Herbert H. Tsang:: Software


  • RNA-DV is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. In RNA-DV, structural modification is achieved through a combination of mouse and keyboard operations. The direct and intuitive interface allows the structure prediction researcher to visualize the structure. Furthermore, RNA-DV provides the necessary tool for structure designers to explore the effect of various structural elements in terms of thermodynamic contributions. Four different thermodynamic energy models (efn2, HotKnots, Major and RNAeval) were incorporated allowing users to observe real-time energy changes while designing the structure. Visualizing and editing of pseudoknotted structure is also supported in RNA-DV.
    • Download source link
    • Online demo link
    • View a demonstration video (click on the photo below)

2) Ebbie-(mis)match v4.3

  • Motivation: Large scale small RNA sequencing projects generate a plethora of data. Generally, only perfectly matched sequences are further analyzed. In some cases 61.8 % of data are unattended. We were wondering if the data was discarded rightfully classified as DNA sequencing errors, or if there were valuable information discarded. Here we present Ebbie-(mis)match (Ebbie-MM) a computational algorithm that analyzes single mismatches of small RNAs to the genome of origin. Using Ebbie-MM, we analyzed a dataset of 7,790 non-redundant small RNAs cloned from Oryza sativa. In this limited dataset, we found 230 1-nt-mismatches of which only 19 % overlapped to themselves. Even with this very limited dataset of 43 overlapping 1-nt-mismatches, RNA base modifications were detectable in small RNAs. Thus, not all sequencing errors should be discarded as they could contain valuable information on RNA base modifications. Ebbie-MM is available under GPL at
    • H. A. Ebhardt, H. H. Tsang, D. C. Dai, Y. Liu, B. Bostan and R. P. Fahlman, "Meta-analysis of small RNA sequencing errors reveals ubiquitous post transcriptional RNA modifications", Nucleic Acids Research (published March 2, 2009)

3) Animation / Computer Graphics

Currently, the following apps that were developed in our class are now in the iTunes store. We are expecting more apps to be in the iTune store soon!

Name Description Release date Link to the iTunes store
iDanceForms by Credo Interactive Inc This software inspires you to visualize dance steps, entire routines or other animations in an easy-to-use 3D environment. For choreography, interdisciplinary arts, dance and animation technology applications. LINK TO DOWNLOAD Aug 23, 2013 iDF_logo.png iDF_screenshot_1.png

4) Various iPhone applications developed as part of the student's research projects. The main themes of these applications are: games, mobile education, and engineering for user with accessibility issues. See HERE for more information and demo.

5) MusicCentric Technologies Inc.

Copyright © 2010, Herbert H. Tsang,

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