exprDB: a flexible relational database for gene expression data

Nature genetics, 1998

Microarray technology makes it possible to simultaneously study the expression of thousands of genes during a single experiment. We have developed an information system, ArrayDB, to manage and analyse large-scale expression data. The underlying relational database was designed to allow flexibility in the nature and structure of data input and also in the generation of standard or customized reports through a web-browser interface. ArrayDB provides varied options for data retrieval and analysis tools that should facilitate the interpretation of complex hybridization results. A sampling of ArrayDB storage, retrieval and analysis capabilities is available (www.nhgri.nih.gov/DIR/LCG/15K/HTML/ ), along with information on a set of approximately 15,000 genes used to fabricate several widely used microarrays. Information stored in ArrayDB is used to provide integrated gene expression reports by linking array target sequences with NCBI's Entrez retrieval system, UniGene and KEGG pathway...

Bioinformatics, 2001

Motivation and Results: A relational schema is described for capturing highly parallel gene expression experiments using different technologies. This schema grew out of efforts to build a database for collaborators working on different biological systems and using different types of platforms in their gene expression experiments as well as different types of image quantification software. The tables are conceptually organized into three categories of information: Platform, Experiment (which includes image scanning and quantification), and Data. The strengths of the schema are: (i) integrating information on array elements using a gene index; (ii) describing samples using ontologies; (iii) reducing an experiment to a single RNA source for precise descriptions yet not losing the relationships between experiments done at the same time or for the same project; and (iv) maintaining both raw and processed (e.g. cleansed and normalized) data and recording how the data is processed. The result is a novel schema, which can hold both array and non-array data, is extensible for detailed experimental descriptions that are precise and consistent, and allows for meaningful comparisons of genes between experiments. Availability: The schema is available at

Bioinformatics/computer Applications in The Biosciences, 2005

The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for microarray data ArrayExpress we had to find novel solutions to many nontrivial software engineering problems. Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high throughput technologies.

Bioinformatics/computer Applications in The Biosciences, 1999

The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. Results: The GeneExpress system developed includes the following major informational and software systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5′-untranslated regions (5′-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. Availability: GeneExpress is available at http://wwwmgs. bionet.nsc.ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/ mgs/links/mirrors.html Contact: kol@bionet.nsc.ru Vol. 15 nos 7/8 1999 Pages 669-686 669 E Oxford University Press 1999 BIOINFORMATICS N.A.Kolchanov et al.

2024

The author discusses the historical growth of thermodynamics, in particular the combination of the first and second laws of thermodynamics. The historical discussion of the important contributions is interesting. The paper is, however, quite long. The paper is in need of a substantial reduction in size and a clearer focus on the most important points of the work.

Cuando somos niños y a medida que vamos explorando el mundo, a modo de experiencia vamos registrando los espacios y cada elemento que los compones, textura, colores olores dureza, la forma en que entra el sol, formas de herrajes de las ventanas las formas de las manijas en nuestras

American Journal of Sociology, 2024

Review of Sun Ra’s Chicago: Afrofuturism and the City. By William Sites. It’s somewhat paradoxical that when writing about Sun Ra, discussing as- pects of his work and life, from music to philosophy, and his role as found- ing figure in Afrofuturism, is made more difficult by the figure of Ra himself. How, or why, is this? It is because in the accounts of his life and work, it is easy to approach and become enamored by Ra as a larger-than-life figure and to stay focused on his idiosyncratic personal traits, more so than the context and times from which he emerged and to which he responded. This is precisely what William Sites’s book Sun Ra’s Chicago does very well: it steps back from engaging with Ra’s performative persona to examine the context in which this performative persona was developed and shaped. As Sites puts it in the introduction, Ra’s “self-presentation as a traveler from a different world can overshadow his creative and often deeply critical en- gagement with this one” (p. 2). By stepping back in this manner, we get a different sense of that critical and creative engagement that leads to emer- gence of Ra the free jazz band leader from outer space.