Corridors for LIFE; ecological network analysis Regione Emilia-Romagna - the plains of Provincia di Modena & Bologna

This report gives the result of an analysis of the ecological network, designed for the agricultural plains of the Provinces of Modena and and Bologna. Three ecosystem types were selected: woodland, wetland, and grassland. Species were selected which can be considered representative of these ecosystems. The LARCH model was used to assess whether these ecosystems still function as an ecological network. We found that the region has a serious fragmentation problem. After implementation of the ecological network the situation would improve much. Larger areas for nature rehabilitation would further improve the functioning of the ecological network

FORM version 4.0

We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Groebner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Lastly, FORM 4.0 has become available as open source under the GNU General Public License version 3.Comment: 26 pages. Uses axodra

Types and concept analysis for legacy systems

We combine type inference and concept analysis in order to gain insight into legacy software systems. Type inference for Cobol yields the types for variables and program parameters. These types are used to perform mathematical concept analysis on legacy systems. We have developed ConceptRefinery, a tool for interactively manipulating concepts. We show how this tools facilitates experiments with concept analysis, and lets reengineers employ their knowedge of the legacy system to refine the results of concept analysis

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Unbiased computation of transition times by pathway recombination

In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these systems, direct simulation of phase space trajectories does not efficiently determine most physical quantities of interest. The last decade has seen the advent of methods circumventing brute force simulation. For most dynamical quantities, these methods all share the drawback of systematical errors. We present a novel method for generating ensembles of phase space trajectories. By sampling small pieces of these trajectories in different phase space domains and piecing them together in a smart way using equilibrium properties, we obtain physical quantities such as transition times. This method does not have any systematic error and is very efficient; the computational effort to calculate the first passage time across a free energy barrier does not increase with the height of the barrier. The strength of the method is shown in the Ising model. Accurate measurements of nucleation times span almost ten orders of magnitude and reveal corrections to classical nucleation theory.Comment: 8 pages, 4 figure