Today Anthony and I brainstormed and are going to try to accomplish a couple things during Spring Break that are useful (a) for boosting my tenure dossier for Provost Office, (b) boosting Anthony’s CV/dissertation for jobs/graduation purposes (May 2013), and (c) useful for science. Really anything with regards to (a) is a last ditch effort, but since lack of peer-reviewed publications was by far the biggest criticism of my dossier, it can’t hurt. Andy and I are submitting a chapter of his paper to PLoS ONE later this week (after he finished uploading the data to FigShare).
We came up with a couple main ideas:
- Add to the SDM project and submit the revised preprint (from 3 or more years ago!) to PLoS ONE for peer review. Anthony is now collecting our scattered links and will post a better summary in his post. The main ideas are (a) post our shotgun DNA mapping software on github, after cleaning it up (b) implement many of the good suggestions Richard Yeh gave us on the preprint (see Anthony’s post for link to these ideas). I believe after doing this that it would be appropriate to move Anthony to lead author and would be worth submitting to PLoS ONE for peer review.
- Finish the revisions for the kinesin modeling paper
Of those two options, as is obvious from my description, we felt (1) made the most sense for strengthening Anthony’s dissertation/CV. This is because he spent a ton of time already on the SDM project.
Also, in parallel, we are thinking about how to use my time to strengthen the deuterium-depletion project. One of these ideas is to modify our existing image analysis software to make it automatically track the lengths of the root growth. I am optimistic that this can be done with Larry’s microtubule tracking software. It will eventually lead to publications, but not in this short time frame.
To make everything more useful, I will make github projects as I find software and get it working. This will be a bit tricky, but overall probably very useful to get our lab out of limbo between visual soucesafe (which nobody is really using except me now) and git, which is far superior–especially for open sharing of our code. To be even more useful, it would be good to move away from LabVIEW, but we’re way to deeply entrenched for me to try to port stuff now.
Locations of some things I found (not really useful for public since it’s on the local harddrive for now):
- DNA unzipping simulation code that Anthony cleaned up a bit: LarryXP->C:\SDM Simulation
- Image analysis software I wrote for Haiqing a while ago: C:\Program Files\National Instruments\LabVIEW 7.1\development_sjkoch_7.1\MT Tracking and analysis\Circles analysis
- A version of the tracking software that maybe isn’t the latest, but compiles on LarryXP: C:\Program Files\National Instruments\LabVIEW 7.1\MT Tracking\Larry Tracking for Andy 2009_fuckINI.vi I remember revising this for Andy after Larry left so that it would ignore some issues we have with the INI files.
- There is also a sub-VI that I wrote that would find the lengths of the tracked microtubules during analysis (I think). This is probably related to the subVI: “length finding sub.vi”
