Friday, March 9, 2012 -- 3DNA's new home

It has been quite a while since my last blog post titled "3DNA base-mutation functionality for the study of pretein-DNA interactions" (dated Sunday, October 30, 2011). Over the past few months, I have been extremely busy laying the groundwork for 3DNA: both in software consolidation and hardware setup.

Here are some background details about what happened:
  • 3DNA now has a dedicated domain name I tried to register with the obvious choice, but found that it has unfortunately been taken already. We thought about several alternatives, and finally settled with the domain name

    This site is the new home of 3DNA, where -- instead of in the blog -- I will post related news and my personal views. Some of the 3DNA-related posts originally published here are being migrated into the "Highlights" section of A side benefit of the switch is that 3DNA users from China and other regions where Google blogger is blocked can have access to the content.

    The site is powered by Textpattern, "a flexible, elegant and easy-to-use CMS". I shopped around for a lightweight CMS to host the new 3DNA homepage. I came across Textpatten and was impressed by the mere 484KB download size (v4.4.1). My positive experience over the past few months has made me love the CMS better.

  • The forum is now hosted under the subdomain, powered by Simple Machines Forum (SMF). While I have been happy with phpBB3, I took the migration opportunity to try something new and found SMF a better option for the purpose of 3DNA. The forum site is where the documentation is located and  my interactions with the user community take place.

  • As a result of the new homepage and forum site, the following three 3DNA-related sites previously hosted at Rutgers University have been retired; links to them are automatically redirected to the corresponding new locations:
    • The former v1.5 site at Over the years, this site has received the most outside links.
    • The v2.0 site at, which accompanies the 2008 3DNA Nature Protocols paper.
    • The former forum site at
To summarize, now 3DNA has a new home at and forum site at With the infrastructure in shape, I can switch gears to focus on the scientific part of the 3DNA project: refinement, further development of its functionality, and better documentation.