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UMBC AAIndex Database
 

Change Log

Current version

The current version of UMBC AAIndex Database and Tools is 1.1.0, updated from version 1.0.1 on August 20, 2007. Features of the new version include:

  • Amino Acid Explorer: Capability to paste custom matrices in text format, instead of typing each of the values individually into its own text box (thanks to Rebecca Halperin and Jack Emery from Arizona State University for the contribution of their code to parse the matrix).
  • Amino Acid Explorer: Fixed a bug that caused Amino Acid Explorer to occasionally freeze while performing graph layout. The bug was caused by concurrency issues that violated Swing's "single-thread" policy.

Previous versions

1.0.1: March 3, 2006

  • Amino Acid Explorer: Improved readability of the distance scale (especially on Mac OS X)
  • Amino Acid Explorer: Enabled Mac OS X users to use context-menus by using a combination of Ctrl+mouse click. Old method (using the right mouse button, which is not available on most Macs) is also still available.
  • Amino Acid Explorer: Upgraded to newer version of TouchGraph code to resolve issues with layout hanging on Apple implementation of Java Virtual Machine
  • Amino Acid Explorer: Corrected problem with accessing the tutorial and UMBC AAIndex web page from the tool on Mac OS X. (There was either an incompatibility or a bug in implementation of LiveConnect on Mac OS X; at least in version 10.3.9.)

1.0.0: November 23, 2005

  • Database/website: Integrated the content of the website with the content of the Freeland Lab Wiki at UMBC. The content of most of the static pages is retrieved from the Wiki. It is also possible to follow the links within the Wiki and browse the content within the UMBC AAIndex website.
  • Amino Acid Explorer: Added ability to remove an index from the tree by right-clicking on it, and selecting an appropriate option from the context menu.
  • Amino Acid Explorer: Added ability to view the metadata of an index from the tree by right-clicking on it, and selecting an appropriate option from the context menu.
  • Amino Acid Explorer: Option to add and edit custom matrices that can later be used in calculation of distances to the indices in a spanning tree.
  • Amino Acid Explorer: Option to view the metadata of the matrices from the database within the tool itself.
  • Amino Acid Explorer: Added ability to show the difference in distances between two matrices and a tree of amino acid indices.
  • Amino Acid Explorer: Rearranged the main window of the tool. The functionalities are now available using a menu bar, not buttons.
  • Amino Acid Explorer: Updated tutorial to conform to the new functionalities and outlook.
  • Database: Ability to download the current snapshots of the database as zip files (AllIndexData.zip and AllMatrixData.zip for indices and matrices, respectively).
  • The database and tools are considered mature enough for public access and publication.

0.4.2: September 14, 2005

  • General: Server-side caching of indices to improve response when computations require significant amount of indices.
  • Amino Acid Explorer: Found and fixed a bug in graph laying algorithm in original TouchGraph code. (Subsequent generations of spanning trees sometimes lead to termination of graph laying thread due to a SecurityException. This caused the graph stabilization process to freeze.)

0.4.1: September 13, 2005

  • Amino Acid Explorer: Option to restrict indices to selected amino acids when calculating the spanning tree and comparing with a matrix.
  • Amino Acid Explorer: Option to select different methods to calculate the distance between any two indices (Statistical Distance and Euclidean Distance).

Initial versions

0.3.x: October 2004

  • Amino Acid Explorer: Tutorial for the tool added.
  • Amino Acid Explorer: Option to add and edit custom indices that can later be used in spanning tree calculation.
  • Amino Acid Explorer: Option to view the metadata of the indices from the database within the tool itself.
  • Amino Acid Explorer: Option to select indices that are in the current spanning tree.

0.2.x: May 2004

  • Amino Acid Explorer: Option to filter indices matching given criteria.
  • Amino Acid Explorer: Index selection window (for spanning tree generation) is radically redesigned.

0.1.x: early in 2004

  • Database: Conversion of the original AAIndex database to XML format and normalization of the indices.
  • Database: Creation of the interface allowing to query the database, retrieve data in XML format, and display data in HTML format.
  • Amino Acid Explorer: Creation of the first tool that shows how an application running on a different computer can connect to the database and take advantage of the data in XML format. The tool allowed to select indices from a list, build a spanning tree, and compute the distance to a single matrix.
 
 
This material is based upon work supported by the National Science Foundation under Grant No. 0317349.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Last modification of the site: August 20, 2007