ChIP-seq quality control

December 14, 2012 § Leave a comment

Aaron Diaz (aad1974 AT gmail DOT com) writes:

“We at UCSF have recently developed a software tool for ChIP-seq quality control and protocol optimization called CHANCE, which appears in the current special issue of Genome Biology.

CHANCE has a graphical interface and doesn’t require any knowledge of programming or statistics. I hope it will be useful and interesting to your readers. The CHANCE program as well as the source code can be downloaded here.”

Take a look and let Aaron know what you think!

Quantitative Imaging: From Cells to Molecules

December 14, 2012 § 1 Comment

 Announcing a new course at Cold Spring Harbor Laboratory: “Quantitative Imaging: From Cells to Molecules”.  Applications are due on January 31, 2013.  Apply here.
Course Description:
This course will focus on advanced quantitative fluorescence microscopy techniques used for imaging a range of biological specimens, from cells to single molecules. The course is designed for cell and molecular biologists with little or no microscopy experience, who wish to begin utilizing microscopy in their own research. Students will gain a theoretical understanding of, and hands-on experience with, state-of-the-art equipment used in quantitative fluorescence microscopy, including: laser scanning and spinning disk confocal microscopy, deconvolution methods, total internal fluorescence microscopy (TIRF), super-resolution methods (structured illumination, STORM, and PALM), and digital image processing and analysis. Students will learn how to design and implement a wide range of imaging experiments using these techniques. Students will use the techniques to address specific quantitative questions and then discuss the results as a group, learning to trouble-shoot the common problems that occur in the course of a quantitative imaging experiment. Among the lectures presented are: microscopy basics, CCD cameras, confocal microscopy, multi-photon microscopy, deconvolution, TIRF, single molecule imaging, imaging ratio-metric “biosensors” (including FRET), and super-resolution techniques. Students will also learn specimen preparation for microscopy, including fixation and immunofluorescence in tissue culture cells, choosing fluorescent proteins, working with live samples requiring environmental control, and more.
Organizers/Instructors:  Jennifer Waters (Harvard) and Torsten Wittmann (UCSF)
Instructors:  Max Krummel (UCSF), Bo Huang (UCSF), and Lisa Cameron (DFCI)
More info and online application:

Hemichordate you are

October 5, 2012 § Leave a comment

Via the Guardian (UK): a new acorn worm has been discovered and named after Yoda from Star Wars.

I wonder what other ways there are to make acorn worms into international news?  Of course, our local acorn worm community (all three of them) are delighted.

To celebrate Yoda purpurata, here are some pictures of Marc’s collection of acorn worm memorabilia, which is — as you will no doubt be able to see at a glance — focused on Y. purpurata‘s slightly better known relative, Saccoglossus kowaleskii.


July 4, 2012 § 2 Comments

Over 500 people from Mexico visited the blog today to read this post, brought here by Yahoo! Image Search, which is clearly running a different algorithm from Google Image Search.

Hola, visitas.  I hope what you find is what you were looking for. I doubt it but one can hope.

Teh internets are very odd sometimes.

For fans of A Game Of Thrones

June 28, 2012 § 1 Comment

this heartfelt video, with the following message:

“George RR Martin, please write and write faster
You’re not going to get any younger, you know
Winter is coming, I’m growing impatient
And you’ve still got two whole damn books left to go
So write, George, write like the wind!”

My favorite lines:

“We don’t mean to dictate how you spend your days
But please, bear in mind, in the time that you’ve had,
William Shakespeare churned out thirty-five friggin’ plays
And if you keep writing so slow,
You’ll hold up the HBO show!”

We need more songs like this.

Wellcome Image Awards 2012

June 25, 2012 § Leave a comment

Check them out here. I want #12 on a t-shirt.

Bad blog craziness…

March 7, 2012 § 1 Comment

We’ve been having a few technical issues today, so I wanted to apologize to anyone who’s noticed.  A script that was running a backup on the images used on the blog went haywire and started re-categorizing all the comments as spam.  Then it corrupted some of the images.  So then we had to restore the whole site from backup, which led to a brief period when the appearance changed considerably because the WordPress theme was wrong.  And then we discovered that the version restored from backup was missing some of the links to the images (though the images still exist), and also some of the category assignments.  Not that the categories are all that useful anyway.

So — apologies if you happened to look in while all this chaos was going on.  Much but not all of it is fixed now; if you spot remaining problems, please let me know (becky AT  Special apologies to comment subscribers, who may have seen a flurry of “there’s been a new comment” e-mails as we tried to restore them.

We love computers.  Really. And they love us.

UPDATE: Oops.  Many of the older posts seem not to have come back.  I guess the fix is going to take longer than I’d hoped.

Computational modeling of signaling course at NIH

March 1, 2012 § Leave a comment

In June, the Laboratory of Systems Biology at the National Institute of Allergy and Infectious Diseases (NIAID, NIH) will offer a short course on computational modeling of cellular signaling processes using the Simmune modeling tool set (June 4-8).

The first part of the course will provide a hands-on introduction that is tailored towards biologists without prior experience in modeling but with an active interest in quantitative and spatial aspects of cellular behavior. The second part of the course will introduce computational modelers with a solid programming background to the possibilities and techniques for using the programming libraries of Simmune in their own projects.

Travel and lodging scholarships are available.  Further information here.

Research Works Act withdrawn

February 29, 2012 § 2 Comments

This is good news: the Research Works Act, which sought to prevent the government from requiring that work that they fund should be made publicly available, has been withdrawn. Elsevier withdrew their support for the act a couple of days ago.

Some are interpreting this as a change of heart on Elsevier’s part.  Mmmm.  I guess that’s within the bounds of possibility.  Or is this a case of “he who fights and runs away lives to fight another day?”.  Note this sentence in Elsevier’s press release: “While we continue to oppose government mandates in this area, Elsevier is withdrawing support for the Research Work Act itself.”


Pay it forward

February 25, 2012 § Leave a comment

Andrew Murray on why teaching is important.  One of his reasons: someone taught you, and you should pay them back by teaching someone else.  Watch the video to learn the rest.

Where Am I?

You are currently browsing the Miscellaneous category at It Takes 30.