Bacterial metagenomics on the JHU campus: analyzing the data, part IV

Do different kinds of biomes (forest vs. creek) support different kinds of bacteria?

Or do we find the same amounts of each genus wherever we look?

Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that we can have a visual picture of which bacteria live in each environment.

The parts of this series are:

I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three).

II. Cleaning up the data

III. Counting all the bacteria

IV. Counting the bacteria by biome

Note: My students found a strange bug that happens if you use Excel on a Windows computer and doesn't happen on Macs. If you use Excel on a Windows computer, you can only graph the data correctly if you copy the data from the pivot table and paste it into a new worksheet before you try to make the pie graphs.

If you don't do this, the PivotTable shows bar graphs by default and then, refuses to let you make two different pie graphs.

Part IV. Pivot tables from Sandra Porter on Vimeo.

For more information about this project, check here, here, here, and here.

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So how was using Keynote compared to Powerpoint?

Enjoyed the videos, but I have a couple of questions about the methods you show. I'm asking because I've experienced a large diversity in abilities in excel (and computers in general). Wouldn't it be simpler to teach the students how to do selections of non-adjacent areas in Excel instead of deleting a series after the fact? Have you tried it both ways and found out that they grasp deleting the series as an easier approach?

I've often wondered if there needs to be a "computer basics" exam that the students take so if they can't perform a series of computer related tasks (e-mail someone, use blackboard to upload a file, etc) they can get help. Learning biology is a challenge, and having to learn computer skills at the same time adds to the stress (although it is much closer to the real world).

I really like Keynote! Thanks for suggesting it! I compared Keynote and PowerPoint and the slides in the video are much nicer than the slides I made with PowerPoint.

That's a good suggestion for Excel, with having students select non-adjacent regions, that didn't occur to me and it's a fine alternative.

The computer basics exam is a good idea, too. I made the videos for an on-line bioinformatics course that I'm teaching, so the goal for the course is to have students learn how to use the computer for doing biological research. It's hard to avoid learning both at the same time.

No problem. Keynote has only gotten better with each iteration, and the graphics always look better in Keynote. Pages is also less frustrating when I'm trying to combine text and graphics compared to Word. Numbers is still lacking in many respects, but I haven't had a chance to mess around with it much, yet.

We rely on detailed descriptions of how make a graph, etc. A video would be better.