On-line Assembling Mitochondrial DNA from de novo transcriptome

This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for reconstructing the DNA from the segments taking k-mers large enough no to generate cycles, once the sequence is ready a Boyer-Moore's algorithm implementation is used to search the genes inside de sequence using starts and stop codons, this solution give a high performance when all genes can be found, and there is no need to read all the segments to reach maximum number of genes, but due to the online nature one cannot be sure about the finals genes givenComment: 3 page

Structured Interactive Music Scores

Interactive Scores is a formalism for the design and performance of interactive scenarios that provides temporal relations (TRs) among the objects of the scenario. We can model TRs among objects in Time Stream Petri nets, but it is difficult to represent global constraints. This can be done explicitly in the Non-deterministic Timed Concurrent Constraint (ntcc) calculus. We want to formalize a heterogeneous system that controls in one subsystem the concurrent execution of the objects using ntcc, and audio and video processing in the other. We also plan to develop an automatic verifier for ntcc

Towards a correct and efficient implementation of simulation and verification tools for probabilistic ntcc

We extended our simulation tool Ntccrt for probabilistic ntcc (pntcc) models. In addition, we developed a verification tool for pntcc models. Using this tool we can prove properties such as the system will go to a successful state with probability p under t discrete time- units. Currently, we are facing a few problems. We can only verify pntcc models using a finite domain constraint system and the encoding of cells ( mathematical entities that can update their value ) is experimental. In addition, in order to reduce the states generated during the verification process we need to implement a procedure to calculate whether two processes are equivalent. In the future, we want to provide multiple interfaces for the tools (e.g., a web ap- plication, a graphical interface and command line interface). We also want to support constraint systems over trees, graph and sets. We want to show the relevance of our tool to model biological and multimedia interaction systems in our tool, verify some properties about them, and simulate such systems in our real-time capable interpreter

A General Overview of Formal Languages for Individual-Based Modelling of Ecosystems

Various formal languages have been proposed in the literature for the individual-based modelling of ecological systems. These languages differ in their treatment of time and space. Each modelling language offers a distinct view and techniques for analyzing systems. Most of the languages are based on process calculi or P systems. In this article, we present a general overview of the existing modelling languages based on process calculi. We also discuss, briefly, other approaches such as P systems, cellular automata and Petri nets. Finally, we show advantages and disadvantages of these modelling languages and we propose some future research directions.Comment: arXiv admin note: text overlap with arXiv:1610.08171 by other author

Current Trends and Future Research Directions for Interactive Music

In this review, it is explained and compared different software and formalisms used in music interaction: sequencers, computer-assisted improvisation, meta- instruments, score-following, asynchronous dataflow languages, synchronous dataflow languages, process calculi, temporal constraints and interactive scores. Formal approaches have the advantage of providing rigorous semantics of the behavior of the model and proving correctness during execution. The main disadvantage of formal approaches is lack of commercial tools