Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis

BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108

Dynamic programming for graphs on surfaces

We provide a framework for the design and analysis of dynamic programming algorithms for surface-embedded graphs on n vertices and branchwidth at most k. Our technique applies to general families of problems where standard dynamic programming runs in 2O(k·log k). Our approach combines tools from topological graph theory and analytic combinatorics.Postprint (updated version

Analytic analysis of algorithms

The average case analysis of algorithms can avail itself of the development of synthetic methods in combinatorial enumerations and in asymptotic analysis. Symbolic methods in combinatorial analysis permit to express directly the counting generating functions of wide classes of combinatorial structures. Asymptotic methods based on complex analysis permit to extract directly coefficients of structurally complicated generating functions without a need for explicit coefficient expansions. Three major groups of problems relative to algebraic equations, differential equations and iteration are presented. The range of applications includes formal languages, tree enumerations, comparison-based searching and sorting, digital structures, hashing and occupancy problems. These analytic approaches allow an abstract discussion of asymptotic properties of combinatorial structures and schemas while opening the way for automatic analysis of whole classes of combinatorial algorithms

An analytic expression of relative approximation error for a class of evolutionary algorithms

An important question in evolutionary computation is how good solutions evolutionary algorithms can produce. This paper aims to provide an analytic analysis of solution quality in terms of the relative approximation error, which is defined by the error between 1 and the approximation ratio of the solution found by an evolutionary algorithm. Since evolutionary algorithms are iterative methods, the relative approximation error is a function of generations. With the help of matrix analysis, it is possible to obtain an exact expression of such a function. In this paper, an analytic expression for calculating the relative approximation error is presented for a class of evolutionary algorithms, that is, (1+1) strictly elitist evolution algorithms. Furthermore, analytic expressions of the fitness value and the average convergence rate in each generation are also derived for this class of evolutionary algorithms. The approach is promising, and it can be extended to non-elitist or population-based algorithms too