Background: Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools ...
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Background: Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Results: Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification o
This special issue of PRIA is devoted to some scientific results and trends of the 25th International Conference on Pattern Recognition (Virtual, Milano, Italy, January 10-15, 2021). Two important events of ICPR-2020 ...
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This special issue of PRIA is devoted to some scientific results and trends of the 25th International Conference on Pattern Recognition (Virtual, Milano, Italy, January 10-15, 2021). Two important events of ICPR-2020 are represented in this special issue: (1) The paper of Professor Ching Yee Suen (Centre for Pattern Recognition and Machine Intelligence, Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada)-the recent winner of IAPR very prestigious K.S. Fu Prize for a year of 2020. The paper based on his lecture "From handwriting to human personality and facial beauty" presented at the ICPR 2020;(2) Special issue "ICPR-2020 Workshop "Image Mining. Theory and Applications." The analysis of the scientific contribution of IMTA-VII-2021 allows us to draw the following conclusions: (1) The construction of a unified mathematical theory of image analysis is still far from complete. (2) There is considerable interest in the development of new mathematical methods for analyzing and evaluating information presented in the form of images. (3) There is a tendency to expand the mathematical apparatus in the development of new methods of image analysis and recognition by involving in this process areas of mathematics that were not previously used in image analysis. (4) The gap between the capabilities of new mathematical methods of image analysis and recognition and their actual use in solving applied problems remains significant. (5) There is an excessive use of neural networks in solving applied problems of image analysis and image recognition, and quite often without proper justification and interpretation of the results. The special issue includes articles based on the workshop papers selected by the IMTA-VII-2021 Program Committee for publication in PRIA. The PRIA special issue "Scientific Resume of the 25th International Conference on Pattern Recognition" is prepared by the National Committee for Pattern Recognition and Image A
dataanalysis as a prerequisite for decision support is still done manually in most companies. This paper describes principles and methods for dataanalysisautomation and a software system that represents the state o...
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dataanalysis as a prerequisite for decision support is still done manually in most companies. This paper describes principles and methods for dataanalysisautomation and a software system that represents the state of the art in this field.
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