An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Innovation, R&D spillovers and productivity: the role of knowledge-intensive services

This paper analyses the performance of companies’ R&D and innovation and the effects of intra- and inter-industry R&D spillover on firms’ productivity in Catalonia. The paper deals simultaneously with the performance of manufacturing and service firms, with the aim of highlighting the growing role of knowledge-intensive services in promoting innovation and productivity gains. We find that intra-industry R&D spillovers have an important effect on the productivity level of manufacturing firms, and the inter-industrial R&D spillovers related to computer and software services also play an important role, especially in high-tech manufacturing industries. The main conclusion is that the traditional classification of manufactured goods and services no longer makes sense in the ‘knowledge economy’ and in Catalonia the regional policy makers will have to design policies that favour inter-industrial R&D flows, especially from high-tech services.

Firms in Scottish High Technology Clusters: software, life sciences, microelectronics, optoelectronics and digital media – preliminary evidence and analysis on firm size, growth and optimality

This paper reports on: (a) new primary source evidence on; and (b) statistical and econometric analysis of high technology clusters in Scotland. It focuses on the following sectors: software, life sciences, microelectronics, optoelectronics, and digital media. Evidence on a postal and e-mailed questionnaire is presented and discussed under the headings of: performance, resources, collaboration & cooperation, embeddedness, and innovation. The sampled firms are characterised as being small (viz. micro-firms and SMEs), knowledge intensive (largely graduate staff), research intensive (mean spend on R&D GBP 842k), and internationalised (mainly selling to markets beyond Europe). Preliminary statistical evidence is presented on Gibrat’s Law (independence of growth and size) and the Schumpeterian Hypothesis (scale economies in R&D). Estimates suggest a short-run equilibrium size of just 100 employees, but a long-run equilibrium size of 1000 employees. Further, to achieve the Schumpeterian effect (of marked scale economies in R&D), estimates suggest that firms have to grow to very much larger sizes of beyond 3,000 employees. We argue that the principal way of achieving the latter scale may need to be by takeovers and mergers, rather than by internally driven growth.

MSight: an image analysis software for liquid chromatography-mass spectrometry.

Images obtained from high-throughput mass spectrometry (MS) contain information that remains hidden when looking at a single spectrum at a time. Image processing of liquid chromatography-MS datasets can be extremely useful for quality control, experimental monitoring and knowledge extraction. The importance of imaging in differential analysis of proteomic experiments has already been established through two-dimensional gels and can now be foreseen with MS images. We present MSight, a new software designed to construct and manipulate MS images, as well as to facilitate their analysis and comparison.

3D visualization software to analyze topological outcomes of topoisomerase reactions.

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases.

Coltop3D: A new software for structural analysis with high resolution 3D point clouds and DEM

Coltop3D is a software that performs structural analysis by using digital elevation model (DEM) and 3D point clouds acquired with terrestrial laser scanners. A color representation merging slope aspect and slope angle is used in order to obtain a unique code of color for each orientation of a local slope. Thus a continuous planar structure appears in a unique color. Several tools are included to create stereonets, to draw traces of discontinuities, or to compute automatically density stereonet. Examples are shown to demonstrate the efficiency of the method.

The MIGCLIM R package - seamless integration of dispersal constraints into projections of species distribution models

The MIGCLIM R package is a function library for the open source R software that enables the implementation of species-specific dispersal constraints into projections of species distribution models under environmental change and/or landscape fragmentation scenarios. The model is based on a cellular automaton and the basic modeling unit is a cell that is inhabited or not. Model parameters include dispersal distance and kernel, long distance dispersal, barriers to dispersal, propagule production potential and habitat invasibility. The MIGCLIM R package has been designed to be highly flexible in the parameter values it accepts, and to offer good compatibility with existing species distribution modeling software. Possible applications include the projection of future species distributions under environmental change conditions and modeling the spread of invasive species.

Modular analysis of gene expression data with R.

SUMMARY: Large sets of data, such as expression profiles from many samples, require analytic tools to reduce their complexity. The Iterative Signature Algorithm (ISA) is a biclustering algorithm. It was designed to decompose a large set of data into so-called 'modules'. In the context of gene expression data, these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different 'resolutions' of the modular mapping. In this short note, we introduce two BioConductor software packages written in GNU R: The isa2 package includes an optimized implementation of the ISA and the eisa package provides a convenient interface to run the ISA, visualize its output and put the biclusters into biological context. Potential users of these packages are all R and BioConductor users dealing with tabular (e.g. gene expression) data. AVAILABILITY: http://www.unil.ch/cbg/ISA CONTACT: sven.bergmann@unil.ch

Implementació del Sistema SAP R/3 mitjançant metodologia ASAP a una organització de caràcter industrial

Aquest treball ha de permetre a l'enginyer encarregat d'iniciar un procés de selecció d'una aplicació de gestió integral i de formar part de la futura implementació d'un sistema SAP R/3, adquirir els coneixements necessaris per a poder iniciar la implementació coneixent les possibilitats i les limitacions del sistema i l'estructura seguida en la implementació, a més dels recursos que hauran d?assignar-s?hi.

Implementació dels mòduls SD i MM del sistema SAP R/3 en una empresa del sector metal·lúrgic

SAP R/3 és un software estàndard de gestió empresarial que engloba tots els processos iactivitats d’una companyia i permet el disseny de l’aplicació a les necessitats de l’empresa.Diferents avantatges, com ara disposar d’una base de dades única, han fet escollir aquestsistema a una empresa del sector metal·lúrgic com a eina de gestió:Aquest projecte té com a objecte la implantació de dos dels mòduls que inclou el sistemaSAP R/3, concretament el mòdul SD (Sales and Distribution), amb el qual es controlen lesvendes de l’empresa, i el mòdul MM (Material Management), mòdul amb el qual es controlatot el que fa referència als materials, la gestió d’estocs i tota la gestió de compres del’empresa

Implantación de SAP R/3 en empresa comercial

El propósito del presente proyecto es el estudio de la implantación de un ERP (Enterprise Resource Planning) en una empresa del sector comercial que se dedica a la venta de perfumes y tiene diferentes comercios repartidos por todo el territorio nacional. Con esta aplicación se quiere controlar en tiempo real el stock y las ventas, y por otro lado se quiere automatizar el proceso de implantación de campañas de marketing y que los comercios apliquen los mismos precios en determinado momento.

Implantació de SAP R/3 a una empresa del sector oleic

Implementació de SAP en una empresa del sector oleic per tal d'incorporar la informació corporativa en una infraestructura única que permeti tenir les dades d'una forma centralitzada, segura i fiable. Reestructuració dels processos, eliminant tasques repetitives i activitats que no aportin valor afegit, per millorar el servei al client.

Integració i gestió dels marcatges laborals del personal d'empresa al sistema SAP R/3

L'objectiu d'aquest projecte és realitzar l'estudi i el disseny per a la corresponent implantació d'un sistema de control dels marcatges per fer el traspàs i poder-los gestionar amb SAP R/3 en un grup d'empreses.

Implantación del sistema ERP SAP R/3

El objetivo del presente trabajo ha sido realizar un estudio de investigación y desarrollo sobre la implantación del sistema Enterprise Resource Planning (ERP) SAP R/3 de una empresa.