Writeup of the paper

[edwintse]

With Round 2 of the competition officially underway (#1), I have begun to draft up the paper/fill out the wiki. This will include all the work done in both Round 1 and Round 2.

The paper is currently being written up in this google doc using the Beilstein JOC template:

https://docs.google.com/document/d/1aD29GjC8RjqrSDcWcEUptS04Z2v10deReRp0eB3kcp4/edit?usp=sharing

I have begun by writing some of the introduction and Round 1 of the competition. If the participants from Round 1 (@holeung, @kellerberrin, @spadavec, @gcincilla, @IamDavyG, @jonjoncardoso) were able to summarise your models and methods that would be super helpful. Any improvements made to the original models during this round can be written up under Round 2.

I am using temporary reference labels for now (surname of the first author and year of publication) so it will be easier to number them at the end.

Please add your author details to the top of the paper as well.

At the same time, all of the information that will be written in this paper will need to go into the relevant wiki pages too.

[mattodd]

@edwintse I wonder if we could ask the participants in Round 1, and Murray himself, to add in text to the paper that indicate their methods? You have some text for this in your thesis. Simplest is to add that into the paper and then ask the submitters to verify that it's looking OK? We also need a link added to the evaluation of the models vs the pathogen box, indicating the ranking order that was obtained. The results of that exercise will need to be summarised in graphical form in the paper.
So there are two discrete things here. If they are complex, or need discussion, start new Issues. The creation of a figure summarising the outputs of round 1, for example, might be substantial.

[edwintse]

I've made a short to-do-list in the readme file here for what needs to be done for the paper. Please add anything relevant to your models/methods or anything you think should be added to the paper. The section of text in blue has been copied over from my PhD thesis so if you submitted a model in Round 1, please check this/edit this to better describe your submissions.

[edwintse]

@spadavec We are approaching the final stages of writing our predictive modelling paper and need some more information about the methods you used during Round 2 of the competition. You can see some examples from other entrants in the experimental section of the paper (link above). It is understandable that some things may not be able to be shared in the paper but we would like to have as much information as possible, so ultimately it’s up to your discretion of what you add. Thanks!

[mattodd]

Hi @spadavec ,
The paper is looking good and we'd love to submit soon. Any chance you can add in some details of your model so we can include it?
https://docs.google.com/document/d/1aD29GjC8RjqrSDcWcEUptS04Z2v10deReRp0eB3kcp4/edit?usp=sharing
(We've reserved a place for you in the SI...)

[spadavec]

@mattodd Sorry for the delay--have been very sick and am now finally able to look at this. Should be able to update in the next day or two.