Paul A. Gagniuc's Projects
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 that are similar.
Jupiter Bioinformatics (V2) uses the local sequence alignment algorithm and a few stored experiments for further experimentation on sequence alignment. It is an open source application designed in native JavaScript, that is able to align two sequences/texts in order to match the regions that are similar.
Jupiter Bioinformatics (V2 - normal) - 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 that are similar. Different interesting experimental designs can be accomplished with it, starting from bioinformatics/genetics to grammar and language studies. In mathematics for instance, such a strategy can be used in research to align the digits of irrational numbers or number sequences in general to find out the similarities between them.
Linear congruential generator (LCG) is an application that demonstrates the generation of pseudo-random numbers. The LCG is a specialized mathematical function (deterministic algorithm) for simulation of “random” numbers. The numbers generated by LCG are called pseudo-random numbers.
This JavaScript implementation detects the areas where two DNA/RNA/protein sequences are similar to each other. All symbols from UTF-8 are accepted by this algorithm.
This software is mapping pixels to LED positions. The coordinates of each LED position is recorded as a string inside an array variable. The array variable is printed as a VB6 source code in a textbox object. Next, the content of the textbox object is manually copied inside the VB6 source code of the Vesta software.
A Markov Chain Generator (MCG) is a prediction machine that uses a transition matrix to generate sequences that are similar to the training sequence. Thus, the output of a MCG mimics the training sequence that led to the values from the transition matrix and the process itself represents a prediction.
The current VB6 application is a detector that uses observation sequences to construct the transition matrices for two models, which are merged into a single log-likelihood matrix (LLM). A scanner can use this LLM to search for regions of interest inside a longer sequence called z (the target).
Here are all the Markov Chain algorithms in java script that are associated with the book entitled Markov chains: from theory to implementation and experimentation.
This application makes predictions by multiplying a probability vector with a transition matrix multiple times (n steps - user defined). On each step the values from the resulting probability vectors are plotted on a chart. The resulting curves on the chart indicate the behavior of the system over a number of steps.
The current JS application is a detector that uses observation sequences to construct the transition matrices for two models, which are merged into a single log-likelihood matrix (LLM). A scanner can use this LLM to search for regions of interest inside a longer sequence called z (the target).
The Markov Chains - Simulation framework is a Markov Chain Generator that uses probability values from a transition matrix to generate strings. At each step the new string is analyzed and the letter frequencies are computed. These frequencies are displayed as signals on a graph at each step in order to capture the overall behavior of the MCG.
This application uses a transition matrix to make predictions by using a Markov chain. For exemplification, the values from the transition matrix represent the transition probabilities between two states found in a sequence of observations.
Markov Chains in Visual Basic 6.0 (VB6) - These applications use transition matrices to make predictions by using a Markov chain. For exemplification, the values from the transition matrix, in any of the three applications, represent the transition probabilities between two states found in a sequence of observations.
This compact chart takes into account both positive and negative values from an input. Thus, this VB chart takes into account a lower bound as well as an upper bound. The lower bound represents the lowest value whereas the upper bound represents the highest value over the input.
Spectral Forecast equation (VB6 app 1.0) - is a demo application designed in Visual Basic 6.0, that is able to mix two signals in arbitrary proportions. Different cases can be seen, with two different waveform signals that are combined depending on the value of a parameter called distance.
This is a demo application designed in Visual Basic 6.0, that is able to mix two signals in arbitrary proportions. Different cases can be seen, with two different waveform signals that are combined depending on the value of a parameter called distance d. This distance d can be defined from zero to the maximum value found above the two vectors.
This is an implementation designed in C#. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in Java. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in Javascript. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in Perl. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in PHP. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in Python. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in Ruby. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This is an implementation designed in VB6/VBA. This implementation is able to mix two signals/vectors (A and B) in arbitrary proportions. This source code uses a novel mathematical model published in the journal Chaos. The model is called Spectral Forecast.
This application searches inside a text sequence for words that resemble those inside a list of similar words.
The projects in this repository show a series of js charts of two types. Both of these types use the HTML5 canvas object. The first type of chart provides a normal linear plot and the second type is a circular model.
This is an application that shows the informational structure of DNA sequences. The objective digital stain (ODS) is represented by a distribution of points on a two-dimensional image, which reflects the information structure inside a DNA/RNA sequence.
This code generates Objective Digital Stains (ODSs) and it is implemented in PHP. On ODSs, the information content (IC) is represented vertically on the y-axis and the frequency of different letters is represented horizontally on the x-axis.
Ordered Sequence Logo based on existing matrices is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet once it is saved as html.
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