Matrix program to analyze primary structure homology

Using persistent homology and dynamical distances to analyze protein binding.

Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is st...

Tandem repeats finder: a program to analyze DNA sequences.

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easil...

Using Program Slicing to Analyze Aspect Oriented Composition

AspectJ language was proposed to make cross-cutting concerns clearly identifiable with special linguistic constructs called aspects. In order to analyze the properties of an aspect one should consider the aspect itself and the part of the system it affects. This part is just a slice of the entire system and can be extracted by exploiting program slicing algorithms. However, the expressive power...

Ripple: a program to collect and analyze digital topographic sequences

Homology Annotations via Matrix Reduction

In this work, we propose an alternative algorithm for annotating simplices of a simplicial complex K with sub-bases of a basis B of its p-dimensional homology group H1(K). Such annotations, summed over p-simplices in any p-cycle z, provide an expression of z in B. This allows us to answer queries of null homology and independence of p-cycles efficiently and improve the running time of the greed...