, and automated memory recovery. Designed for Windows 95, 98, ME, NT, and 2000, it features dynamically generated charts, LEDs, VU-style indicators, System Tray monitoring, configurable optimization rules, and a proprietary trial-key licensing system. This repository preserves the complete software archive, including all versions, source code, installation kits, licensing tools, original interface assets, documentation, CD images.

DMF is one of several projects preserved in this historical software collection. Taken together, these archives are also snapshots of how software was imagined and built at the time: interfaces drawn almost pixel by pixel, custom controls, hand-built charts, compact algorithms, unusual licensing mechanisms, and complete CD-based distribution kits. Beyond their original functions, they preserve the visual language, technical constraints, and practical ingenuity of an earlier period of personal computing.


More on the Historical Software Archive [+]

Mini AVI (2003 - 2004)

Mini AVI 2.1 player interface

Applied Genetics 1.2 (2007 - 2008)

Applied Genetics 1.2 on Windows 11
Algorithms in Visual Basic for Applications

More [+]
Binary files inside EXCEL VBA Spectral Forecast in EXCEL

  • Paul A. Gagniuc. An Introduction to Programming Languages: Simultaneous Learning in Multiple Coding Environments. Synthesis Lectures on Computer Science. Springer International Publishing, 2023, pp. 1-280.

  • Paul A. Gagniuc. Coding Examples from Simple to Complex - Applications in Python. Synthesis Lectures on Computer Science. Springer International Publishing, 2024, pp. 1-245.

  • Paul A. Gagniuc. Coding Examples from Simple to Complex - Applications in MATLAB. Synthesis Lectures on Computer Science. Springer International Publishing, 2024, pp. 1-255.

  • Paul A. Gagniuc. Coding Examples from Simple to Complex - Applications in Javascript. Synthesis Lectures on Computer Science. Springer International Publishing, 2024, pp. 1-240.

  • Paul A. Gagniuc. Antivirus Engines: From Methods to Innovations, Design, and Applications. Cambridge, MA: Elsevier Syngress, 2024. pp. 1-656. ISBN: 9780443329524

  • Paul A. Gagniuc. Markov chains: from theory to implementation and experimentation. Hoboken, NJ, John Wiley & Sons, USA, 2017, pp. 1-256. ISBN: 978-1-119-38755-8.

  • Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, Hoboken, NJ, USA, 2021, pp. 1-528. ISBN: 9781119697961.

More [+]
Gagniuc

gagniuc.github.io

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  1. Bioinformatics-HTML5-Implementations Bioinformatics-HTML5-Implementations Public

    These All-in-one Bioinformatics HTML5/JS files accompany the book entitled: Algorithms in Bioinformatics: Theory and Implementation, and they are compatible with all internet browsers.

    HTML 6 1

  2. Information-Content-vs-Information-Entropy Information-Content-vs-Information-Entropy Public

    This is an application designed in HTML5/Javascript of a scanner that makes a comparison between two methods, namely between Shanon entropy (Information entropy) and self-sequence alignment (Inform…

    HTML 7

  3. Jupiter-Bioinformatics-V2-dark Jupiter-Bioinformatics-V2-dark Public

    Jupiter Bioinformatics (V2 - dark) - local sequence alignment, is an open source application designed in native JavaScript, that is able to align two sequences/texts in order to match the regions t…

    HTML 13

  4. Spectral-Forecast-equation-for-matrices Spectral-Forecast-equation-for-matrices Public

    A more complex example that uses the spectral forecast equation is related to matrices. A question that can be asked this time would be: given two matrices A and B, what would a third matrix (M) lo…

    HTML 5

  5. Spectral-Forecast-equation-for-signals Spectral-Forecast-equation-for-signals Public

    One of the easiest applications to understand the spectral forecast equation is related to signals. A question that can be asked would be: given two signals A and B, what would a third signal M loo…

    HTML 5

  6. Chaos-and-Noise Chaos-and-Noise Public

    Chaos & noise is an implementation that suggests by experiment that the universe is deterministic. Initially, the experiment was used to show why there are limits in predicting the behavior of phys…

    HTML 26 1