is powered by a responsive design (so the page will look good even on the smaller screens of smartphones and tablets)
natively supports social links
takes advantage of WordPress’s menu-ing system (so I can more easily customize menu’s without going into a theme’s custom menu setup flow)
takes visitors to my homepage directly to the About Me page which also now features one of the few photos that doesn’t make me look terrible instead of drops users into a confusing, touch-unfriendly link carousel
I’ve also made a couple of other tweaks and customizations to update information / fix formatting to fit better with the new theme, but if anyone spots any bugs, please let me know in the comments! 🙂
The basic challenge is that the ophthalmology research world uses an arcane but very difficult-to-do-by-hand scoring system for taking data on a glaucoma patient’s vision (see image below for the type of measurements that might be collected in a visual field test) and turning that into a score (the AGIS visual field score) on how bad a patient’s glaucoma is (as described in a paper from 1994 that is so old I couldn’t find a digital copy of it!).
So, I started by creating a program using the C programming language which would take this data in the form of a CSV (comma-separated values) file and spit out scores.
While I was pleasantly surprised that I still retained enough programming know-how to do this after a few weekends, the programming was an awkward text-based monstrosity which required the awkward step of converting two-dimensional visual field data into a flat CSV file. The desire to improve on that and the hope that my software might help others doing similar research (and might get others to build on it/let me know if I’ve made any errors) pushed me to turn the tool into a web application which I’ve posted on my site. I hope you’ll take a look! Instructions are pretty basic:
Sorry, only works with modern browsers (Internet Explorer 9, Firefox 7, Chrome, Safari, etc) – this simplified my life as now I don’t need to worry about Internet Explorer 6 and 7’s horrific standards support
Enter the visual field depression data(in decibels) from the visual field test into the appropriate boxes (the shaded entries correspond to the eye’s blind spot).
You can click on “Flip Orientation” to switch from left-eye to right-eye view if that is helpful in data entry.
You can also click on “Clear” to wipe out all the data entered and start from scratch. An error will be triggered if non-numeric data is entered or if not all of the values have been filled out.
Note: the software can accept depression values as negative or positive, the important thing is to stay consistent throughout each entry as the software is making a guess on depression values based on all the numbers being entered.
Click “Calculate” when you’re done to get the score
Hope this is helpful to the ophthalmology researchers out there!
Instead of hosting my blog on Blogger, I’ve decided to move it over to a self-hosted WordPress blog which not only gives me a whole lot more control over content and styling (and has vastly more versatile plugins and themes), but allows me to start consolidating my online presence into, hopefully, a coherent presence. [This will also hopefully finally get Serena and Teresa to stop with their “Wordpress is so much better than Blogger” comments everytime they talk to me about my blog :-)]
The process, while complicated, was not as painful as I expected:
1. Design – With the help of my lovely girlfriend, I picked out the Berita theme from BizzArctic. It presents a very cool landing page with a slider and a sophisticated menu-ing system across the top. I then did some simple copy & paste to create a CV page (from an existing resume) and an About page (borrowed heavily from my LinkedIn profile). A quick scan of my Google Reader and some of my friend’s blogs helped me fill out the Links page, and a quick scan of my hard drive put together the various pieces of my Portfolio.
2. LifeStream – Through WordPress’s plugin directory, I found LifeStream which makes it easy to embed a LifeStream page and sidebar widget which aggregates my activities on Google Reader, Twitter, and my blogging life in one place.
3. Import – WordPress comes with a powerful import tool which made the actual moving of posts from Blogger to WordPress painless. Handling the URL’s (steps below) proved to be a bit more challenging…
5. Setting up a URL re-direct on Blogger – This too, thankfully, was very simple (just follow the steps after “Update your Blogger settings” as it sets up the Blogger URL re-direct – the playing around with the DNS is needed for it to be completely seamless, but I don’t think its necessary) and step #4 above makes it so that the URL re-directs from Blogger go to the correct WordPress page.
