CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis

CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays. R and packages from the Bioconductor project are used as an analytical engine in combination with the R function Sweave, which allows automatic generation of analysis reports. These report files contain all R commands used to perform the analysis and guarantee therefore a maximum transparency and reproducibility for each analysis. The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at

GOLD.db: genomics of lipid-associated disorders database

BACKGROUND: The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders. DESCRIPTION: The GOLD.db provides a reference for pathways and information about the relevant genes and proteins in an efficiently organized way. The main focus was to provide biological pathways with image maps and visual pathway information for lipid metabolism and obesity-related research. This database provides also the possibility to map gene expression data individually to each pathway. Gene expression at different experimental conditions can be viewed sequentially in context of the pathway. Related large scale gene expression data sets were provided and can be searched for specific genes to integrate information regarding their expression levels in different studies and conditions. Analytic and data mining tools, reagents, protocols, references, and links to relevant genomic resources were included in the database. Finally, the usability of the database was demonstrated using an example about the regulation of Pten mRNA during adipocyte differentiation in the context of relevant pathways. CONCLUSIONS: The GOLD.db will be a valuable tool that allow researchers to efficiently analyze patterns of gene expression and to display them in a variety of useful and informative ways, allowing outside researchers to perform queries pertaining to gene expression results in the context of biological processes and pathways

MARS: Microarray analysis, retrieval, and storage system

BACKGROUND: Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. RESULTS: MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. CONCLUSION: We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

<p>Abstract</p> <p>Background</p> <p>The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches.</p> <p>Results</p> <p>We have developed the MAss SPECTRometry Analysis System (MASPECTRAS), a platform for management and analysis of proteomics LC-MS/MS data. MASPECTRAS is based on the Proteome Experimental Data Repository (PEDRo) relational database schema and follows the guidelines of the Proteomics Standards Initiative (PSI). Analysis modules include: 1) import and parsing of the results from the search engines SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA; 2) peptide validation, 3) clustering of proteins based on Markov Clustering and multiple alignments; and 4) quantification using the Automated Statistical Analysis of Protein Abundance Ratios algorithm (ASAPRatio). The system provides customizable data retrieval and visualization tools, as well as export to PRoteomics IDEntifications public repository (PRIDE). MASPECTRAS is freely available at <url>http://genome.tugraz.at/maspectras</url></p> <p>Conclusion</p> <p>Given the unique features and the flexibility due to the use of standard software technology, our platform represents significant advance and could be of great interest to the proteomics community.</p

Digitalized Mobility

In our research commentary, we take up the topic of the digitalization of mobility and show how digital technologies impact mobility and transport. We describe the four main characteristics of Digitalized Mobility, (i) people and goods, (ii) infrastructure, (iii) mobility and transport data, and (iv) data-driven services, so-called digitalized mobility services. In a conceptual, multilayered model with the three building blocks (1) mobility and transport artifacts, (2) data storage and processing and (3) Digitalized Mobility Services, we outline how data-based services ultimately emerge from the data generated within the mobility and transport ecosystem and illustrate this process in a fictitious case study. Finally, in our research agenda, we capture research questions on digitalized mobility relevant to the IS community

Characteristics of High-Temperature Torrefied Wood Pellets for Use in a Blast Furnace Injection System

As the iron and steel industry needs to cut its CO2 emissions drastically, much effort has been put into establishing new&mdash;less greenhouse-gas-intensive&mdash;production lines fueled by hydrogen and electricity. Blast furnaces, as a central element of hot iron production, are expected to lose importance, at least in European production strategies. Yet, blast furnaces could play a significant role in the transitional phase, as they allow for the implementation of another CO2-reducing fuel, carbonized wood reducing agents, as a substitute for coal in auxiliary injection systems, which are currently widely used. Wood carbonization yields vastly differing fuel types depending on the severity of the treatment process, mainly its peak temperature. The goal of this study is to define the lowest treatment temperature, i.e., torrefaction temperature, which results in a biogenic reducing agent readily employable in existing coal injection systems, focusing on their conveying properties. Samples of different treatment temperatures ranging from 285 to 340 &deg;C were produced and compared to injection coal regarding their chemical and mechanical properties. The critical conveyability in a standard dense-phase pneumatic conveying system was demonstrated with a sample of pilot-scale high-temperature torrefaction

A Research Agenda for Vehicle Information Systems

As modern cars have transformed to computers on wheels, digitalization is an important driver of ser-vice and business innovation within the automotive domain. As a new class of information systems (IS), vehicle information systems (Vehicle IS) are enabled through the data generated by a plethora of different sensors within modern vehicles, meshed up with data from a variety of different other sources. Expecting the awareness on and the needs for Vehicle IS to steadily increase in the future - as a result of the continuing provision of driver assistance systems towards fully automation - we investigate existing literature on Vehicle IS published by the academic IS community. To get an overview on topics discussed so far as well as publication activity in general, we use the AIS Electronic Library as an indicator. We then provide a definition of the term ‘vehicle information system’ and give an overview of relevant research directions with a set of example research questions, which we deem important for the academic IS community to advance the state-of-the-art in designing Vehicle IS