The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data

M. A. O'Neill, C. C. Hilgetag
<span title="2001-08-29">2001</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="" style="color: black;">Philosophical Transactions of the Royal Society of London. Biological Sciences</a> </i> &nbsp;
Many problems in analytical biology, such as the classi¢cation of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow e¤cient computational representation and analysis of such data. The system can also be used as a general development tool for database and classi¢cation applications. As the
more &raquo; ... mplexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a £exible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in di¡erent analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-de¢ned cost functions, thus providing £exible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal e¡ectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identi¢cation system (DAISY), a system for the automated classi¢cation of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture-and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed ( as open-source software under the GNU license agreement.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1098/rstb.2001.0912</a> <a target="_blank" rel="external noopener" href="">pmid:11545702</a> <a target="_blank" rel="external noopener" href="">pmcid:PMC1088514</a> <a target="_blank" rel="external noopener" href="">fatcat:i23zkpatkjfcbhqkois53lwyvm</a> </span>
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