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Overview

The Structural Proteomics Application Development Environment (SPADE™) is a free, Python-based, structural biology analysis and modeling toolkit. The beta release under the liberal BSD license was announced on June 4, 2008 at the annual OCCBIO conference at the University of Toledo[1]. SPADEweb is actively seeking support for the existing infrastructure, which is being promoted to attract a community of interested developers and users. Please get involved to find out how SPADE can help you.


In addition to standard structural bioinformatics accessories (molecular viewer, solvent accessibility calculation, secondary structure recognition, protonation and hydrogen bond calculation), SPADE offers algorithms for fold recognition alignment, pairwise or multiple structure alignment, efficient nearest neighbor collection, standardized project and code file organization, undo/redo functionality, with a slew of other features and usability enhancements.


SPADE users download new datasets and software applications using built-in automated software deployment tools. This arrangement allows a bazaar-like commercial model where developers create SPADE-ready applications to provide either for free or for a charge. Registration of at-cost software applications with SPADEweb requires developers pay a fee to access the deployment tools, and to post information and documentation on SPADEweb. This covers overhead for the project, including code and website maintenance, and costs associated with project dissemination.


Two applications are currently available through SPADE. SequencePad is a sequence alignment editor that applies an interactive phylogenetic tree window to assist deliberate sequence selection, a critical standard for proper evolutionary conservation analysis and protein-protein interface patch prediction. RAVE is a toolkit that facilitates the application of reactive probes and mass spectrometry toward determining the details of protein structures and empirical verification of models for macromolecular structures. RAVE saved projects can be viewed with a BSD-licensed toolkit but generating new projects is not free. SequencePad is free.


The resulting project and organization strongly encourage development of marketable strategies in the field of structural biology, including independent public and proprietary software development contracts, as well as incorporation of existing specialized public and proprietary software into this highly capable, open source front-end. Potential also exists for use in the class room setting, and detailed instruction manuals can be produced. A general bioinformatics text should be adapted from existing works using SPADE to illustrate concepts.


References

  • Deacon J. Sweeney, Gerald M. Alter, and Michael L. Raymer (2008). "Introducing SPADE, the Structural Proteomics Application Development Environment" Ohio Collaborative Conference on Bioinformatics (OCCBIO) 2-4 June 2008, University of Toledo.


History

SPADE™ emerged from a multiple-template structure modeling program that required several structural biology tools, including protein structural data and visualization tools, sequence and structure alignments, and solvent exposure and secondary structure assessment and prediction algorithms. The original software was written in C/C++ and included a few tens of thousands of lines as well as several exclusively-licensed dependencies.


The package capabilities were eventually expanded to predict protein-protein interface patches from smoothed evolutionary conservation values. It became clear that the reusable tools would lend themselves to the rapid development of other libraries and applications. A leaner, more flexible language would be highly advantageous to this, and Perl and Python were examined for their concise, script-like grammar rules. Python was eventually selected for its popularity with programmers of all levels of expertise.


The files were rewritten starting with a highly organized MolecularSystem object. A clear hierarchical separation of its object-oriented components stabilized, and a full-featured MolecularViewer object was written to visualize the three-dimensional structures. The files were organized into simple categories, the MolecularComponents, Scripts, Tools, Applications, Systems, and Databases directories located in the main folder. This arrangement allows one point of access for each file category, and obviates the locations of core components.


The phylogenetic tree editor (SequencePad™) was the first application developed for SPADE. Its main goal is to support quality control for sequence alignments, in particular for protein interface patch prediction. The RAVE™ application was developed to support reactivity-based structure analysis. In effect, RAVE complements SPADE by providing empirical data for meaningful evaluation of structural models.


Getting Involved

There are several ways to get involved in the project. First be sure to join the mailing list to keep up with project planning, platform testing, and new releases. Try out SPADE and its combined MolecularViewer and MolecularSystem objects on your favorite PDB-format protein structures. Bug reports benefit the project. Please assist by reporting them in the Bugs section of the SourceForge page.


Try out the available test cases and provide feedback (in the Forums toward debugging and alteration of the existing code. A CVS will eventually be established to facilitate collaborative development efforts.


If there is a new application you are initiating, please consider the SPADE context for your development project. To view or suggest project ideas, please visit the Feature Requests section of the project page on SourceForge.


Thanks To

The majority of code contributions have come from members of the Wright State University Bioinformatics Research Group, under the exceptional oversight of Michael Raymer and Travis Doom. Experimental data used for RAVE development were generated in the protein chemistry lab of Gerald Alter, by Twinkle Christian, Lauren Mitchell, and Jon Nuss. Greatly appreciated feedback has been provided by these experimental scientists. Mass spectrometry support was generously provided by Billy Grunwall and David Cool at the WSU Proteome Analysis Laboratory. Funding was received from the WSU Biomedical Sciences Ph.D. program and the BiRG lab, with support from the National Science Foundation.

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Copyright © 2001-2013 Deacon Sweeney. All rights reserved.

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