Ed's Big Plans

So a more or less solid date has been set for the Masters’ defense– it’ll more likely happen on July 15th.

The final pre-defense revisions for my thesis have already been sent in, and I’ve just signed the request for examination form today.

The primary focus of any slide show I put together for the presentation must be about all of the new work put into the NGN with less emphasis on the background. I’ve also been advised to mention the math while not going into its detail.

I should get going on those slides.

Brief: Andre has recruited me for the Operators team since the DNAClass is complete.

Brief: Not a lot to report, papers are being edited and written– I’ve just finished the QSAR briefing, NGN design and experimental design sections of the IEEE paper… Thesis corrections are due Monday…

Brief: Met with Stefan today. The conference paper we’re working on has a page limit of eight pages, not six– but I’ve just been told this must include everything including the references and of course figures. With respect to the thesis, the request for examination paperwork has just been completed, and the abstract for the thesis document has been submitted. A few corrections are to be completed on the thesis document. Present work focuses on said corrections, the conference paper and software completion for Chris’ project. There is presently no benefit to working on anything more in parallel.

So, I’ve been assigned the Recombinatron DNA submodule and spent a good part of yesterday morning and afternoon working on it at the UWiGem office. I’ve brain stormed out what features the submodule should have and have finished a sizeable chunck of it.

While doing so, I managed to learn how to use the Python yield keyword (along with raise StopIteration); and all about abstract functions and how to manipulate them underneath the hood. Abstract functions include items like “len()”, “some_collection[5:7]” and “some_object >= another_object”.

Basically, the DNAClass submodule will be the atomic type that will be passed between the different larger modules of the project. Each DNAClass instance (DNAObject) encapsulates a read-only string that is to be iterated in a loop either forward or backward, along with the ability to be sliced as a string. This all must be transparent to the user.

I might go into detail later, but for now, here’s a good resource– Python.org / Emulating Sequence Types (hard to find / hard to google) and also the Ordered Dictionary [odict] class by Nicola Larosa and Michael Foord. The odict source is an excellent primer actually, it contains many many useful comments that’ve really helped me figuring out iterators, the slice object and abstract functions.

Finally, I only really have two items left that are mandatory– fixing up slices when a “None” object is used, and then the iterator-iterators…

The iterator-iterators (terrible idea actually) would be a list of iterators, so that each iterator will start at a different position in the loop of DNA all of which correspond to the same token.

I’m thinking now that I should replace it with an accessor that returns a list of positive integers corresponding to the tokens of interest instead; this can still be transparent to the user AND have the benefit of not being unwielding to implement. Having nested yield statements is just asking for trouble.

Update: Done. An initial version has been committed to the repository.

Brief: Draft accepted with minor revision notices by Dr. Stacey. Approval for defense documents to be finished soon along with revisions implemented.