Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

Generating derivative structures: Algorithm and applications

We present an algorithm for generating all derivative superstructures--for arbitrary parent structures and for any number of atom types. This algorithm enumerates superlattices and atomic configurations in a geometry-independent way. The key concept is to use the quotient group associated with each superlattice to determine all unique atomic configurations. The run time of the algorithm scales linearly with the number of unique structures found. We show several applications demonstrating how the algorithm can be used in materials design problems. We predict an altogether new crystal structure in Cd-Pt and Pd-Pt, and several new ground states in Pd-rich and Pt-rich binary systems

On Role Logic

We present role logic, a notation for describing properties of relational structures in shape analysis, databases, and knowledge bases. We construct role logic using the ideas of de Bruijn's notation for lambda calculus, an encoding of first-order logic in lambda calculus, and a simple rule for implicit arguments of unary and binary predicates. The unrestricted version of role logic has the expressive power of first-order logic with transitive closure. Using a syntactic restriction on role logic formulas, we identify a natural fragment RL^2 of role logic. We show that the RL^2 fragment has the same expressive power as two-variable logic with counting C^2 and is therefore decidable. We present a translation of an imperative language into the decidable fragment RL^2, which allows compositional verification of programs that manipulate relational structures. In addition, we show how RL^2 encodes boolean shape analysis constraints and an expressive description logic.Comment: 20 pages. Our later SAS 2004 result builds on this wor

Model counting for complex data structures

We extend recent approaches for calculating the probability of program behaviors, to allow model counting for complex data structures with numeric fields. We use symbolic execution with lazy initialization to compute the input structures leading to the occurrence of a target event, while keeping a symbolic representation of the constraints on the numeric data. Off-the-shelf model counting tools are used to count the solutions for numerical constraints and field bounds encoding data structure invariants are used to reduce the search space. The technique is implemented in the Symbolic PathFinder tool and evaluated on several complex data structures. Results show that the technique is much faster than an enumeration-based method that uses the Korat tool and also highlight the benefits of using the field bounds to speed up the analysis

VeloCité – Development of an Energy Storage System for an E-bike

AbstractWithin the framework of the development of an energy storage system for a lightweight electric bicycle the electric behavior of LiFePO4 cells was investigated. We propose a systematic and efficient procedure for identification and parameterization of a cell model based on measurements in the time domain. An equivalent circuit model approach was adopted using parameters dependent on temperature and state of charge. The model was parameterized for a wide range of operational conditions concerning temperature, state of charge and cell current. Finally, the accuracy of the proposed model is shown by the comparison of simulation results with real measurements of the given cell using a highly dynamic driving cycle