Appendix C

Data Base Perceptualization Scenario

 

If I am someone who is interacting with large biomedical data sets, I may need a set of primitive objects each of which can represent some elemental of the vast data field.  For example, let's say I am a user who is responding to a flood of sensor data which has suddenly detected germs of some kind following an explosion on a battlefield, or in a subway terminal--take your pick.  So off go my sensors which are distributed all around the area of detonation.  As the data starts to come into the Grok Box interface environment, below is a rough picture of the kind of thing I am fantasizing I would see in an array of screens spread out before me as the expert medical/military bio-counter terrorism response dude.  The fantasy scenario would unfold in the following order.  BTW, this is pure scientific speculation as you know I am no scientist.  This is what I would want to see were I in such a situation. 

 

  1. a single, simple object which appeared soon after the explosion hovers in a large screen directly in front of me.  Let's say this single prominent object is a simple circle, white in color.  This 2 dimensional object is suspended against a black background as a heavy stream of live data continues to flow unseen into the system and I wait for what to do next.
  2. Suddenly, the object begins to three dimensionalize—fill out into 3 space and following the filling out quickly turns from white into a very intense green color.  As the bio expert dude, I know that this means the explosion has released not a toxic chemical, in which case the sphere would have turned into a black color, but has released a germ the identity of which I have no clue about yet. 
  3. The object now hovers in its new state in front of me
  4. Next, I reach my virtual hand out and touch the sphere object (had there been more than one germ or chemical, the system would have put two, three, or four objects in front of me).  By clicking the one, or a particular one, the machine knows to begin the process of identifying that germ/chemical represented by the object. 
  5. The sphere is now going to change/morph in ways which will tell me whether the organism is a virus or a bacteria.  For example, if a virus, the shape may become like that of a 10 or 20 (icosahedral) sided dice; or else, the object may change into a shape more akin to a spiral.  If the organism is a bacteria, the object may change into the rough shapes of a paramecium or an ameoba.  Perceptually/culturally, such shapes have been associated with the two kinds of organisms mentioned and so are reasonable first iterations of how we may visualize that streaming sense data which intially identifies the kind of germ we are dealing with.
  6. Once the object assumes one of these shapes (in this case, the organism is a virus as indicated by the sphere changing into a 20 sided shape), I reach out again and touch it.  At this point, the object begins to open and out of  it comes an array of say 6-12 squares which all fill my screen along the x axis.  So from left to right along the bottom of the screen are laid out these square objects.  The background is still black. 
  7. Next, I see distinct, individual, simple geometric forms appearing some distance above each rectangle.  These are initially (perhaps) 3 dimensional and white as they come out of the square and hover above it until the data begins to stream into and morph the object.  By this process, I know the machine has begun the biochemical analysis of the germ’s elemental components (Topper…each of these objects above the rectangles represent the “primitives” I need you to create)
  8. The still objects above the squares, after a time, will begin to change in accord with the specific data that comes into them.  That is, data from sensors, and soon from queried database stores, are going to be effectively streaming right into the individual objects, thus structuring them--loading them with meanings/significance in real time with real data.  Presuming the ground sensors to have sufficient biologic/biochemical sensitivity, as the user I would like to see the first object on the left representing perhaps parts of the amino-acid/protein schema of the viral particle.
  9. Once the object has been morphed by the data, I will then take that molecular/structural information and instruct the system in such a way that an array of qeuries are sent out over the network/web to begin the intensive database searching which will result in the identification of critical features of a suspected weaponized virus.
  10. Let’s say for the sake of simplicity that there are 10 individual databases distributed throughout the US which contain information relevant to the identification and neutralization of the virus in question (its likely there would be many more than this!).  So in response to my queries, data from these 10 data bases begins to stream back.  Critical at this stage in the processs of visualizing all of this data to myself, for the sake of the example, is to connect each data base with one of the objects above the squares.  These objects may themselves become multiple objects once the data starts getting represented. 
  11. Next, the individual objects and their associated squares spread out into their own space at the outer sections of the very large screen I am interacting with.  The center of the screen remains empty.  In their respective locations the initial objects begin to break up into multiple distinct objects which are now undergoing intensive alterations and enrichments so as to represent the raw data coming in from their respective database.
  12. For example, several groups of objects are taking data from sources dealing with the capsids of possible viruses (ie the viral protein coat). As the identity of a virus will depend a great deal on the structure of its capsid, each object in this group may be representing properties, morphologically and abstractly (not necessarily in terms of mirroring the shape of a certain molecule), of different parts of the viral protein coat.  
  13. Another group may be taking data from a source dealing entirely with content related to RNA virsuses in general
  14.  Another group may be taking data from a source dealing entirely with content related to DNA virsuses in general
  15. As the system learns more about the germ it is dealing with it refines its search parameters.
  16. A set of objects may then be visualizatin data from a data base whose sole content is recent research on a family of RNA viruses known as Filoviridae. 
  17. as the filtering and visualization are going on the second to final stage in the process of identifying the virus is intitiated.  This involves particular data object shapes from each of the groups either

·        bonding in specific ways to form compound objects; this bonding/fusing occurs according to the morphic/textural/chromic/dynamic rules of “grammar” which the system knows to apply to the abastract objects for the particular content set being dealt with (ie, molecular microbiology, biochemistry, pathophysiology, immunology, and pharmacology).

·        Staying singular.      

  1. the final stage of the metavisualization which will yield the identity of the entire virus, or else key antigenic regions of it for the targeting of drug and/or immune actions is now primed and ready for execution. 
  2. in this final stage I as the user am watching all these grouped objects at the periphery of the screen space. Some of the groups are going to have information absolutely critical and others will have information at a 2nd or 3rd layer of importance.  The system will alert me to the simple or compound objects to which I must attend. 
  3. Because of my own specialized training with this technology, I have understandings of what is going on such that I, and not the machine, have to make the final decisions as to how and in what order the relevant objects are to be grouped together.  So I begin the final stage by dragging the prepared data objects from the perimeter and placing them in the center of the screen within specific regions. 
  4. With each placement, the compound object grows and complexifies. 
  5. The process of ‘agglutination’ of the various peripheral objects has resulted in a highly significance rich complex entity which provides me information as to the idenity of the virus in question: an RNA virus, Family: filoviridae; Genus: unknown; Species: Ebola-Zaire; Special Features: altered (ie weaponised) into aerosol.