Supplementary Material for "Browsing RNA Structures by Interactive Sonification"

Grond F, Janssen S, Schirmer S, Hermann T (2010)
Bielefeld University.

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OA 6.2. Complementary Information Fused by Sound
OA 6.3. Adjusting the Sonic Information
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Abstract
This paper presents a new interactive sonification technique to browse ribonucleic acid secondary structures using a combined auditory and visual interface. Despite the existence of several optimization criteria for searching an optimal structure within the numerous possible structures of an RNA sequence, it is still necessary to manually inspect a huge number of the resulting structures in detail. We describe briefly the background of RNA structure representation and typical search scenarios. Then we discuss the audio-visual browser in detail, with a special focus on the sound design, data-to-sound mapping and interactive aspects. The sonifications we propose turn RNA structures into auditory timbre gestalts according to the shape classes they belong to. Various research-relevant phenomena become clearly audible such as transitions among shape classes and different free energies of selected folds. Both can be simultaneously assessed in an interface that allows for an integrated audio-visual perception.
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This Supplementary Material for "Browsing RNA Structures by Interactive Sonification" is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0. Any rights in individual contents of the database are licensed under the Database Contents License: http://opendatacommons.org/licenses/dbcl/1.0/
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Grond F, Janssen S, Schirmer S, Hermann T. Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University; 2010.
Grond, F., Janssen, S., Schirmer, S., & Hermann, T. (2010). Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University.
Grond, F., Janssen, S., Schirmer, S., and Hermann, T. (2010). Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University.
Grond, F., et al., 2010. Supplementary Material for "Browsing RNA Structures by Interactive Sonification", Bielefeld University.
F. Grond, et al., Supplementary Material for "Browsing RNA Structures by Interactive Sonification", Bielefeld University, 2010.
Grond, F., Janssen, S., Schirmer, S., Hermann, T.: Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University (2010).
Grond, Florian, Janssen, Stefan, Schirmer, Stefanie, and Hermann, Thomas. Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University, 2010.
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File Title
6.1. Pointing and Learning
Description
The combination of visualization, sonification and interaction has the special advantage that the user may point into an abstract representation of the sound stream. Since the sonification is played while browsing the shapes together with the image of the secondary structure representation and the shapestring notation, the meaning of the sound may be learned by interactively playing back the sound by combining two complementary visual pieces of information with one sonic representation. This is shown in example video V1, where the interplay of the browser elements is demonstrated.
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OA Open Access
Last Uploaded
2016-03-18T15:53:43Z
File Title
6.2. Complementary Information Fused by Sound
Description
Even for the experienced reader of shapestring notations it takes a while to establish the correspondence with the secondary structure representation. This is due to the fact that the shape information, particularly at abstraction level 3 and 4, is not always easy to see in the image. The interactive sonification of the 5 secondary structures on the display often reveals surprising differences or similarities. This is examplified in example video V2, where the noticeable difference in sonification originating from different groups of unpaired regions in the structure are pointed out.
Access Level
OA Open Access
Last Uploaded
2016-03-18T15:53:43Z
File Title
6.3. Adjusting the Sonic Information
Description
As mentioned before, the user has the possibility to adjust the gain of the sonification for each of the shape abstraction levels 3, 4 and 5. This interaction from the user adapts the sonification to task specific requirements. If the shapes are for instance sorted according to abstraction level 5, then the corresponding sonification is of less interest and the gain can be set to 0, whereas the sonification of level 4 and 3 get more importance. In example video V3 browsing interaction with different sorting criteria is demonstrated together with gain control for the abstraction level 3,4,5.
Access Level
OA Open Access
Last Uploaded
2016-03-18T15:53:43Z
File Title
S.mel.1021_pSymA_NC_003037_730322-730242
Description
The following movie shows an audio visual interface browsing some shapes of the following RNA string:

ATCTCATATTTTTGCAAGTGCCGGCAAATCAGGCGGCATGAGGCGGC
TTTTCAAGGCAGAGGAGGGCCAGGGTCGCCGGGG
Access Level
OA Open Access
Last Uploaded
2016-03-18T15:53:43Z
File Title
S.mel.1021_chromosome_NC_003047_735453-735533
Description
The following movie shows an audio visual interface browsing some shapes of the following RNA string:

CTCTTCCGTCAGTAAGCGGCGCCCCGGCTAGGGGGCGGCTTCGTCCCGC
TCTGAAGGAGAAAAACCGCGGCTCGCAAAGGG
Access Level
OA Open Access
Last Uploaded
2016-03-18T15:53:43Z

This data publication is cited in the following publications:
1893988
Browsing RNA Structures by Interactive Sonification
Grond F, Janssen S, Schirmer S, Hermann T (2010)
In: Proceedings of the 3rd Interactive Sonification Workshop. Bresin R, Hermann T, Hunt A (Eds);KTH, Stockholm, Sweden: KTH School of Computer Science and Communication (CSC): 11-16.
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