Petri Net-Based Graphical and Computational Modelling of Biological Systems

In silico modelling of biological pathways is a major endeavour of systems biology. Here we present a methodology for construction of pathway models from the literature and other sources using a biologist-friendly graphical modelling system. The pathway notation scheme, called mEPN, is based on the principles of the process diagrams and Petri nets, and facilitates both the graphical representation of complex systems as well as dynamic simulation of their activity. The protocol is divided into four sections: 1) assembly of the pathway in the yEd software package using the mEPN scheme, 2) conversion of the pathway into a computable format, 3) pathway visualisation and in silico simulation using the BioLayout Express3D software, 4) optimisation of model parameterisation. This method allows reconstruction of any metabolic, signalling and transcriptional pathway as a means of knowledge management, as well as supporting the systems level modelling of their dynamic activity.

A simple notation scheme to describe time-averaged ostracod assemblages (Crustacea, Ostracoda) by their taxonomic composition

A simple notation scheme is presented for the description of Quaternary freshwater ostracod assemblages by means of their taxonomic composition. The notation scheme also allows diagrammatic description of the fauna and assists in palaeoecological interpretation of sequential samples.

Robot deboning for beef forequarters

SUMMARYInitial development of a robotic meat cutting system based on force feedback control and continuous path planning is described. Forequarter beef cutting is attempted where each carcass processed will be compared to a database containing cut information for previously processed beef carcasses. Using the database information, cut start and end points can be defined along with initial path direction for each cut. A robot then drives a powered knife through the carcass utilising force feedback control to follow bone profiles, thus removing meat from the forequarter. An original cutting scheme suitable for robotic butchery of a beef forequarter is defined, along with a notation scheme for describing the cutting procedures.

Characteristics of Matrices Items

A range of self-completion matrices items is analyzed in terms of the general characteristics of the matrix, its cell attributes, and operations required upon cell attributes. Symmetrical items include purely symmetrical, identity and Latin square arrangements. Non-symmetrical items are evolved by summation of cell attributes or by various operations upon cell contents. A notation scheme for matrix items is appended.