6. Correcting internal links – While steps #4 and #5 fix most of the URL issues, I wanted to fix the internal links so that people who read my blog wouldn’t have to deal with the ugly Blogger re-directs everytime they clicked on the many internal links I have in my blog. Thankfully, because WordPress relies on a SQL database to store all of the post content, a simple SQL command in phpMyAdmin was all that was needed to fix all the internal links.
7. RSS feed – Because most of the regular traffic I get on the blog comes through RSS readers, I wanted to make the transition seamless. Thankfully, I’ve been using Feedburner for quite some time so all I needed to do was switch out the source feed, and then I used the FeedSmith plugin to re-assign my blog’s RSS feed <META> tags to point to my Feedburner feed so that new subscribers would get the right one. So, most of you RSS readers won’t see any difference unless you actually click over to the page itself.
And voila! While I’m sure there are still a few kinks to work out (i.e. alas I’ve lost all the old Disqus comments from my Blogger days and the pictures on my blog are subject to the whims of Picasa/Google hosting), the new blog has been set up. So, please, check it out, let me know what you think, and for those of you with your own blogrolls or who haven’t yet figured out how to use RSS, please update your bookmarks & links!
As my RSS Feed provider, Feedburner, is now part of the Google empire, they’ve decided that (for some reason) every feed needs to be moved to a different system. I’ve updated all the links on my blog accordingly, but please re-set your RSS feeds to my new feed address: http://feeds2.feedburner.com/bnjamminsblog
And thus concludes the second year of this blog’s existence. In line with all the other “year-end” posts on the blogosphere that come around this time of year, here are highlights from my life as reflected in the past year of this blog:
If you had told me four years ago that I would be working in consulting, I would have responded with a basic question: “What’s consulting? And, why am I doing it?”
As recently as a year ago, I was positive that I would be pursuing a PhD in Systems Biology (or something similar such as Computational Biology or Mathematical Biology). The field was deeply exciting to me. It was (and still is) full of untapped potential. I spoke eagerly with professors Erin O’Shea and Michael Brenner about how I could prepare myself and what I could study. Having worked in the lab of professor Tom Maniatis for almost two years at that point, and having been exposed to the joys of doing collaborative scientific work, I was fairly certain that being a graduate student doing research full-time was what I wanted.
With almost a sense of smugness, I looked down at the more “business-y types”. I thought what they were doing lacked rigor, and was hence not worthy of my time. I believed it was mere mental child’s play compared to the rigor and intellectual excitement of trying to decode complex gene networks and how invisible molecules could determine whether we were healthy or sick.
So what happened? Well, I can think of four main reasons. The first and most immediate was that I was part of the organizing committee behind the 2006 Harvard College Asian Business Forum, which was the HPAIR (Harvard Project for Asian and International Relations) business conference. The experience was very rewarding and eye-opening, but more than that, it was an impetus to follow the paths of the many excited delegates, many of whom were early professionals looking into business jobs like consulting and finance.
The second factor was a growing awareness of what life in academia meant. Yes, I was well aware of the struggles that junior academics had to go through on their way towards tenured faculty. But at the same time, towards the end of the summer, with several experiments facing setbacks and the doubts in my mind over my ability to be a good researcher, I began looking to other alternatives.
The third consideration stems from the fact that I have always been interested in application. My approach towards science has always been rooted in searching for possible applications, whether commercial or for the public interest. Even the reason that I chose to specialize in Systems Biology stemmed from a belief that traditional molecular and cellular techniques will face sharply diminishing returns with regards to finding the causes and cures for diseases. Having lived almost all of my pre-college life in the Silicon Valley, I was geared to seeing fruiftul science as science that moved from “bench to bedside” and my highest aim was to transition brilliant ideas to profitable ones.
The final factor is of course that it’s always exciting to try something new, especially something competitive — and even though I cursed recruiting at times, it could feel like a fun competition. Although I did not expect to receive a job offer from any firm, I did better than I expected in the interview process and received an offer which I simply found too interesting to turn down.