The SimDB project aims at creating a public repository for molecular dynamics trajectories and other conformational sampling data of biological macromolecules. The SimDB resource will enable research groups worldwide to easily examine, share, and compare simulation data. You can take a look here how far we have come.

Rather than simply collecting and providing access to very large trajectory data sets, the SimDB design incorporates a comprehensive set of analysis functions so that only the analysis results have to be sent back to a database user. More information about the SimDB architecture is available here.

SimDB can be accessed at http://simdb.bch.msu.edu.

Stage 1 focuses on the development of the fundamental SimDB components. The highlighted areas represent components that have been implemented already and were tested and used for a set of trajectory analysis web services.

Stage 2 adds more advanced features such as a special interface for comparative analysis of dynamics between multiple simulations of the same or similar systems. Other components that will be added during this stage address the need for a distributed resource management system as well as authentication protocols for controlling access to trajectory data and computational resources. We will also extend the set of analysis functions further during this stage.

In Stage 3 methods for access outside the web service will be developed. As a result, user clients will be made available that allow download of trajectory data in different formats and prepare other input files for running analysis programs.

SimDB Architecture

A brief introduction to the current design of the SimDB architecture and the different pieces that it uses.

Raw Data Server Protocol

This document outlines the protocol used by Raw Data Servers, which store raw trajectory data sets.

Perl Module for Raw Data Servers

A Perl module has been created to allow for the development of clients to interact with Raw Data Servers.

History

A short history of the SimDB project