EMSL Scientific Grand Challenge: Membrane Biology
Membrane Biology GC Resources
- Meet the Team
- Advisory Committee
- What Are Cyanobacteria?
- Project Achievements
- In the News
- 2005-2007 Progress Report
- Presentations
- Related Links
Additional Information
Achievements: Software
The experimental tasks of the Membrane Biology Grand Challenge have provided the data required for the generation of models and model systems. Several analytical and visual analytics software applications developed by the project have been made available for use on data generated by the Membrane Biology Grand Challenge team that focusses on:
- Interactions of membrane proteins and membrane systems
- Energy production
- The central "clock" apparatus which in part drives the switch from N-fixation to photosynthetic energy production and back.
The suite of analytical tools for managing, browsing and interrogating datasets includes Similarity Box, ScalaBLAST, SEBINI and PQuad, and they are all available for general use.
Similarity Box
What it is: A genome context mining and browsing tool.
What it does: Combines sequence similarity with chromosomal or plasmid location information to give evolutionary or functional superfamily classification information. For example, consider three different proteins which are all highly conserved across many species. Similarity Box can be used to draw evolutionary inferences across species by grouping together species in which the genes encoding for these three proteins appear as neighbors.
It incorporates an interactive dendrogram viewer and powerful clustering tools into a single application and allows users to mine information from sequence-derived analysis such as BLAST hits or bidirectional similarity scores in conjunction with genome context or position of genes on genomes of closely-related organisms. More information on Similarity Box.
ScalaBLAST
What it is: A high-performance BLAST engine.
What it does: Uses multiprocessor environments to share a target database across memory, thereby eliminating the need for frequent file access. It is a highly scalable implementation of the NCBI BLAST algorithm and has been used to perform whole genome or multiple genome BLAST calculations against a variety of databases on the EMSL MSCF supercomputer, MPP2. Compared to BLAST, ScalaBLAST is up to 1500 times faster on real datasets, making it possible to perform the equivalent of three years' work on a dedicated single machine in less than a day. More information on ScalaBLAST.
SEBINI
What it is: A platform that aids in more accurate reconstruction of the topology of regulatory and interaction networks, with much less effort, in less time.
What it does: Allows users to upload datasets from microarray studies or proteomics analysis, or create synthetic networks of various topologies, and extract inferred regulatory or interaction networks using a collection of network inference tools, including mutual information algorithm, pearson correlation, and bayesian network structure learning algorithms. More information on SEBINI.
PQuad
What it is: A viewer for combining sequence and proteomics data. A viewer for proteomics peptide and protein data exploration.
What it does: It is a visual tool for browsing proteomics results mapped back onto the original genome under study. It is helpful for visualizing differentially-expressed proteins from two conditions and for discovering operons, co-regulation, and differential expression. More information on PQuad.
