Whither lurk multitouch, tactile computing, and lab instrument hacking?  I’ve started to work on the SmartLab project again.  You can see what I am up to on the SmartLab tumblr.

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 at ActiveResearch.”

In a whirlwind two weekends, I’ve given a DIYbio talk with Kay Aull and Mac Cowell at CodeCon 2009 and will be at the Cambridge Science Festival (details), BarCamp Boston 4, and The Maker Revolution (Sunday at 1:00pm). CodeCon was a fantastic experience - San Francisco was enjoyable as always, and it was stimulating to be around so many incredibly bright folks. Thanks again to Len, Bram, and all the organizers for putting it together and for hosting the BioHack! track. I hope to record the talk material with Kay and Mac, titled “DIY Synthetic Biology: From Design to Construction with New Model Organisms,” so that it is available online in the near future.

Monday, Jan 5 2009: Tonight is the first night of nublabs’ Kitmakers course.  I’m excited to see how it goes! I’m primarily interested in building equipment for do-it-yourself biology, such as an inexpensive, high quality gel electrophoresis apparatus. – cut to Thursday, Jan 8 – …and today was the second night.  There were notably fewer people tonight, but it rocked anyhow.  I learned how to use the Bridgeport mill to do basic manual milling and how to use the digital readout, turned some aluminum in a lathe, and watched an intro to MIG welding. Then, with Alex’s help, I put together a variable DC power supply with a variac, bridge rectifier (three of them, actually - but only because we blew two), and a resistor+capacitor to smooth the resulting voltage.  Photos: Next week I’d like to test the power output on an oscilloscope, and start working on building a “draft” of an enclosure.

Hey folks!  It’s been a while (whew… 6 months?) since my last update here.  Here are a few things I’ve been up to, and what my plans over the next few months are:

1. Built and delivered awesome web applications with thoughtbot, and will help to roll out a beginning Rails thoughtbot training course later this January.
2. Attended RailsConf, RubyConf, the Lone Star Ruby Conference, and spoke at Boston.rb on Clearance, a small auth plugin for Ruby web apps.
3. Started learning more biology in earnest by taking a cell- and micro-bio course at Harvard Extension and working with DIYbio.  While the lecture is a very good one, as lectures go, I preferred the lab to the lecture and, as such, intend to do more hands-on learning in 2009.  A few projects I would like to undertake include:
   1. Working through Shoestring Biotechnology: Budget-Oriented High Quality Biotechnology Laboratories for Two-Year College and High School.
   2. Working on at least one piece of equipment with DIYbio folks, such as Open Gel Box 2.0.
   3. Participating in a DIYbio iGEM team.

If you are interested in keeping tabs on what I’m up to, I’d suggest either my twitter feed or the DIYbio Google Group, as these are my highest-touch interactions these days.

Tags from del.icio.us/jasonpm via wordle.net:

A little while back, I resigned from my position at VistaPrint to take a great opportunity at thoughtbot, inc in downtown Boston.  I’ll be starting with them on Monday, June 9, and am super excited to join their small and dynamic team.  Initially, I’ll be working on tools for the Nature Publishing Group like Nature Network.

I got to hang out with some of the team at RailsConf, see some top-secret Tee-Bot designs, go on some exciting Portland excursions and adventures, and I might have even learned a little Ruby or Rails along the way.

DIYbio is an organization for the ever expanding community of citizen scientists and DIY biological engineers that value openness & responsibility.  DIYbio aims to be an “Institution for the Amateur” – an umbrella organization that provides some of the same resources afforded by more traditional institutions like academia and industry, such as access to a community of experts, to technical literature and other resources, to responsible oversight for health and safety, and an interface between the community and the public at large.

Check out diybio.org and, if you’re in the Boston area, drop by our meetup next week!  Read Jason Bobe’s summary of the first meeting at the DIYbio blog, and keep an eye on the DIYbio mailing list for details.

An easy way to import a Mephisto blog into WordPress is by using a Python script for extracting a WordPress-friendly WXR file from Mephisto (which can be imported via the WordPress web admin interface), which eventually worked like a charm. I had to modify it to use MySQL, and to look at a different date field for publication (my Mephisto install was returning Null in the field m2wp.py was looking at).

1. Go grab m2wp.py.
2. Download m2wp-mysql.diff. (Update 6/6/08: fixed the missing trailing newline)
3. Run patch m2wp.py m2wp-mysql.py.diff -o m2wp-mysql.py.
4. Now you can run python m2wp.py -h and you’re off and running!

A less effective method is to transform Mephisto’s Atom feed into RSS, and import that into WordPress. This is a pain, because the feed does not contain comments, but here is how I did it before I discovered m2wp.py:

1. Get the XMLStarlet command line XML toolkit.
2. wget http://atom.geekhood.net/atom2rss.xsl
3. wget http://mymephistoblog.com/feed/atom.xml
4. xml tr atom2rss.xsl atom.xml > rss.xml
5. Go to http://mywordpressblog.com/wp-admin/admin.php?import=rss
6. Import your rss.xml
7. Pull comments over by hand.

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
• The little b language: shared models built from reusable parts
• BioComputing resources from Luca Cardelli