What I've Done with this Blog

Dec 2011 - Mobile Friendly

I've been meaning to do this for a while, I've updated the look of the blog.

The previous design was inspired by an old design of über minimalist Ev Bogue. Back then I was wandering around the world as a nomadic minimalist.

I've since been folded back in academia and it's time for a change. The new look has two goals:

  1. Emphasise the article nature of most of my (longish) posts
  2. Responsive-Web-Design

Resize the window and make it real narrow. You will see the design collapse into a linear layout. Perfect for reading on a mobile† device.

†I really mean iPhones, but I need to stay in the good books of @pansapien.

Jan 2011 - Rebranding

I started this blog over 6 years ago. At the time, I thought it was both hilarious and ironic to have a blog named "Trapped in the USA". The name seemed apt because it started off as a travel blog. But over the years, I found that my best writings revolve around science, whether it be about molecular dynamics or commenting in science articles. I think I may need to rename this blog (also due to another reason over events recently transpired).

Anyway, here's a couple I just brainstormed:

  1. mechanical sludge
  2. the zen of blobs
  3. bouncing balls of proteins
  4. we are all protein
  5. simplicity in science
  6. it's really quite elementary

While I'm still stewing this over, I'd love to hear your suggestions in the comments!

Aug 2009 - Switched commenting over to Disqus

I run this blog on Textpattern, a nice clean Content Management System. I like the way they do things, their aesthetic gives me joy, and I grok their programming model.

However, their commenting system is sorely lacking. I have experienced constant pain with dealing with comments of Textpattern. I imagine this is because Textpattern is a small operation (at least compared to Wordpress or Movable Type) and they don't devote a lot of resources to comments. For a while, I was just sucking up and taking the punches from the hordes of comment spam.

Then my comp-sci life-line Mark Reid told me about Disqus, something that I had probably used but been oblivious to. After seeing it in glorious action, I've finally decided to switch the commenting on this blog to Disqus.

May 2007 - Minimalist design

I got sick of my old design, and have been itching towards an all white design. I love the creamy goodness of white. Long live white background. After all, if it's good enough for Benedectine monks of the 16th century, it's good enough for us.

If you like the logo on the left, it was created by my good buddy Benoit Adam, who made these watercolors for me.

Feb 2007 - Moved to Textpattern

I've done it. After a good 5 years on the venerable blogspot.com, I have cut the cord, jumped the gun, and moved away from blogger.

It wasn't easy.

Blogger doesn't have an export function. There is no big red button to press that can gracefully back-up your blog. No sirree. There are some rather convoluted procedures. But what's worse, with the new version of Blogger (to which I switched over without thinking), the convoluted procedures to back-up your site does not work.

I was pulling my hair out. I ended up writing a python script (blogger_extracter.zip) that will scrape the actual web-site, and pull-out all the html files of each individual entry. That's the only way to do it if you want to keep the comments.

Run "python fetch_blogger.py http://yourblog.blogspot.com" making sure that you've got monthly archives on the front page. The script will make a directory "yourblog.blogspot.com" with the html files of all your individual entries.

Then I wrote another script blogger2movabletype.py that converts the html files into MovableType text file format. With that, I can import all my blogger posts into pretty much any blogging software out there. This one may not work on your blog unless you have the same template files as mine. But it's a short script and you can hack at it.

The reason why I switched is that, after years of squatting on servers of the scientific laboratories that I've worked in, I finally got embarassed with not having my own personal server. A dominion on which I could reign supreme without typing out ridiculous url's such as dillgroup.ucsf.edu/~bosco. So I bought

I used to hand-code html files. But that's stupid. There's plenty of great and free software to handle web-sites. In the process, I tried Movable Type, Word Press, Pivot, NewsBruiser – most of them had a wonderful set of features, but I wasn't satisfied.

Finally, I came across TextPattern. And as soon as I loaded up the Admin page, I fell in love. This was the first blogging/content-management software that was manifestly designed, by a force-ful intelligent, and gifted designer. It had a beautiful, sparse aesthetic, and it was pleasantly missing the design-by-committee look that some of the other packages had. So here I am. I am looking forward to working here.

July 2006 - Move to Infogami

I've slowly been transferring my web-site from my academic research group's server (with the rather unweildy url of http://www.dillgroup.ucsf.edu/~bosco , which is now defunct) to my new infogami web-site (http://bosco.infogami.com).

And I've really enjoyed the transition. For what I want to do, infogami fits the bill. Perfectly.

I don't really want to build my own server, I just need somewhere free to store it.

I don't want to write fancy html/ajax/flash widgets, I just want to write text in an attractive template.

I don't want to register a domain name, I want someone to give me a sensible one for free.

Infogami fits all these requirements.

Yes it is a wiki, but you don't have to host it. Yes it is a wiki, but you don't have to register a domain name. Yes it is a wiki, but you won't have to write one single linux shell script. Yes it is a wiki, but you don't have figure out how to install it.

But unlike a wiki, infogami makes it very easy for you to change the template. To make it look good. It's really hard to change the look of some wikis - and boy are they sometimes ugly. This is because Aaron Swartz is a damn fine programmer who keeps it simple, who knows how to keep the templates in infogami simple and flexible.

To all those people who say infogami is just a glorified wiki, you've missed the point about infogami. Infogami aims to cut-out all the headaches involved in setting up the wiki on some computer.

But what I like most of all is the text editor in infogami - it's bare-bores functionality is precisely it's strength. The text editor always sizes to the window size. i like that. I never have that window within a window scrolling rat-race. I love the mark-down format - it's power wrapped in simplicity - it can handle clean text and embed complex html.

I use to be a total coding monkey - I'd spend hours writing code for recreation. Now I am more interested in writing prose - which is, contrary to popular geek wisdom, a much harder thing to do than programming. Very few writers can write to the level of a typical New Yorker article.

Now I just want a web-site where I can put essays and articles up with a minimum of fuss, and which allows me edit easily. The wiki format makes it so easy to edit a file. No more save and ftp on some random computer, requiring multiple clickety-click steps.

Like a good English butler, Infogami serves me when I need something and dissappears into the background when I don't.