Ensembl website

The Atmospheric Chemistry Transport modelling system used is based on the off-line coupled CAMx and HIRLAM models has been developed to simulate particulate and gas-phase air pollution on different scales. It has been used to simulate short and longterm releases of different chemical species and air pollution episodes. At present it is run in a pre-operational mode 4 times per day based on 3D meteorological fields produced by the HIRLAM NWP model. Currently this modelling system is setup to perform chemical weather forecasts for a series of chemical species (such as O3, NO, NO2, CO and SO2) and forecasted 2D fields at surface are available for each model as well as an ensemble of models (based on 12 European regional air quality models). The simulated output is publicly available and it is placed at the ECMWF website (http //gems.ecmwf.int/d/products/raq/forecasts/) of the EC FP6 GEMS project. 

The retrieved data can be (1) a set of promoter sequences, which can be analyzed further with different bioinformatic tools, (2) a list of genes that contain similar conserved motifs to the query sequence, and (3) a list of genes that contain similar patterns in their promoter region to the query sequence. Besides these data, the websites also provide a starting point for further analysis, because it contains links and cross-references to other databases like ENSEMBL, GOA, or EPD. 

Obtain Moldyn from the textbook website (http //statthermo.sourceforge.net/). Moldyn is a set of codes which simulates point mass particles that interact with Lennard-Jones forces. Moldyn uses the velocity-Verlet integration algorithm in the NVE ensemble. Read the README file on how to run the programs and do this homework problem. 

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