Paul A. Gagniuc's Projects
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.
Here are all the Markov Chain algorithms in PHP that are associated with the book entitled Markov chains: from theory to implementation and experimentation.
A sequence of digits that never ends and never exhibits any clear patterns, is scratchy for any questioning mind. The main question in regard to this project is: Are there patterns in the digits of irrational numbers? PI laboratory is a scanner that tries to show patterns in the digits of irrational numbers, in a graphical manner.
Predictions with Markov Chains is a JS application that multiplies 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 n steps.
This section contains all the original presentations from the supplementary materials related to the book entitled: Algorithms in Bioinformatics: Theory and Implementation. The presentations contain original content related to biology, bioinformatics, genetics, genomics, physics, as well as algorithms or software programming implementations.
A total of 44 poster presentations and 404 source code examples reflected in nine computer languages, namely: C#, C++, Java, JavaScript, PERL, PHP, Python, Ruby and VB.
PromKappa 1.0 is a complete application made in Visual Basic 6.0 (VB6) that generates Objective Digital Stains (aka DNA patterns).
PromKappa V2.0 generates Objective Digital Stains (also called DNA patterns in the past). This is the second version of the application and it is made in Visual Basic 6.0 (VB6).
PromKappa 3.0 is a complete application made in Visual Basic 6.0 (VB6) that generates Objective Digital Stains (aka DNA patterns). The main output of the application consists of a series of images that are saved in the 'chart' (or 'chart_comp') folder and which can be later analyzed using different methods.
Photon-pixel coupling is a novel method that allows a parallel sampling of an unlimited number of sensors. In the case shown here, 200 sensors are sampled in parallel at video rate frequency. This implementation is done in Visual Basic 6.0 (VB6).
This JavaScript implementation detects the areas where two RNA sequences are complementary to each other. All symbols from UTF-8 are accepted by this algorithm.
Self-sequence alignment represents a novel mathematical model for measuring the information content in biological sequences, such as DNA, RNA, or proteins. Nevertheless, the use of this model is not limited to biological sequences. Thus, any symbol inside a sequence can be considered.
Sequence Logo - block style 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 a html file.
Sequence Logo - block style with axes (native Java Script) 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.
Sequence Logo - relative style is an alternative that provides full control over how the graphics of a Sequence Logo should look like, and is an alternative to an application called WebLogo. All the inner workings of this open source application are written in native javascript.
Sequence Logo - relative style with axes 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 a html file.
Sequence Logos based on maximum values 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.
Sequence Logos using logarithms 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 a html file.
Signal processing with Spectral Forecast - is a demo application designed in Javascript, that is able to mix two signals (A and B) in arbitrary proportions. Different cases can be seen, with two different waveform signals that are combined depending on a value d.
Simple JS implementation of Objective Digital Stain (ODS) produces ODS images from DNA sequences. 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.
This highly responsive VB6 application is an implementation of the global sequence alignment algorithm. It allows the modification of the alignment parameters (match, mismatch, gap), and it shows the pairwise alignment as well as the score matrix in real time. The purpose of it is to seeks the optimal alignment between two text sequences.
It demonstrates the use of a single "for-loop" in traversing a matrix. The example shown here is made in 10 programming languages: C#, C++, Java, Javascript, PERL, PHP, Python, Ruby and VB/VBA.
It demonstrates the use of a single "for-loop" in traversing three-dimensional arrays. The example shown here is made in Javascript.
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) look like if it must resemble both A and B in a certain proportion?
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 look like if it must resemble both signals in a certain proportion?
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) look like if it must resemble both A and B in a certain proportion?
Spectral forecast is a novel general-purpose prediction model recently published in the journal CHAOS. The model revolves around three known states: two extreme outcomes (A and B) and one measurement (P). These states are represented by either vectors or matrices that include sets of homologous parameters.
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