Database & Applications
Biolayout
Visualisation of biological data as networks is becoming increasingly popular for the analysis of 'omics' and other high dimensional data. These data are derived from a wide variety of biological relationships, such as interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathway, gene regulatory cascades, gene expression, etc. Biolayout Express3D is a program designed for the visualisation, clustering and analysis of large network graphs in two and three dimensional space derived primarily, but not exclusively, from biological systems.
Development of Biolayout Express3D is an ongoing collaboration between the groups of Dr Tom Freeman, Division of Pathway Medicine, University of Edinburgh and Dr Anton Enright, Sanger Institute, Cambridge and is directly funded by the BBSRC
BioLayout Express3D: To view the website of BioLayout Express 3D [click here]
EPCC
DPM and Edinburgh Parallel Computing Centre (EPCC) have collaborated on several occasions to successfully deliver applications requiring both biological and HPC specialist knowledge. For more information about our collaborative projects please [click here]
GPX MEA
The GPX Macrophage Atlas (GPX-MEA) is a web resource for expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators.
Experiments within GPX-MEA have been selected via an extensive literature and database survey using defined criteria. Data sets within GPX-MEA have been manually curated and have undergone a multi-parameter quality assessment analysis.
Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. Significantly, the database offers access to MIAME-compliant experimental information and analysis files and includes experiments and raw data previously unavailable to the public.
This is the first example of a focussed macrophage gene expression database which will allow the researcher to efficiently explore patterns of transcription and obtain novel insights into biology of this cell system.
GPX: Macrophage Expression Atlas [click here]
GPX
In addition to the macrophage-specific data-set, GPX also contains data from a diverse range of transcription profiling studies carried out at GTI. Public access to published datasets is available via GPX Discovery [click here]
GPX software is also available to download. Please [click here] for installation instructions. To Download the GPX software please [click here].
PDQ Wizard
PDQ Wizard is a web based tool that enables the rapid classification and prioritisation of large lists of gene and protein identifiers (GenBank, RefSeq, UniGene, Entrez Gene, Gene Symbols, SwissProt) using the PubMed biomedical literature database. The use of free text terms as primary input is also permitted. The classification is based on the number of literature references retrieved for each identifier and modifier pair. The system also provides novel features to:
- Further classify results
- Highlight relevant publications
- Manually inspect literature references
Try PDQ Wizard [click here]
PDQ Wizard Database Statistics
| Identifier | Count |
| Entrez Gene Ids | 1 464 437 |
| Primary Swiss Prot Ids | 190 089 |
| UniGene Ids | 215 052 |
| GenBank Accession Numbers | 2 996 223 |
| MRNA RefSeq Ids | 491 691 |
| Synonyms | 512 278 |
Download PDQ Wizard Software [click here]
Installation Manual [click here]
Alternatively the software can be downloaded from the NeSCForge website