Developing CSS can be a drag. Stylesheets stuffed with selectors. Cross-browser dilemmas. Reload. Reload. Reload.
BluePrintCSS aims to change that. It’s a framework for developing CSS that simplifies many common CSS tasks, letting you get to the good stuff faster.
FF 0 comments, 0 likes. hide
Less than 15 hours after deciding to port our existing SVN repositories into mercurial via BitBucket — largely on the presence of BitBucket’s issue tracker — GitHub GitHub has now released an issue tracker. Lots of Jquery goodness, but no API yet.
Perfect timing.
FF 0 comments, 1 likes. hide
Multiple factor security questions are only for the one-dimensional. They stymie those with more developed and extensive tastes. Perhaps that is the point.
They’d be more useful if they stuck to tried and true questions with definite answers:
* Your mother’s maiden name
* The name of your high school
* The worst president in U.S. history
But no. They have to be clever. Today I was trying to log on to my TransUnion account to check my credit report (COMCAST - YOU SUCK! I paid for the stupid modem already). They have the following as one of their security questions:
What is your favorite movie?
My favorite movie? Who has one favorite movie? Isn’t it entirely dependent on your mood? I dunno, maybe it’s The Big Lebowski. Amelie? No. Surely it’s Rancho Deluxe. Triplets of Belleville? There is no way I would have picked that - it’s too long. Shorter names, hmm. Incredibles. The Incredibles?
Here are some other useful questions from McSweeney’s.
FF 0 comments, 0 likes. hide
I get email. Lots. Absurd amounts. It’s 5:03 AM, and this is my situation from yesterday and last night:
One thing that seriously slows me down are chronic bottom posters.
For those not familiar with the issue, there are two prevalent quoting styles when replying to email. Top posting, or placing your reply at the top of possibly a long thread of messages, or bottom posting, sticking it at the bottom.
Bottom posting
On Jan 20, 2009, at 6:46 PM, So-and-So wrote: > Dear Webmaster, > Your website is broken. Please fix it. > Sincerely, > So-and-so Dear So-and-so, Thank you for letting us know of the problem. It is now resolved. The Web Team
Top posting
Dear So-and-so, Thank you for letting us know of the problem. It is now resolved. The Web Team On Jan 20, 2009, at 6:46 PM, So-and-So wrote: > Dear Webmaster, > Your website is broken. Please fix it. > Sincerely, > So-and-so
For long threaded discussions, bottom posting makes it much easier to read the thread IF YOU ARE BEHIND ON YOUR EMAIL. Judicious editing and quoting of past replies makes it even cleaner. Interspersing replies works for only short threads. After one or two replies it becomes entirely too messy. Don’t even try.
But when you get hundreds of emails a day, bottom posting is a drag.
Don’t make your recipient scroll to the bottom of every long thread with every single reply. Assume they are reading the thread and probably don’t want to re-read it. Stick your answer right up at the top. Yes. It’s expedient without sacrificing legibility or too much formality.
Hopefully you’ve “replied to” and included the original message(s). If the recipient has a brain lapse or is chronically behind on email they can scroll through the earlier messages. No biggie.
Expression pattern images are some of the most information-rich data housed at model organism databases. They are time consuming to generate. They are time consuming to collect and annotate.
Moreover, copyright restrictions mean that many images remain captive at publisher’s websites, unable to be placed within the rich intellectual framework that exists at sites like WormBase and FlyBase. How many near identical images are stashed away in darkened confocal rooms? How many possibly informative rejects are tossed out due to the puny limitations of publication? Gabijillions?
I wanted to build an easy to use expression pattern image resource that got around these limitations. The system would allow people to add their own photos for display within a broader intellectual context, comment on photos, add tags, search for a variety of criteria, etc. The problem? Developer cycles. This is a lower than low priority project and there aren’t enough hands to go around as it is.
