Angles of movement are used to represent the transitino from one nucleic acid to the next.
The twelve possible transitions are described
by moving in some direction from each successive step in the sequence,
considering the current step to be the center of an imaginary clock.
The twelve hours of this genomic clock
are assigned to transitions as follows:
Mouse
In the following example, we present an
initial mapping from DNA to music in the form of an audio legend. We use
an invented sequence as follows:
Transition from one letter to the next is represented by twelve notes from a C major scale played on marimba. This includes each of the twelve possible transitions. The sample sequence is designed to highlight these transitions.
Amino acid triplets are assigned a string section sound. Hydrophobic AA's sound much higher than other AA which sound below the marimba pitches. All notes again are selected out of a C major scale.
Ribosomal-l14 with a long 'staircase' tripeptide in the middle of it.
Ribosomal-14 with 30 acgt from salmon inserted in the middle of it. Left side plays the original sequence, Right side plays the mutated slightly longer sequence.
Acute biological warfare defense by rapid anti-sense determination using advanced strategic audio biowar defense workstation (asabd) to direct the synthesis of dna and rna active drug in the cbd(chemical and biological defense) command outpost is the goal of this feasibility project.
The key to this design is the use of advanced computer audio, haptic and graphic information display to characterize the threat, and search for candidate matching anti-sense and binding site reagents in minutes. interpretation of this data is augmented by computer, but experienced multi-media human pattern perception and experience is key to the determination of the threat, selection and synthesis of the defense reagent. we see this as a prototype system as the bio-warfare defense equivalent as the sonar(auditory) combined with radar(visual) advanced threat analysis system.
Computer aided surgery, inc. seeks to build
from its base in the conceptualization, design, and implementation of advanced
tactical audio displays for neurosurgery and break the new high ground
in strategic threat display and tactical countermeasure selection and synthesis.
We propose to prototype, using elements of our existing sgi computer graphics
and lake dsp sonification, novel display technology of sniffer and Merlin,
and other multiple reagent binding data and build a display system to enable
the user to rapidly characterize a digital morse decomposition of the affinity
tree data. display of the tree should then enable the user to make tactical
decisions about defensive reagents that can block the dna binding site(s)
and order their dispersal to civilians or troops at risk.
Genometry
Genometry is a geometric and sonic representation of the structure of dna sequences. the representation can include several levels of data sequence history. for instance, a no history representation is concerned with only the four individual nucleic acids, a, c, g, t. on the other hand, a two character history is concerned with the current letter, and the prior letter. this is considered a two character transition from one letter to the next. for acgt dna data, there are twelve such transitions. three character transitions consist of the amino acid combinations. there are 64 possible three character combinations which condense to 20 amino acid forms.
Genometry uses colored lines at specific angles to represent sequence information. each angle is calculated from each successive point, considering that point the center of an imaginary circle. the length of the line can be adjusted to display more or less data. the angles are calculated from a horizontal line as a move of 0 or 360 degrees.
Different historical views have different sets of angles to represent the information. individual nucleic acids use angles of 270, 360, 315 and 45. this creates a line that will move always to the right and lines which never cross.
The sonic representation of this lowest level of organization assigns various parts of a drumset to the letters a, c, g and t. not just one sound is heard for each letter, but rather a representative sound from a particular drum set group. for 'a' we hear a snare drum, for 'c' a cymbal, for 'g' a high hat closed cymbal effect, and for 't' we hear tom toms and bass drum. this technique utilizes patterns for each group that do not repeat quickly and so add to the musical quality of the listening experience.
For the visual representation of two letter transitions we use a set of 12 angles generally corresponding to the positions on the face of a clock. for the numbers 6 - 11, however, we add 15 degress to their normal positions. the following code snippet lists the assigned angles.
static int gc = 300; // 1 oclock
static int ta = 330; // 2 oclock
static int ag = 360; // 3 oclock
static int at = 30; // 4 oclock
static int cg = 60; // 5 oclock
static int ga = 105; // 6 oclock
static int ac = 135; // 7 oclock
static int gt = 165; // 8 oclock
static int tc = 195; // 9 oclock
static int ca = 225; // 10 oclock
static int tg = 255; // 11 oclock
For the amino acid display we use a set of 20 angles assigned to highlight the following characteristics.
strongly acidic (-) - d,e near 9 o'clock
hydrophobic - a,i,l,f,w,v spread near 6 o'clock
polar - n,c,q,s,t,y spread near 12 noon
all others are neutral (p, g, etc) spread
in 4 directions nw, ne, se, sw
Various techniques will be employed to sonify dna information.
controlled by mouse or 3d tracking device. allows for both 'formal' and 'informal' repeatable tours of the data. allows waiving/scanning over/thru the data with resulting sound that reflects the data terrain.
the data will be organized into as many as 7 zoom levels corresponding to current levels seen in the genome viewer by will gilbert at http://bioinformatics.unh.edu.
- the functionality of regions will map to changes in music.
scales of instruments, pitches, dynamics, rhythms, patterns, and control changes, along with key word driven textual musical translations identify regions and sequences in the dna data by musical texture. additional musical underpinnings highlight intelligent context information of functional sections identified from gene research.
a formal method allows a tour of the data within an appropriate length of time not to exceed 5-10 minutes.
a sonic counterpart will highlight and
identify agct transitions. the sequence of musical events that correspond
to the twelve possible transitions between acgt are represented visually
by geometric elements employing twelve angles or other such visual components.
presenting agct sequences as natural looking coastlines and shapes allows
the visual pattern recognition facilities to be integrated with sonic equivalents
reinforcing the pattern matching capabilities of the user.
- fly over the data in a sonic plane.
Use 3d sound to identify where we are and rhythmic presentation to identify how fast we are travelling. up high we hear comglomerate sounds. as we zoom in, we get individual components such as proteins, then individual cgta. (or however many levels of groupings that are identified)
- represent large (3 billion) sequences as sound wave forms that are simply played.
In a sense we create a drum head out of the data and play it. if the drum head is played on a few positions we hear harmonic differences due to the underlying data characteristics.
- the dna shaker.
A kind of dna shaker facilitates data touring. consider the shakers boundaries being defined by the dna data itself. at any particular level and/or area of interest, a set number of sound beans can be shaken around within that data space. when the conceptual beans hit the side of the shaker, the data is played at that location. the sound response is fast, as in a real shaker. users define the level of detail and the zoom data level heard at any one time. simple gestures or other input control the zoom level. the user selects the data areas that become the shaker's surface.