Cell cycle draft V 0.4

Draft 0.4 continues to build out the cell division elements that were introduced in V0.3.

This update presents the completion of (what I hope is) the most challenging part of creating this vis - an animation of chromosome movement coordinated in time with the movement of the arrow around the cell cycle diagram.

Some of the transitions that occur in the cell during mitosis may benefit from some additional tweaking, but overall I am happy with this version. all the action is packed into a small section of the cycle which is ok. It accurately represents what happens in real cells.

V0.4 Status

• The biggest change is the addition of chromosomes in the dividing cell that move in a realistic way:
  • The chromosomes appear in the nucleus of the single cell when the illustration loads.
  • As the cell begins to increase in size in G1, the chromosomes uncoil, transitioning from visible chromosomes to diffuse chromatin. The chromatin represented as a light grey fill in the nucleus.
  • In the S phase, the chromosomes replicate. As they replicate the grey fill in the nucleus darkens. This is subtle. There may be a better way to show duplication here, but it may not be necessary. Another planned graphical element (see next steps) may help.
  • All the rest of the action occurs during mitosis. At the end of G2 the DNA transitions back to condensed chromosomes, the chromosomes line up at the center of the cell, the nucleus breaks down, chromatids migrate to opposite sides of the cell, cytokinesis happens, the nucleus reforms around the chromosomes and the chromosomes transition back into chromatin.
• The timing of cell division has been modified. In V0.3 the actual division of the cell (cytokinesis) takes place over the entire mitosis phase. In v0.4 has it compressed into the end of the phase after the chromatids have migrated to the sides of the cell.
• The speed of the cycle is faster in this draft. This was done to help with development which involved a lot page reloading to see how changes in the code altered the visualization. The final version will give the user the ability to control the speed.

Next Steps:

• The transitions of the chromosomes from condensed to diffuse (chromosome to chromatin) is not smooth. May be worth modifying this transition to reduce the abruptness.
• Still no interactivity in the illustration. Settle on the controls and interactive elements and start building them. At the very least speed controls and a pause button need to be added.
• Add a third element to the illustration showing how cell contents change over the cycle. The plan is to have a graph that shows changes in size and the amount of protein, RNA and DNA present in the cell as it transitions through the cycle.
• The dialogue box at the top right needs to be rethought. It is currently focused on checkpoints, but should probably be refocused onto describing what is happening in each stage.
• Consider what additional cell components are needed: centrioles, spindle fibers, organelles etc...