Search Based Software Engineering in Membrane Computing

This paper presents a testing approach for kernel P Systems (kP systems), based on test data generation for a given scenario. This method uses Genetic Algorithms to generate the input sets needed to trigger the given computation steps

Testing Identifiable Kernel P Systems Using an X-machine Approach

This paper presents a testing approach for kernel P systems (kP systems), based on the X-machine testing framework and the concept of cover automaton. The testing methodology ensures that the implementation conforms the speci cations, under certain conditions, such as the identi ably concept in the context of kernel P systems

Comparison and Mapping Facilitate Relation Discovery and Predication

Relational concepts play a central role in human perception and cognition, but little is known about how they are acquired. For example, how do we come to understand that physical force is a higher-order multiplicative relation between mass and acceleration, or that two circles are the same-shape in the same way that two squares are? A recent model of relational learning, DORA (Discovery of Relations by Analogy; Doumas, Hummel & Sandhofer, 2008), predicts that comparison and analogical mapping play a central role in the discovery and predication of novel higher-order relations. We report two experiments testing and confirming this prediction

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license

Motility at the origin of life: Its characterization and a model

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first" approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an impoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate timescales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct timescales, which are typically associated with metabolism, motility, development, and evolution. On this view, self-movement, adaptive behavior and morphological changes could have already been present at the origin of life. In order to illustrate this possibility we analyze a minimal model of life-like phenomena, namely of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis we suggest that processes in intermediate timescales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced timescales of chemical self-individuation and evolution by natural selection, respectively.Comment: 29 pages, 5 figures, Artificial Lif

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

The PDBTM database (available at http://pdbtm .enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ~400 to 1700 entries but also new structural elements have been identified, in addition to the well-known a-helical bundle and b-barrel structures. Numerous ‘exotic’ transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community

Containment and reciprocity in biological systems : a putative psychophysical organising principle

The stuff of life, the living substance that is common to all biological organisms, is the aqueous society of biochemical activity ongoing in every cell in every living body. The basic biochemical ‘reactions’ of life are largely similar with variations of a theme played out in different cells living in different environment, e.g. the core biochemical metabolic processes of all life likely stem from an ancient, early-earth ancestor (Smith & Morowitz, 2004). However, even more common to life than shared biochemistry are the basic structural properties of all cells and all living organisms into complexes of compartmentalised units. In this paper, I will argue there are common feelings driving the generation of these ubiquitous structures in nature and that these feelings may constitute one of several primary forms of feeling in living systems

Ontology-assisted database integration to support natural language processing and biomedical data-mining

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language

Life as an Explanation of the Measurement Problem

No consensus regarding the universal validity of any particular interpretation of the measurement problem has been reached so far. The problem manifests strongly in various Wigner's-friend-type experiments where different observers experience different realities measuring the same quantum system. But only classical information obeys the second law of thermodynamics and can be perceived solely at the holographic screen of the closed orientable two-dimensional manifold implied by Verlinde's and Landauer's mass-information equivalence equations. I conjecture that biological cell, as a dissipative structure, is the smallest agent capable of processing quantum information through its holographic screen and that this mechanism have been extended by natural evolution to endo- and exosemiosis in multicellular organisms, and further to language of Homo sapiens. Any external stimuli must be measured and classified by the cell in the context of classical information to provide it with an evolutionary gain. Quantum information contained in a pure quantum state cannot be classified, while incoherent mixtures of non-orthogonal quantum states are only partially classifiable. The concept of an unobservable velocity, normal to the holographic screen is introduced. It is shown that it enables to derive the Unruh acceleration as acting normal to the screen, as well as to conveniently relate de Broglie and Compton wavelengths. It follows that the perceived universe, is induced by the set of Pythagorean triples, while all its measurable features, including perceived dimensionality, are set to maximise informational diversity.Comment: This research is incomplete and partially incorrec