Just a quick note. Nick Loman notes that he intends to use material from my Basics: Sequencing series in his undergrad lectures. That is pretty awesome, and I feel an urge to reciprocate by using one of the things he’s blogged about, but given that I teach mathematics on a blackboard, I’m not entirely sure how to do so*.
To clarify, the images and material in those posts, and indeed everything written in this blog, can be used freely for any purpose. I would like it if you would provide a link back here, or note who created them verbally, but that is by no means required.
* Ohh ooh I’ve got one, a question for my first year Elementary Mathematics for Biologists students:
Question 1
The Sanger Centre owns 42 sequencing machines, of which 2 are 454 and 40 are Illumina. Throughout the rest of the UK, there are 12 Illumina machines, 9 454s, and 3 SOLiDs (1). Perform a chi-squared test of independence to see whether there Sanger Centre has significantly different purchasing priorties than the rest of the UK. Is this test valid in this instance?
(1) According to data found at http://pathogenomics.bham.ac.uk/blog/2009/08/sequencing-in-the-u-k/
Answer 1:
The contingency table is:
ILMN 454 SLD TOT SC 40 2 0 42 UK 12 9 3 24 TOT 52 11 3 66 The expected values are thus:
ILMN 454 SLD SC 33.1 7 1.9 UK 18.9 4 1.1 Chi-squared score is thus ~19.04. This is larger than the 95% critical value of 6.0 for df = 2.
This test is not valid in this case, for two reasons. Firstly, the expected values are very low, and thus the normal approximation is unlikely to hold; we should instead use Fisher’s exact test. Secondly, each purchase of a sequencing machine is not independent of the result of the last purchase; you are more likely to buy the same machine again, since you have invested in equipment, software and training for that type of machine.
Haha, good one. I can steal this example for the medical students’ critical appraisal course too. Who knew that blogging would be so productive?
But I wouldn’t dream of using your materials without attribution so rest assured. I will also be encouraging the students to engage directly with the blogosphere as part of their studies!
By the way…have you heard of the Science Carnival, Scientia pro Publica, explainign science for ordinary people? http://scienceblogs.com/grrlscientist/2009/08/scientia_pro_publica_-_will_p.php they’re lookinf for people to host at the moment (as well as submit posts), I thought you might be interested.