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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.
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.
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).
- Go grab m2wp.py.
- Download m2wp-mysql.diff. (Update 6/6/08: fixed the missing trailing newline)
- Run
patch m2wp.py m2wp-mysql.py.diff -o m2wp-mysql.py. - Now you can run
python m2wp.py -hand 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:
- Get the XMLStarlet command line XML toolkit.
wget http://atom.geekhood.net/atom2rss.xslwget http://mymephistoblog.com/feed/atom.xmlxml tr atom2rss.xsl atom.xml > rss.xml- Go to http://mywordpressblog.com/wp-admin/admin.php?import=rss
- Import your rss.xml
- Pull comments over by hand.
Sardines is an experiment in organizing a tiered, distributed wiki that is motivated by Open Science.
Imagine research that takes place in a lab and is recorded and documented on an electronic platform such as a blog or wiki. It’s reasonable to conceive that the researcher may want to keep a closer hold on their findings for a short time in order to polish and confirm, before releasing it into the open.
This being said, it would be nice if the data, before being released publicly, were available within the entire research lab or institution. It’d also be great if the publication process seemed relatively seamless and that the interfaces for local private edits and global public edits be similar. To cap it all off, people “downstream” (i.e. in the lab) should automatically get updates when changes are made available “upstream.”
Example
Distributed document versioning
In this example, there is one public server and two private servers; labs Alpha and Beta each have a private instance of the server running so that they are assured of privacy. Lab Alpha has published version 3 of its research, although they have an internal copy which is more recently updated. The published version is available on the public server and is made known to Lab Beta’s server. Lab Beta has private research which it has not yet released.
Notes
It may very well be the case that this idea constitutes “too much software,” and a simple published-state property on a central wiki would suffice.