Derpy Day!

March 1st is known as Derpy Day. You may be curious about what Derpy Day is, and why all the BCRC computer screens currently have a picture of a pony. Here's a little background on what today is all about:

  • Derpy Day is named after Derpy Hooves.
  • Derpy Hooves is a Pegasus pony from the show 'My Little Pony'
  • Derpy Day celebrates indiscriminate friendships.
  • A few simple and fun rules on how to celebrate Derpy Day are-
    1) You must eat a muffin
    2) You must write someone a letter
    3) You must take a goofy picture of yourself cross-eyed

Come celebrate Derpy Day with us, and help yourself to a muffin! :)

Derpy Day

March 1st is Derpy Hooves Day in the BCRC. Stop by to see our decorations and have a muffin, while they last.

Duplexing fixed on ronkonta

I noticed last week that there was an off-by-one problem with duplexing on ronkonta: it would print the first page of two-sided jobs single-sided and then print the rest two sided. I updated the firmware and the printer now appears to be working correctly.

MAMP and Drupal

I've setup a Drupal sandbox using MAMP in the BCRC. To use it, go to the Application folder and double-click on MAMP. Click the button to start the servers. It will ask for an administrative username and password, but you can just click cancel. Once MAMP is running, if you visit a web-browser, you can visit a local instance of Drupal 7. Read more for details.

Unexpected Zoom in on Desktop Screen

Today there was a student that accidentally zoomed in on her desktop screen on her computer. I assumed that I could zoom out using Command -, like I do on my MacBook, but it didn't work. In case this happens to anyone the solution is Option-Command + or -, if you want to zoom in our out.

Raven Pro updated

Raven Pro, a piece of software used for the Biocommunication class, needed some updates, so I've built a package that includes the updates. If you notice the application behaving incorrectly, let me know.

Mongoose Dem

Good Morning,

Dr. Brewer recently returned from St. Croix where he and Buzz Hoagland, Professor of Biology at Westfield State University, spent the summer researching the population of Small Indian Mongoose (Herpestes javanicus) inhabiting Sandy Point National Wildlife Refuge.

Below is a documentary created to summarize some of the work that they have been doing. Enjoy!


R opportunities and resources

OEB is organizing an R study group: Studying, Originating, and Understanding R Coding Executables (SOURCE). There is a sign-up sheet for a mailing list that includes a survey of what people are interested in learning about.

I have also installed RStudio in the BCRC after Sheila Patek requested it for her class. I hadn't seen it before -- it looks pretty useful, although I haven't had a chance to play with it much. Check it out!

Now Hiring

The BCRC may have positions available for undergraduates. Preference given to students with work study. Looking for people interested in biology, technology, and other cool stuff. Contact Steven Brewer.

Updates for Fall2012

I have been updating software in the BCRC and Biology computing labs for the fall semester including updates to the MacOS and many software packages, including Adobe Creative Suite, MS OFfice, Firefox, Libreoffice, Scribus, and others. If you notice something not working, please bring it to my attention.

Note that we did not upgrade to the newer versions of the MacOS: We are not using Lion or Mountain Lion. We have several software packages that people depend on that won't work after we update to Lion. And for most things, Snow Leopard (the version we have installed) seems to work better for most people.

New printer: ronkonta

After much discussion, we decided to replace sigelonta (the old color printer) with a new Laserjet 5200 printer called "ronkonta". Our existing black-and-white printer, provizonta, is probably not going to last much longer. In this way, we have a backup printer now and, when provizonta fails, ronkonta can take over.

Provizonta has returned

After an extended tour of the Lederle Lowrise and OIT, Provizonta has returned to the BCRC to great acclamation.

In other words, printing is available again -- thanks for your patience.

Provizonta recovering nicely

Provizonta had to be hospitalized after its fuser seized up. But I am informed it is recovering nicely and will be up and about in just a few days and ready to print your documents in no time.

