Biomedical subjects

Tim Rayner

Publications and source records attributed to Tim Rayner.

3 recordsLinked to original sources

PubMed2005

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.

ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data sets represent approximately one-quarter of the experiments in ArrayExpress. The majority are based on Arabidopsis (Arabidopsis thaliana); however, there are other data sets based on Triticum aestivum, Hordeum vulgare, and Populus subsp. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. AtMIAMExpress exports data in MAGE-ML format for upload to any MAGE-ML-compliant application, such as J-Express and ArrayExpress. It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis community. Plant data are queryable both in ArrayExpress and in the Data Warehouse databases, which support queries based on gene-centric and sample-centric annotation. The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk.

Academies and Institutes↗

PubMed2004

The ArrayExpress gene expression database: a software engineering and implementation perspective.

MOTIVATION: 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 non-trivial 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. RESULTS: ArrayExpress has been online since February 2002, growing exponentially to well over 10,000 hybridizations (as of September 2004). It has been demonstrated that our chosen design and implementation works for databases aimed at storage, access and sharing of high-throughput data. AVAILABILITY: The ArrayExpress database is available at http://www.ebi.ac.uk/arrayexpress/. The software is open source. CONTACT: ugis@ebi.ac.uk.

Algorithms↗

PubMedDate not supplied

The effect of a dissolvable hyaluronic acid-based pack on the healing of the nasal mucosa of sheep.

INTRODUCTION: There is a paucity of knowledge about the healing of the nasal respiratory mucosa after endoscopic sinus surgery (ESS). Nasal packs often are placed after ESS in an attempt to reduce adhesions but the effect of these packs on the healing of the nasal mucosa is not known. METHODS: A standardized normal animal model (the sheep) was used to examine the healing of the nasal epithelium after ESS. A full-thickness wound was created in the nasal mucosa and either packed with a dissolvable hyaluronic acid-based pack or left unpacked to serve as control. The wounded areas were biopsied at 28, 56, 84, and 112 days postinjury and epithelialization, and cilial regeneration was assessed by light microscopy and scanning electron microscopy. RESULTS: The wounds with the dissolvable hyaluronic acid-based packs showed no differences in reepithelialization up to 84 days postwounding. However, a significant increase in reepithelialization was observed on day 84 in packed wounds compared with unpacked controls, indicating an increased rate of healing at that time point. In addition, there was a significant increase in the epithelial height in the packed wounds on day 28, indicating that packing was affecting the epithelial maturity of the mucosa. No significant difference was observed in cilial regeneration between the packed and control wounds. CONCLUSIONS: Application of the hyaluronic acid-based nasal packs to wounds after ESS may improve reepithelialization of the nasal mucosa but appears to have minimal effect on reciliation at the time points studied in normal-healing wounds.

Adjuvants, Immunologic↗