Pending

List of pending tasks for TXTL modeling toolbox
RMM, 12 Sep 2012

This is a list of small and large things to be done in the TXTL modeling
toolkit.  Feel free to add items.  Names in [brackets] are people who are
working on this task.

* New function: txtl_plot(t_ode, x_ode, names) - smart plotting of protein
  concentrations, resources and DNA, mRNA concentrations (using TXTL naming
  conventions to extract variables to plot)

* Modify DNA degradation to use an enzymatic reaction:

    RecBCD + DNA <-> RecBCD:DNA -> null

  Coordinate with Zach, Jongmin, Vincent.

* Better modeling for tetR: dimerization

* Add plac promoter, lacI gene (including dimerization, inducer effects, etc)

* Add sigma28 and RNAP28 (tricky; need to generalize RNAP representation and
  expand RNAP70 models to include sigma70).  Also need to add sigma28-based
  promoters (p28?).  Coordinate with Dan (and Vincent).

* Add ClpXP-based protein degration, as well as degradation tags (tricky;
  need to generalize protein specification to allow tags, such as
  deGFP-LVA).  Coordinate with Zach.

* Circuit example: feedforward loop [Zach?]

* Circuit example: genetic switch, including trying to switch between states
  using different inducers.

* Figure out how to implement induction at a time later than the initial
  time in a simple way.  Need to see how the simbiology toolbox handles
  this.

* Create a version of the toolbox that allows testing of genelets, including
  a transcription only buffer.  Could be tricky.

* Establish methods to optimize parameters in a given model to match
  experimental data.  Use simbiology methods that already exist, if any.
  Coordinate with Clare C and Jongmin.

* Put in more realistic parameters for the existing parts (with Zach, Clare,
  Clare C, Jongmin)

* Code up model for Julius Lucks's RNA-based circuit (might be tricky).
  Coordinate with Clare H.

* Code up model for Domitilla Del Vecchio's circuit and try to match
  experimental results [Enoch?].

* Build model and do some predictions for TX-TL versions of Victoria and
  Emzo's circuit.  [Victoria?  Emzo?]