3048144
An analysis of extensible modelling for functional genomics data
BackgroundSeveral data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types. Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time.ResultsIn this paper we review the data formats that exist in functional genomics, some of which have become de facto or de jure standards, with a particular focus on how each domain has been modelled, and how each format allows extensions. We describe the tasks that are frequently performed over data formats and analyse how well each task is supported by a particular modelling structure.ConclusionFrom our analysis, we make recommendations as to the types of modelling structure that are most suitable for particular types of experimental annotation. There are several standards currently under development that we believe could benefit from systematically following a set of guidelines.
4157117
Data Access and Integration in the ISPIDER Proteomics Grid
Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources.
11348191
A note on the Gamma test
This note describes a simple technique, the Gamma (or Near Neighbour) test, which in many cases can be used to considerably simplify the design process of constructing a smooth data model such as a neural network. The Gamma test is a data analysis routine, that (in an optimal implementation) runs in time O(MlogM)as M→∞,where Mis the number of sample data points, and which aims to estimate the best Mean Squared Error (MSError) that can be achieved by any continuous or smooth (bounded first partial derivatives) data model constructed using the data.
9096556
A language extension for expressing constraints on data access
Controlled sharing of information is needed and desirable for many applications and is supported in operating systems by access control mechanisms. This paper shows how to extend programming languages to provide controlled sharing. The extension permits expression of access constraints on shared data. Access constraints can apply both to simple objects, and to objects that are components of larger objects, such as bank account records in a bank's data base. The constraints are stated declaratively, and can be enforced by static checking similar to type checking. The approach can be used to extend any strongly-typed language, but is particularly suitable for extending languages that support the notion of abstract data types.
20473212
Towards a formal theory of defeasible deontic conditionals
The paper outlines the approach to the analysis of deontic conditionals taken in earlier work of Jones and Pörn, comparing it briefly with two main trends within dyadic deontic logic, and discussing problems associated with the augmentation principle and the factual detachment principle. A modification of the Jones and Pörn system is then presented, using a classical but not normal (in the sense of Chellas) deontic modality, to provide the basis for an alternative analysis of deontic conditionals. This new analysis validates neither the factual detachment nor the augmentation principles. However, influenced by the approach of Delgrande to default reasoning, it is shown how a restricted form of factual detachment might be accommodated within the revised system.
14346877
The Construction of Smooth Models using Irregular Embeddings Determined by a Gamma Test Analysis
One of the key problems in forming a smooth model from input-output data is the determination of which input variables are relevant in predicting a given output. In this paper, we show how the Gamma test can be used to select that combination of input variables which can best be employed to form a smooth model of an output. For time series prediction this amounts to the selection of an appropriate irregular embedding. We give some simple zero noise examples of time series analysis, and illustrate how using these techniques a binary message encoded into a chaotic carrier can be retrieved without knowledge of the dynamics used to generate the carrier. Provided the underlying dynamics are such as to produce a smooth embedding model with bounded partial derivatives, the sampling distribution is dense in input space, and any associated distribution of measurement error has the first few moments bounded, so that the typical prerequisite conditions of the Gamma test are satisfied, we conclude that the Gamma test is an effective tool in the determination of irregular time series embeddings. These techniques can also be useful in practical applications which involve filtering seismic data to detect anomalous events.
206840293
Formal Specification of Security Requirements using the Theory of Normative Positions
We use a number of the examples presented in [Ting 1990] to illustrate how the formal theory of normative positions may serve as a tool for clarifying, and making precise, the specification of security requirements, particularly in regard to access control. We describe the basic features of the theory of normative positions (which has its roots in the analytical theory of law), and of the modal logics (deontic and action logics) involved in its formulation. We then indicate three levels of software we have under development, which aim to turn the analytical procedures into a practical tool. Our concluding remarks relate our discussion of Ting's examples to some particular issues in the formal specification of computer systems.