CULSPIN is a free application in the field of chemical-theoretical graphs (applied mathematics) programmed in the Python language and used by the module wxPython to create the graphical environment. This module is also used in the creation and help display (plain HTML format) and the graphical spirals generated by the application. CULSPIN runs on the Microsoft XP/Vista operating system. CULSPIN transforms any sequence of letters into a graphic representation that uses the Ulam spiral as a template (arrangement of natural numbers in the form spiral) and in which those nodes that belong to the same class (have the same letter) are connected.
In addition, based on that graph, CULSPIN calculates two families of Indexes Topological (TIs). These indices can be calculated at several levels: for each one, the classes in each Ulam gnomon, for each of the classes in the entire graph and for each gnomon independent of classes. On the other hand, the 2D graphs (Graphs-U) generated by the application, in addition to being viewed, they can be exported for the purpose of to be able to use them in other programs to calculate other families of TIs. All index Numerical numbers can be saved and/or exported and with them you can perform various statistical analysis or create QSAR (structure-property relationship) models. examples of sequences are the amino acid chains of proteins, nucleic acids, and protein mass spectra. CULSPIN can be used to study different systems, from simple systems of atoms in anti-cancer small molecules, to complex systems of metabolic, social, computational networks or systems biological.
Related Algorithms:
CULSPIN is a variant of the MI algorithm MARCH-INSIDE: Markov Chain Invariants for Networks Simulation and Design MARCH-INSIDE (MI), is a well-known method introduced by Prof. Humbert G Díaz (Gonzaléz-Díaz et al.) as early as 2002 for the calculation of Markov Invariants (Moments, Shanon entropies, Mean Markov values) of molecular graphs and complext netxorks using a Markov chain stchastic approach.
MI is the basis for posterior softwares developmed a posteriori by other authors in co-authorship with Prof González-Díaz or independently. Some of these are: Sequence to Stars Networks (S2SNET) by C.R. Munteanu and González-Díaz H. https://github.com/muntisa/S2SNet); R-Markov Topological Indices (RMARKOVTI) by C.R. Munteanu https://github.com/muntisa/RMarkovTI, S2SNET Phyton (PyS2SNET) by C.R. Munteanu https://github.com/muntisa/pyS2SNet, etc.
CULSPIN transforms sequences of characters (text, gene, proteins, etc.) into Ulam's spirals. The Ulam spiral or prime spiral is a graphical depiction of the set of prime numbers, devised by mathematician Stanisław Ulam in 1963 and popularized in Martin Gardner's Mathematical Games column in Scientific American a short time later. It is constructed by writing the positive integers in a square spiral and specially marking the prime numbers, https://en.wikipedia.org/wiki/Ulam_spiral. After that, the software CULSPIN visualize the Ulam's spiral representations of the input. Next, it uses the MI algorithm to calculate different invariants of the sequence studided using Markov Chains (https://en.wikipedia.org/wiki/Markov_chain). Last, CULSPIN export the values of the numerical parameters ready for use as inputs in Artificial Intelligence / Machine Learning (AI/ML) studies.
Contact: In case you want to develop new collaborations, applications, etc. related to MI algorith please do not hesitate to contact us at: https://www.linkedin.com/in/humbertgdiaz/
What can CULSPIN do? • Read sequences of letters organized by rows or columns from files txt; • Read FASTA format sequences stored in TXT files; • Read numerical sequences or series, organized by rows or columns from of TXT files; • Read numerical data corresponding to signals from Mass Spectra (MS) to from multiple TXT or CSV files; • Convert strings or strings of numbers and MS data into strings of letters; • Transform any sequence of letters into its corresponding Grapho-U. connecting the nodes that belong to the same class (they have the same letter); • Calculate two families of TIs using the generated U-Graphs and show their values in a table; • Graph and Visualize the U-Graph of the sequence that is selected; • Export the connectivity information of the Grafo-U in CT files or NET; • Save the calculated TIs in TXT or CSV files.
Repository files: The application uploaded to this repository can be used: without compiling it, if you have installed Python 2.4 or 2.5 and wxPython version 2.8 for guarantee absolute compatibility: ▪ CULSPIN_v_1_0.py in the CULSPIN_v_1_0_codes folder ▪ Compiled with the py2exe module, on Microsoft Windows XP/Vista: ▪ CULSPIN_v_1_0.exe in the CULSPIN_v_1_0_exe_distribution folder Note: for correct operation, the files and subfolders are required included in both distributions.
▪ Programming language: Python, wxPython, HTML;
- Operating system: Microsoft XP and Vista. File Lists Memory: CULSPIN v-1.02 List of original modules Source files (Python): CULSPIN_v_1_0.py FiltersSeq_v_1_0_imp.py BuildSpiral_v_1_0_imp.py ▪ CalcIndices_v_1_0_imp.py Grid_v_1_0_imp.py SpiralGraph_v_1_0_imp.py HelpHtml_v_1_0_imp.py About_v_1_0_imp.py Supplementary File List Supplementary files for the graphical interface: ❝ bibliohelp.jpg ❝ about.png* ❝ about.ico* bitmaphelp.jpg build.png help.ico* ↓ calculate.jpg ↔ export.png ↔ icon.ico ❝ cha01graphhelp.jpg ❝ gtk-quit.png* ↓ classnumericas.jpg ↔ help.png* ↑ fshdefinition.jpg ↔ makecopy.png* ↑ gnomoneshelp1.jpg ↔ open.png* gnomoneshelp2.jpg reload.png* ↔ gridindices.jpg ↔ save.png* ↑ indiceslevels.jpg ↔ spiral.png start.jpg starthelp.jpg inputfileformat.jpg listbox1.jpg listbox2.jpg listbox3.jpg menubar.jpg MyAbout.jpg acionsculspin.jpg spiralnum.jpg ڀ tableindiceshelp.jpg
- Images taken from the free KDE sources of a Linux distribution; the rest They are own creation. File Lists
Memory: CULSPIN v-1.03 Supplementary files examples of input files, useful for checking the proper functioning of the application: ❖ testing codes leter byrow1.txt ❖ testing ms D50.csv Testing codes leter byrow2.txt Testing ms daf-0780.csv test codes leter byrow3.txt Testing codes letter bycol1.txt test codes num bycol1.txt test codes num bycol2.txt test codes num byrow1.txt test fasta.txt ↔ testing ms 1.txt ↔ testing ms 2.txt Testing ms daf-0625.txt ❝ testing ms f05 h.txt