title: Chromosome Territory Modeller and Viewer.
abstract: This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi-a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters. ChroTeMo has been developed as a fully probabilistic modeller. Due to this feature, the comparison between the experimental data on the structure of a nucleus and the results obtained from ChroTeMo can indicate whether the distribution of chromosomes inside a nucleus is also fully probabilistic or is subjected to certain non-random patterns. The presented tools have been written in Python, so they are multiplatform, portable and easy to read. Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license.
authors: Institute of Computer Science, Faculty of Material and Computer Science, University of Silesia in Katowice, Sosnowiec, Poland.
authors: Magdalena A
authors: http://orcid.org/0000-0002-3931-0474
authors: MA
authors: Tkacz
authors: Institute of Technology and Mechatronics, Faculty of Material and Computer Science, University of Silesia in Katowice, Sosnowiec, Poland.
authors: Kornel
authors: K
authors: Chromiński
authors: Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
authors: Dominika
authors: D
authors: Idziak-Helmcke
authors: Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
authors: Ewa
authors: E
authors: Robaszkiewicz
authors: Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
authors: Robert
authors: R
authors: Hasterok
mesh_terms: D019985:Benchmarking; D058431:Brachypodium / Q000166:cytology* / Q000235:genetics; D002466:Cell Nucleolus / Q000378:metabolism; D032461:Chromosomes, Plant / Q000378:metabolism*; D008954:Models, Biological; D012984:Software