New Year update

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.

The Pradipta 416

The Few, The Proud, The Pradipta 416

and

http://groups.google.com/group/pradiptas-rolodex

del.icio.us.tags

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

DIYbio is alive!

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.

Jason joins team thoughtbot!

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.

Mephisto to WordPress

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.

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

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.

Bricklet currently consists of:

  • A proposal for a Part Description Language
  • A proposal for a Parts Sharing Framework that supports a web of registries, selective publication, document revisioning, and provenance/attribution.

Our intent is to implement ideas from the synthetic biology community and the BioBricks Technical Standards Working Group. We want to exercise these ideas with the hope of gaining insight into both their advantages and limits, with the intent to iterate in the future. Eventually, we may like to submit our ideas as patches to a project like Brickit to reuse existing functionality and build development mindshare.

We are tracking the requirements, design, and implementation on the Bricklet page at Google Code page. Mac and I will be presenting our progress at the Standards and Specifications in Synthetic Biology Workshop at the end of this month.

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!

I gave a session that introduced synthetic biology, iGEM, their motivations, and surrounding issues. I’ve uploaded my slides in PDF (1.5MB): Synthetic Biology at BarCampRochester.

Here are a few takeaways from some of the sessions I attended:

There was a great session and discussion about intellectual property: copyright, patents, and trademarks – in particular how these apply to software and why patents aren’t necessarily evil (although the patent duration is surely out of touch with the speed of the software market). I’ll be reading more about Open Innovation, with an eye toward its applicability to both software and science.

Al Biles led a brainstorming session about the nature of creativity and what it means to be creative. This was an open-ended discussion with an exploratory nature, and was quite enjoyable. Al differentiated between P-creativity, which is an act that is original from an indivudal’s perspective, and H-creativity, which is an act that is original with respect to all known history. He also recommended Margaret Boden’s “Dimensions of Creativity.”

I learned about the difficultly of accessing supposedly open governmental data in the US due to its distribution in proprietary or obtuse formats. Consider a database that is made accessible by taking screenshots from within the Oracle admin tool, printing these out, scanning them back in, and distributing the lot as a PDF. Fighting the good fight, there are projects like those at the Sunlight Foundation that focus on making this data more readily accessible.

Then, there are projects like EveryBlock, which collates such data and lets you filter it by location, so you can learn about happenings in your neighborhood from crimes to business licensing to permit issuances. This is a great trend, and I hope to see it grow both in the domain of making data accessible and making it useful.

Following up on the political theme, I was in a thought-provoking session called “So you want to become a lobbyist?” that took a look at the importance of some of the “nuts and bolts” political issues like redistricting, and how effective grassroots movements are on a local scale (the consensus: very effective). Remy made an interesting point that grassroots means person-to-person, whether that’s door-to-door or online.

Sam & Katie gave a refreshing talk about relationship branding: 2 cool kids = 1 cool brand: thinkskinc.com.

Justin Thorp has a great post that he wrote post-BarCamp about starting your personal branding in college that is spot on. Having attended a fair number of conferences, I was also caught slightly off-guard by the lack of biz card trading. Go go day job plug for business cards!

Finally, if you’re in the Rochester, NY area, definitely check out the Society of Lectors, a group of folks who hold regular meetings to give BarCamp style presentations on a wide gamut of topics. Go brush up on your presentation skillz, and learn something new!

Managing your research

There are a few activities that, arguably, comprise the bulk of science.

They are, of course, not linear.

And each one generates many artifacts.

…many, many, many artifacts.

Wouldn’t it be nice to keep track of all these? (Especially in a distributed team!)