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.

Firefox 8.0

Workstations in the BCRC will be updated to Firefox 8.0 overnight. Other labs in our network will receive it over the next few days. Also included are new versions of Flashblock, Flash Player, and Shockwave.

Using the No-Script Firefox Add-on

For Technology Tuesday on Nov 22, 2011, I will offer an overview of the No-Script Firefox add-on -- an important tool for improving browser security.

One of the most serious current vectors for security issues in computing are client-side scripts (Javascript and Flash in particular). In many ways, when you let these scripts run on your computer, it's like letting a stranger sit at your computer and do whatever they want (watch your keystrokes when you type passwords, for example). It's not supposed to be like that, but all too often it turns out that they actually can. It's worth taking steps to be aware of the issue and protect yourself.

Unfortunately, browsers don't provide simple tools to manage which sites you allow to execute code on your computer. In Firefox, there is a powerful Add-on called No-Script, which lets you choose on a site-by-site basis, which to allow to execute scripts on your web-browser. I will offer a walk-through of how to install and manage the add-on to help you make informed decisions about security and web-browsing.

RSS and Feeds

The BCRC is experimentally hosting an instance of the TinyTinyRSS Feed Reader that can be used to subscribe to (and publish) RSS and Atom feeds. Most modern websites (like this one) can provide a feed (or feeds) of articles, often by author or category -- or even the comments. Most scientific journals also provide feeds that generally include the abstract. If you're suffering from information overload, a feed reader can help you organize things to stay current with a much larger number of information sources than would be possible almost any other way.


Hi everyone,
It's already November and I can't believe how fast time has gone by. It's getting colder outside but it's always warm at the BCRC :)

I started working on creating a hard copy of the BCRC Staff Manual. I also plan on creating tutorials/tips on the things that I've learned here for future references. mferony, did you figure out how to print the slides for powerpoint?

I also started playing around with the TinyTinyRSS we got from Steve. I'm not much of a FeedReader but I will start learning to~ I subscribed to 1 site that I particular check on a daily basis and now finding out what TinyTiny can do :)

If anyone has any special tips that they think should be included in the HardCopy of the Staff Manual, please print it out or send it to me so I can add it.

First Blog

Hi Everyone!

I know it's a little late for my first post, but better late than never right? My name is Tanya, and this is my first semester working as a Consultant in the BCRC. I'd have to say that so far my favorite thing is changing the ink cartridges in both printers. I also sow the post of changing the posters and I think that's a great idea. We should find some recent science posters, or biographies of some important people in the field.

Poster Printer Payment

We've changed how we handle paying for poster printing: we can no longer accept payment via checks or cash. We can now accept UCard payments. And we can still bill people provided you will give us a speedtype number to simply the billing. Hopefully this will represent a simplification for everyone.

~New Ideas~

Hi everyone,
It is a rainy chilly day outside but really nice and warm here at the BCRC. I've recently been given the opportunity to teach a faculty member in learning to use gimp. As a photoshop person, it was a little tough to grasp. But through some web tutorials it is getting easier.
I also had an idea that maybe we should make a tutorial on "How to Print" for various applications available as a book page because then in the future any new BCRC consultant can refer to it. I'll try to get started on it when my GIMP adventures slow down.


New Application: 4 Peaks

I have added the application 4 Peaks to the installed software in the BCRC, Intro Labs, and ISB 264, 264, and laptops. The application is a sequence trace file analysis program that can read and translate among many different formats, recognize motifs, and do many other sequence analysis tasks. It should be on all the computers on Sept 29.


Hey guys,
My name is Jobin and this is my first year at the BCRC. I see that msyed(sorry I don't know your actual name) was talking about a new poster , well I've been working on one for the Biology Imagery outside of the BCRC. I have a couple of pictures that were on Umass Biology departments website and was wondering if you guys have any input. I'll make a list of which ones I have now and send them out in my next blog post but if you see one that really catches your eye then give me a heads up. Also if anyone has any pictures from a lab they may work at and want that to be included then send that over with a brief description.



I see that some of the posters seem to be old, maybe we should order some new posters?