Questions from our mailbag: How do I cite FinchTV?

One of the questions that appears in our mailbox from time to time concerns citing FinchTV or other Geospiza products. A quick search with Google Scholar for "FinchTV" finds 42 examples where FinchTV was cited in research publications. Most of the citations seem to follow the same conventions.

We recommend citing FinchTV as you would any other experimental software tool, instrument, or reagent. The citation should include the version of the program, the company, the location, and the web site. Other Geospiza products (FinchLab, Finch Suite, and iFinch) may be cited in similar manner.

In our case, a citation would most likely read:

FinchTV 1.4.0 (Geospiza, Inc.; Seattle, WA, USA; http://www.geospiza.com)

If you're not sure which version of FinchTV you're using, open the About menu. The version number will appear on the page.

It would also be a good idea to check with the journal where you plan to submit the article. Most journals have a set of instructions for authors where they provide example citations.

Entering information in iFinch via FinchTV, part I

Teaching is a hard habit to break so I teach short courses now and then.

This year, I've been having my students use FinchTV to enter their blast results into iFinch. This also works with FinchLab and other Finch systems, too.

This has been pretty helpful. The data get stored for each chromatogram and we can all view the results (I'll address this part in a later post.)

How does this work?

1. Log in to your Finch account. Open a chromatogram in FinchTV either by clicking the FinchTV icon or the link from the Chromat Read page that says Open in FinchTV.

2. When you're ready to enter information, click the Commit button (outlined below).



3. You'll see a message appear asking if you're sure. Say "yes."

4. Enter the information that you want to store. Since we were using FinchTV to connect to NCBI blast and identify our bacteria, I'm entering the conclusion from my blast results.

5. Then I click the "OK" button.



6. If I refresh my web browser page, I can see that the version number for my read is now at "2", and I can see that my information has been stored in the database.



In a later post, I'll show how we get that information out.

Stay tuned...

iFinch in education: metagenomics with JHU, part I.

iFinch is the perfect bioinformatics tool to accompany a class. I used it Fall quarter in a class that I teach at Shoreline Community College (Washington) and I'm using it right now in an on-line class that I teach at Austin Community College (Texas).

We cover several different topics in the class, but I have a fondness for long projects where we can use multiple techniques and tie everything to a common theme.

This semester we're working with bacterial sequences that were obtained from students at John Hopkins University. I've been collaborating with an instructor there for several years and now we have four years of data to dig our teeth into.

This video describes the first part of the project that we're working on.



JHU bacterial metagenomics project from Sandra Porter on Vimeo.

Capturing your images from FinchTV: PCs with Windows

As many of you know, FinchTV is wonderful tool for viewing and editing the trace files from your chromatograms.

Naturally, many people would like to be able to generate images from FinchTV for publications and talks.

In this post, I'm going to describe how to capture your images from FinchTV if you're using a PC with Windows. In the next post, I'll write about capturing images on Macs.


If you're using a PC with Windows

1. Open some kind of program for storing the image - this could be any image editing program or even a program like Microsoft Word.


2. Open FinchTV and find the part of the trace that you want to capture.


3. Hold the shift key down, then press the Ctrl key, and the PrintScrn key. This will capture whichever window is active. Since you were just working with FinchTV, you should have captured the FinchTV window.


4. Open a new document in Word, PowerPoint, or whatever image program you're using.


5. Click the Ctrl key and the V key to paste the image in the document.


6. Edit as necessary.

Addendum: I've also been told that Snagit is another really nice screen capture program for PCs.