UPDATE: Provizonta should be back to work sometime on Friday April 20. We're still waiting on hardware support. :-(

The program "structure" installed in BCRC

I have recently installed the command-line version of structure which "implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers." The program is on your PATH if you open a terminal window and type "structure". To run the program, you really need the "mainparams" and "extraparams" files -- the original ones are in /usr/local/share/structure, if you need to start with something.

I have also set up the workstations to run structure in an automated way, if you have many analyses you want to run -- contact me to get directions on how to use that. Or if there are similar analyses you would like to run using the BCRC computers.


I have installed Octave via macports in the BCRC. Just start a terminal and enter "octave" at the command prompt...

There are many resources to getting started with Octave, including this brief introduction and this programming tutorial. This Reference Card handy.

There are many extensions to octave with additional functions and tools. I've installed the octave-bioinfo tools already, but others may be of interest.

*Happy New Year :)*

Hi Everyone~
It is another exciting new semester here at the BCRC. I hope you all had a nice winter break and all happy to be back.

I just created instructions on printing double sided using microsoft applications and preview. I had also just created on how to print multiple slides on powerpoint. The next one will be how to do that in preview as well.

if anyone figures out any other great tips. Please blog about them and I'll add it in our staff manual and/or How Do I... page.

Enjoy a wonderful semester!

Synchronizing Folders

Someone asked me recently if there was an easy way to synchronize folders between two computers. Unfortunately, the easy ways tend not to work very reliably. But here is a method that's a little more complicated, but should be extremely reliable. You'll need to do some unix things and you'll need a place on the server where you can keep all of the files.

Note: You could avoid using the server as an intermediate space, but then you'd be limited to a system that only works inside the building. Or, rather, making it so it would also work outside the building would make it a lot more complicated.

We'll assume you're going to keep a folder in your home directory on a laptop and a desktop synchronized with a folder located on a lab hard-drive on marlin. Don't try to set this up with a folder in your home directory unless you've made prior arrangements with the technical staff, unless you only want to use it for tiny things.

Read more to learn how.

~New Content~

Hi Everyone,
I really enjoyed the new blog entry by Tanya who wrote the instructions on scanning transparent slides. ^^ Good job Tanya!
I've added it to the "How Do I" page. I've also added links on how to print as well as the link to Poster Printing.

Our hardcopy of the BCRC staff manual is coming out rather nicely. I have included a "Tips & Tricks for the Consultant" section. At the moment it includes:
*Printing in the BCRC
*Poster Printing
*Using the Scanner
*Making a Poster with Scribus

I plan on continuing to upgrade our manual with more tips and tricks. Feel free to write your own instructions to help others as well.

Good luck on the rest of Finals and have a wonderful winter break. ^o^


Scanning Transparency Slides


The steps to scanning transparency slides are as followed:
1. Place Slides onto the scanner starting with the bottom left corner, and continuing to the right with a good amount of space in between. They do not all have to be in the same row.
2.Open Applications on the Macintosh HD, and look for VueScan.
3. Under Input-
Make sure scan resolution is 1600dpi, Mode is on
Transparancy, and Preview Resolution is on 200dpi.
Under Output-
Make sure the profile checked is TIFF
All other options should already be on the right setting.
4. Scan in the slides.
5. Select a slide, and use the cursor to crop the image with a little bit of the black edges to make sure you have the full image.
6. Click Scan (Don't worry about the window that pops up of the image, you can exit out of it)
7. Repeat until all transparencies have been scanned in.
8. Go to Pictures in Macintosh HD, and the scans should be there. Right click the space under the scanned photos to create a new file. Name them Scans-XXXXXX, the X's will be the first five numbers that every scan has in common. (After the first round have been scanned in, you may need to adjust the name to make sure they are different. Increase the number +1)
9. Open Scratch on the Desktop, and drag the new folder over.
10. Later you could go into GIMP to edit the photos.