Talk:Mathematics of Reaction Networks

I think it is probably about time some discussion was started over the direction of this wiki. I have been slowly chipping away filling in the background sections of this site so the site basically has all the emphases, biases, and limitations that come from that.

At any rate, I would like to start some discussion on the following topics:

• Direction - I envision this site as serving the double purpose of being a primer for new students in CRNT (along the lines of Marty Feinberg's lecture notes or Jeremy Gunawardena's CRNT for in-silico biologists write up, but more dynamic and up-to-date). At any rate, I would like to see summaries of main results and, eventually, accessible examples (drawn from the literature where possible) which illustrate the results. (I know this site is envisioned to encompass more than CRNT, but that is my focus.) I also see it as a place where the most current research topics can be enumerated and connections between researchers easily made. I imagine, among other things, reference lists and suggestions of what current projects are being studied and by whom. Are there other features I have omitted here that would be beneficial in this wiki?
• Terminology and notation - I have been using terminology and notation familiar to me, but I recognize it varies within the literature and what I use may not correspond to those most widely accepted in the wider community. (In particular, I have been using n to denote the number of species, m to denote the number of complexes, ${\vec {y}}_{i}$ to denote the stoichiometric vectors, etc., and realize other notations are widely used - e.g. N or m to denote the number of species, ${\vec {z}}$ or simply $y_{i}$ to denote the stoichiometric vectors, etc.) Comments and criticisms would be welcome.
• Tasks - As the pages get deeper and more detailed, it will become more and and more important to have people who specialize in the particular topics contributing to the wiki pages. Once the background section is ironed out, I plan on contributing mostly significantly to:
  • Dynamical equivalence
  • Deficiency theory

I know the literature related to these topics fairly well, but would not be able to say the same of, for instance, injectivity or multistationarity.

At any rate, feel free to post here or message me privately if you have any comments. -- Mjohnston (talk) 14:53, 13 October 2012 (BST)

Sounds sensible. Here are my thoughts (such as they are):

• Direction — The plan is for the wiki to be the main content of the site, but also to have a few small other bits and pieces. For example, it would be good to have a centralised repository for CRN related software. I also want to post up news of CRN related conferences, workshops etc, although the Upcoming Events page (link in left bar) of the wiki would probably suffice for that. Wiki-wise, summaries of main results and examples would be very helpful, agreed. Until/unless there are contributions from specialists in more general reaction network theory, the focus will have to remain on chemical reaction network theory. I am conscious that you have contributed nearly all of the content so far, and we need more people to get actively involved. Ideally I'd like a front page (possibly one level above the wiki) that gives very short summaries of various areas, and provides useful links to introductory articles for new researchers in the field, as well as links to "state of the art" type articles so that researchers who've been working on RNs longer can quickly find out about the new results. This second part will require active participation from people as they publish new results though.
• Terminology and notation — Sticking with the terminology you're familiar with seems reasonable. If other people prefer different terminology, we can debate which to use once they start contributing. In the long term I think it would be preferable to choose the clearest/most logical terminology where there is a conflict, but those are quite subjective measures! In the meantime, translating things to different terminology to what the author is familiar with only slow down the rate of adding content.
• Tasks — I'm intending to tackle monotonicity, and to have a go at injectivity/multistationarity. It's difficult to find time though, particularly as I'm having ongoing problems with RSI.

-- Pdonnell (talk) 18:24, 15 October 2012 (BST)

I reorganized the main page (and tried to correct the affected internal links) to emphasize the research goals of the page. I would like to chip away at the background sections more, but it a bit much having it on the main page. Comments and thoughts welcome. -- Mjohnston (talk) 18:30, 3 November 2012 (UTC)