Posted by Jason Morrison | May 6th, 2009

See you at RailsConf!

If you’re going to RailsConf this week, let’s grab some drinks and catch up! I’m looking forward to hanging out with my awesome coworkers, my Ruby friends from all around, and giving a lightning talk on the BioWeatherMap Initiative at the ActiveResearch “Science on Rails” evening (Tuesday at 7:30pm). Update: I’ve uploaded my talk from ActiveResearch to SlideShare:  “BioWeatherMap...

Posted by Jason Morrison | Apr 16th, 2008

Biological Simulation Languages

From the “publishing old drafts for kicks” department, some interesting notes on Biological Simulation Languages: SPim Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus http://lambda-the-ultimate.org/node/2447 The little b language: shared models built from reusable parts http://lambda-the-ultimate.org/node/2671 BioComputing resources from Luca Cardelli http://lucacardelli.name/BioComputing.htm

Posted by Jason Morrison | Apr 14th, 2008

Bricklet announcement

Mac Cowell and I have been working on a new project, coined Bricklet. Bricklet is an open and extensible platform for storing and sharing standardized synthetic biology parts with the goal of fostering a rich ecosystem of synthetic biology software. <p>Bricklet currently consists of:</p> <ul> <li>A proposal for a <a href="http://bricklet.org/part-description-language/">Part...

Posted by Jason Morrison | Apr 7th, 2008

BarCampRochester3

Last weekend, I has the pleasure to attend BarCampRochester which was a great time. Thanks to the organizers and sponsors for making this happen! <p>I gave a session that introduced <a href="http://www.syntheticbiology.org/">synthetic biology</a>, <a href="http://www.igem.org">iGEM</a>, their motivations, and surrounding issues. I&#8217;ve uploaded my slides in <span class="caps">PDF</span>...

Posted by Jason Morrison | Mar 21st, 2008

Managing your research

There are a few activities that, arguably, comprise the bulk of science. <p><img src="http://jayunit.net/assets/2008/3/21/prp-slide1.png" style="border: 1px dashed #ccc; padding: 10px; " /></p> <p>They are, of course, not linear.</p> <p><img src="http://jayunit.net/assets/2008/3/21/prp-slide2.png" style="border: 1px dashed #ccc; padding: 10px; " /></p> <p>And...

Posted by Jason Morrison | Feb 28th, 2008

Traffic is a routing problem

2 ideas and then 1 idea: <p>1. <span class="caps">GPS</span> devices need more information about real-time traffic information. The best source for this is other GPSes that are also stuck in traffic. If they could communicate, they could intelligently route traffic to optimally spread traffic over primary and alternate routes. There are products that do this. iPhone and Android would also...

Posted by Jason Morrison | Feb 6th, 2008

lolscience

I actually had to register for a LiveJournal account today (ack), but it was for a good cause: to post to lolscience. <ul> <li><a href="http://community.livejournal.com/lolscience/25744.html">imma chargin mah mRNA!</a></li> <li><a href="http://community.livejournal.com/lolscience/26008.html">teh central dogma: it goes &ldquo;VRMMMMMMMM&rdquo;</a></li> </ul>

Posted by Jason Morrison | Feb 6th, 2008

Cell signaling, computer architecture, functional programming, and AI blackboards

While thinking about synthetic biology, I find it useful to identify analogues of biological systems in a discipline I am already familiar with, computer science. This helps me better understand the new concept and can also raise questions about the new system that already have discussions around them in the CS world. Of course, the fidelity of such metaphors is not 100%, so I have to take care to ground such...

Posted by Jason Morrison | Jan 28th, 2008

Installing redland-1.0.7 from source on Ubuntu 7.10

The Ubuntu packages for the Redland RDF libraries seem to have an issue, at least for the Ruby bindings (see Ruby objects to cyclic dependency about the “cyclic include detected” issue), so I installed it from source. <p>In case I need to do this again (or someone else does), here are the steps I took for installing Redland on Ubuntu 7.10:</p> Get the GNU MP Bignum library: sudo apt-get...

Posted by Jason Morrison | Jan 16th, 2008

Bio eye for the CS guy (or gal!)

Lately, as a result of my fascination with Synthetic Biology, I have been reading biology and bioinformatics references voraciously. More on Synthetic Biology to come, but I encourage you to read up on it. It suffices to say that it greatly appeals to me, coming from a Computer Science and engineering background. When you throw “refactoring” and “bacteriophage” into the same paper...