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Can I autoclave this thing?
Its my water bottle. Will there be any damage to the paint?
Cut It Out, a new game by NEB
I’ve played some citizen science games designed to help make new discoveries in bioinformatics. Of course I don’t remember what any of them are but I have heard of “Fold It” and I’ve just never played it. Anyways, today I got an email from New England Biolabs about a game they developed that lets you create sequences and find restriction enzymes to cut them. It’s actually pretty fun, but I have no idea if they use this game to do anything actually scientific. But if you need to kill some time and destress from the lab then this could be worth some minutes.
The game is here: Cut It Out
Have fun.
2012 Spring Break Catch-up
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”
Somewhere out there…
I check my site stats every day. I know more or less who is coming to check out my notebook. Except people who come to my notebook via search engine and social media. Every day or most every day, someone searches “iheartanthony research.” I want to know who you are. If you are that person, then leave a comment in this post introducing yourself. It would be nice to meet the person who remembers iheartanthony research, but can’t directly type research.iheartanthony.com in the url bar. Hahaha, I jest (but only slightly), but I do want to meet you stranger.
Looking at my site stats, I’ve been getting a lot of Google search referrals. Especially to this post. How on earth is that possible? Talking to a friend who came across that post via Google+, I realized WordPress says that Google+ is Google Search in the referrals section of the analytics. Something to keep in mind in the future…
One of these hands is not like the other
I’m in a silly mood right now and so I thought I’d share a silly thing…
I ran out of my normal medium gloves (not Nitrile… I know!) and had to go with one medium and one x-small. The extra small looked so ridiculous that I had to take a picture of it. It makes my hand look like a genetic experiment gone wrong; my fingers are all bloated and webbed.
Hope this brightened your day slightly…
Stephen Chu, US Secretary of Energy Twitter Transcript #secofenergy
Dr. Stephen Chu came to UNM to address the student body in a town hall type setting. I decided to capture some quotes and thoughts from the assembly on twitter. You can check out everything here:
I have no idea how long that link will be active. If anyone knows of a way to get permalinks to tweets, I’d be appreciative.
Here are some other thoughts from the meeting:
- The person who asked the first question was a total loser. He asked Secretary Chu about lobbying in Congress, and while that stuff is pretty rampant, the Secretary isn’t running for office. Ask him about science and technology, loser!
- I was disappointed by the attention to industry and the focus on fuel costs. There was a lot of answers pertaining to financial situations. While a large part of the audience probably enjoyed these answers, I was not satisfied.
- I wish there was more focus on how the academic community could lead the charge into clean/green energy (since most of the questions were about that). There was only a little emphasis on the fact that we were at a university center and that were are all the future of the country. Shame.
I guess that’s really all I have to comment on. Like I said you can read the quotes in the twitter stream to find out what Secretary Chu had to say about various policies with regards to the US energy situation.
Merry Christmas!
Happy holidays to everyone out there. I hope Santa brought you all something amazing!
I updated the FigShare figures and slightly modified the excel files. Check it out.