I started wondering if I could leverage a site like Flickr to create a Poor Man’s Expression Pattern Database. Flickr is a key exemplar for Web 2.0 community style features. Tags, contacts, comments, an API.
I took approximately 6000 public, highly curated expression pattern images from WormBase. We display these on Expression Pattern Summary pages.
I wrote a script exploiting Flickr’s REST-like API to programmatically upload images.
For each image, the script added a text description of the expression pattern with hyperlinks back to WormBase genes, anatomy ontology terms, gene ontology terms, strains, transgenes, etc. Images were posted to a dedicated user named, ahem, wormbase.
Tags were added to each image corresponding to the unique gene ID, public gene names, and anatomy ontology terms.
Here’s an example image on Flickr.
I wasn’t happy with the current Perl interfaces to the Flickr API so I wrote my own (Flickr::API::Simple; note that I haven’t released this to CPAN yet and probably never will).
To pull the correct images, tags, and comments from Flickr, individual expression pattern pages levy a query for images at Flickr from the wormbase user with tags corresponding to either the expression pattern ID or the current gene being displayed. Information is displayed inline on the page but served from Flickr.
Since the goal of this project is to allow *anyone* with images to post them for display at WormBase, we needed a open account or group to do that. But since people are nuts, I wanted to constrain it a bit to people who I knew. Attribution is critical. To do this, I created an invite-only group on Flickr called, erm, WormBase.
If a user has an image that they would like to share on the WormBase site proper, all they need to do is:
* Upload the image to their account
* Post the image to the WormBase group on Flickr
* Tag the image with the unique gene ID
These images will automatically be displayed on WormBase Expression Pattern pages using the exact mechanism as above: Expression Pattern pages search Flickr for images belonging to the WormBase group (instead of user), tagged with the current gene.
That’s it! A Poor Man’s Expression Pattern database with integration and cross links to a public genomics repository.
We get tagging, searching (clustered tag analysis), social features like commenting and blog integration for (nearly) free. We don’t have to spend six months time in development.
Cost: $24 bucks a year for a Flickr Pro account. This gives 24 GB of storage. Ridiculous. No electricty costs. No sysadmin. No maintenance. $24 dollars or 6 pints.
Time: about 2 hours of programming time to figure out the Flickr REST-like API. About 2 days of running time to upload images (I’m on a slow link).
FF 11 comments, 12 likes. hide
In a speech to the NAACP, John McCain wrote:
First, how many Nobel Prize winners would want to teach in America’s public schools. I don’t think he realizes that this would be a serious pay cut for most Nobel Laureates.
Second, there is much more to be an effective teacher than simply having “knowledge, wisdom, and experience.” Nobel laureates are usually good for ribald seminars but I’m not certain I’d want them teaching my kids. And I don’t even have kids 
FF 0 comments, 0 likes. hide
I’ve now implemented such a system as an extension to Catalyst, the open source Perl web framework. The system isn’t yet ready for general distribution, but I’d like to share my approach.
First, I’ve gathered ten years of web access logs from WormBase, a generic model organism database where I work as the project manager.
Next, I correlated IP addresses with requests and tried to trace browsing patterns from one object to the next. This isn’t an exact science since we haven’t historically tried to uniquely identify users.
Data is loaded into a simple MySQL schema with object and object2related tables. Expediently simple.
Recommender systems [Wikipedia] seek to provide users with information related to what they are currently browsing. These are now ubiquitous in e-commerce sites such as Amazon, where each page contains a list of items viewed or purchased by other users.
I’ve long felt that a recommender system could revolutionize the browsing and mining of biological data. The idea would be to provide users with a list of related objects based on browsing history of cadres. See this post for some preliminary implementation notes.
I am worried that a recommender system won’t be received with open arms. Given that my current implementation is based on web log analysis it presents serious privacy issues. It’s conceivable that it’s use could inadvertently reveal the identity of uncloned and unpublished loci.
The Wild Type