# 0.00.16 (61742) Feb 24, 2012
2/24/12 Publishing version to dev for possible demo
Added most of the user interface for the 2nd tab.
Made the molecules that don't directly interact with the DNA stay above it when doing random walk.  This should serve to prevent some confusion about what is interacting with the DNA.
Added label for mRNA that fades in during synthesis and out when synthesis is complete.
Fixed an issue where polymerase could attach to DNA in locations that overlapped with transcription factors.
Made the node for the grabbed biomolecule always move to the top of the z-order for its layer.
Added support for multiple positive transcription factors per gene, added to gene 2 only so far.
Made the positive and negative transcription factors offset somewhat so they aren't right on top of each other (requested by MK).
3rd tab: Adjusted the range of the graph, the parameter ranges, and the default values in order to make the "noisy" nature of the single cell more apparent and yet still stay on the graph when all values are maxed out.
Made ribosomes larger, since it was pointed out they they are in reality about 5x larger (by mass) than the polymerase.
Made the polymerase and transcription factors do the 1D walk more quickly and detach sooner.
Prevented user interaction with mRNA destroyers when they are destroying.
Prevented user interaction with protein until it is fully grown.
Prevented user interaction with ribosome when it is translating mRNA.
Prevented user interaction with polymerase when it is transcribing.
Added infrastructure to prevent user interaction with biomolecules in some circumstances.
Fixed an issue where ribosomes wouldn't be able to perform another translation until they were moved by the user.
Fixed an issue that was preventing multiple polymerases from transcribing at the same time.
Made it easier to get transcription factors and polymerase to attach to the high-affinity sites on the DNA molecule.
Made biomolecules fall of the DNA strand if they are block transcription and the transcribing polymerase bumps into it.
# 0.00.15 (61246) Feb 13, 2012
2/13/12 Deploying to dev for a review meeting.
Reinstated the 2nd tab and put a new drawing on it that represents a revised design.
# 0.00.14 (61129) Feb 8, 2012
2/8/12 Deploying to dev for use in interviews.
Added first cut at an indicator the tell the user when their protein collection is complete.
Fixed an issue where the DNA strand would get pulled too far apart by the polymerase if it had been previously attached to the strand.
Added the ability to prevent transcription factors from attaching to DNA is there is a different biomolecule in its way.
Reduced the number of polymerase, ribosome, and rna destroyer molecules in the tool box from 3 to 2 in order to avoid false connection to the number of proteins in the collection area.
Made the placement hints brighter and with a more apparent stroke so that they will be more easily seen (especially on the DNA strand).
Added a floating clock control to the last tab.
Adjusted parameter ranges and chart range to keep protein level on the chart in last tab.
Lengthened the DNA strand on the 1st tab so edges aren't seen when zooming in/out.
Fixed an issue where background cells were too large.
# 0.00.13 (61026) Feb 6, 2012
2/6/12 Deploying to dev for review and feedback.
Added counter to protein collection area for number of instances of a given protein.
Added better hint for indicating that user needs to move protein into collection area - area flashes when protein produced.
Made the DNA shape change when being transcribed.
Changed wording in protein capture are to make it clearer that it is protein TYPES that complete the collection.
Changed labels on transcription factors to use words rather than "+" and "-" symbols.
Tweaked model params on last tab to make it more responsive to changes.
Increased protein size to make them, and the capture area, more eye catching.
Optimized cell placement algorithm.
# 0.00.12 (60483) Jan 20, 2012
1/20/12 Publishing to dev for potential use in classroom setting.
Temporarily removed the Protein Levels tab so that a version with only working tabs can be published.
Renamed tabs.
Changed the background color on all tabs to be black when outside of a cell.
Changed cell placement algorithm on 3rd tab to look more random and therefore realistic.
Added a dialog that shows real E. Coli cells in the 3rd tab.
Change cell shapes to look roughly like E. Coli.
Added zoom in/out feature on 1st tab.
Completed integration of numerical model on 3rd tab.
Got mRNA destroyer working.
# 0.00.11 (59967) Jan 6, 2012
1/6/12 Snapshot of version reviewed with biology expert.
Implemented first cut of third tab, which allows the user to tweak cell parameters for one or several cells and see how protein levels change.
Fixed an issue where mRNA would be above the ribosome in the z-order in some cases, which looked weird.
Added placement hint for mRNA destroyer.
Added "capture signal" to the protein capture area.  This is a flashing node that surrounds the location where the protein is moved when captured.
# 0.00.10 (58851) Nov 29, 2011
11/29/11 Deploying to dev as a snapshot for use in discussions with design team.
Added infrastructure and stubbed out implementations (i.e. static pictures) for 2nd and 3rd tabs.
Made biomolecules move directly and quickly to attachment sites, rather than doing a "directed wandering".
Changed the motion of wandering biomolecules to be faster and have a longer mean free path.
Implemented the ability to capture proteins in the collection box.
Added protein collection box node.
Added protein production from ribosomes.
Got mRNA positioning and winding algorithm working, supports multiple simultaneous translation and translation during transcription.
# 0.00.08 (56347) Sep 9, 2011
9/9/11 Snapshot for review and some initial testing.
Added some random shaping to the mRNA to make it be a bit curvy.
Got hints for transcription factors and polymerase working.
Added ability for polymerase to produce mRNA
Added ability for polymerase to exhibit the "transcription motion" on the gene.
# 0.00.07 (55950) Aug 31, 2011
8/31/11 Deploying to dev to capture a snapshot
Added 1D random walk when attached to DNA for molecules with general DNA affinity.
# 0.00.06 (55793) Aug 25, 2011
8/25/11 Taking a snapshot before making some major changes.
Fixed an issue where biomolecules removed from the DNA would jump back to it.
# 0.00.05 (55514) Aug 19, 2011
8/19/11 Deploying to dev for review by design team.
Added attachment sites and the ability for polymerase and transcription factors to attach to DNA.
Added negative transcription factor.
Added support for hints and added initial set to first gene.
Added gradients to biomolecules.
Made strand longer so that ends are not seen when overall aspect ratio is reasonable.
Made 1st gene be centered at (0,0) in model space so that initial scrolling doesn't occur.
Made shape of RNA Polymerase look like suggested by design team.
Improved layout of biomolecule tool box
Retitled "Tool Box" to "Biomolecule Tool Box"
# 0.00.04 (53478) Jun 24, 2011
Made ribosomes into a single unit instead of two subunits
Added tool boxes and ability to add/remove biomolecules using these tool boxes
6/24/11 Publishing to dev for review of DNA look and navigation.
Added base pairs to DNA molecule
Improved the size and coloration of the prototype genes.
Added genes to the model
Improved panning behavior
Made DNA strands curved instead of linear