Published iFold Papers in Bioinformatics.

Here are the papers that were in Bioinformatics, Volume 22, Number 21. You can check out the site on a production server at http://ifold.dokhlab.org.

Base Paper [Adobe PDF]
Supporting Information [Adobe PDF]

 

7 of 8 Semesters Complete.. What’s Next?

So, with the exception of my honors presentation/semi-completed thesis/deliverable, two finals, and another presentation… I’m 88% complete with being an undergraduate. The other day I remembered some random event and was telling a friend.. “Do you remember last year when…”. After I finished the story, she looked at me and said, “Yeah… but Adi, that was in freshman year.” I was confused; I was so sure that it happened last year.

Even though I’ve gone through almost four years of college, it still seems like C-Tops was just last week. And that scares me. I don’t want the last few experiences of college to past by like a fleeting daydream. My worst fear is sitting in an office somewhere a few years from now, looking back on these past four years and missing it all — all of it. The parties, the dance battles, the allnighters with Pokey Stix, the classes, Kamikazi, the teachers, the friends, the acquaintances, that damn pit preacher, that meditative experience of walking through the quad in a sea of people, jumping across puddles of rain in the pit, being a freshman and eating at Lenoir with random people. But I know it’ll happen. I know i’ll miss it all.

Regardless, I’m trying my best not to think of it this last semester. I was originally going to graduate in December and I know now that would have been a horrible idea. I need a semester to take it all in, to relive everything that I’ve missed and live everything that I haven’t done. I need a freaking conclusion to this four-year novel. As far as work is concerned, most of it is stuff that I’ve always wanted to do independently but never had the time or the resources.

1. Work on my honors project, thesis, and presentation… and probably take a grad. info theory class to help it.
2. Consolidate all of the web design work, web development work, and graphic design work I’ve done in the past years into one place.
3. Work on designing and developing one of my ideas and push it out to the public for free (but get money through advertising!) I want to see what people like and what they don’t like. I have these conceptions of what users like right now, but I think that’s kind of pretentious without actually knowing what target audiences are interested in.
4. Build/hack the HTPC…
5. Start work on the carputer (…car + computer). I can’t actually do anything to my car until June when the warranty expires, but there’s always LOTS of time to spend $1,000 :] I should probably also figure out how I would cut out the dashboard and stuff before I actually do it…
6. Start developing applications in .NET. Ha, this is kind of obvious…

So lots of fun, but mostly lots of relaxing before summer, travel, moving to Seattle, and starting work with Microsoft on August 13th!

 

Like.com: Image Rec + AI. WOW.

Just played with the just-launched Like.com, a site whose design reeks of Web 2.0 but whose functionality is seriously unparalleled. This new webapp is from the creators of Riya.com and has stuff that would have Vannevar Bush rolling in his grave. For example: you can search for watches (or browse by watches) select which ones you like, and the backend feeds the user-friendly interface with tons of watches that look like it. What’s more, you can select which of the following attributes you like: the color, the shape, or the pattern on the watch, and the frontend immediately updates to show you watches based on your preference. THEN you can select a part of the watch you like, and find watches with that part! It’s eerily accurate. You can also change what color you’d prefer. Finally, you can look at pictures of celebrities and search based on the products that they’re wearing — you can drag a box around their shoes, or their watch, or whatever, and find products exactly like it!

Whew.

Keep a close eye on this one. Froogle-like functionality + Like.com + cool domain name = a killer app.

 

Interviewing with YCombinator

I went to Boston this past weekend to pitch an idea with Phil to YCombinator, a venture firm started by Paul Graham — the guy who sold his online store to Yahoo in ‘98 for 48,000,000 dollars. The entire weekend was an incredible escape from school and work (unfortunately as I write this now I’m right back in the heart of it). We applied with a completely different idea than what we pitched. In fact, we had a few ideas so we didn’t really know what we were going to pitch until the day before. Regardless, we put our faith behind an idea that did have a lot of technical problems. While we could have touted the amazing user experience and the sheer amount of pain points that the product could have addressed, in the end we were pushing our beautiful pie-in-the-sky design that would have solved all of these technical problems. I think Robert Morris noticed that the most. Phil and I both agreed that we probably would have done a lot better if we had a demo or if we had come better prepared to tackle the technical issues… or if we had went with the idea that Paul had suggested we do!

The night before the interview we had dinner with about 10 of the teams that were interviewing. Seriously, I met some of the most diversely smart people in the bottom of that Italian restaurant. The guys who probably impressed me the most were the three-member Weebly team. They have an amazing beta of their product with an impressive userbase and a great team organization. A few days ago they were mentioned in TechCrunch and received another 2000 users.

While I was pretty disappointed in not getting YCombinator, it was still awesome getting the opportunity to meet Paul, Robert, Trevor, and Jessica. And hey, everything happens for a reason. I was always upset at the possibility of leaving my friends and abandoning my senior year to work in Mountain View on the startup — although I definitely would have done it if we were given funding from YCombinator. A few hours after Phil called me and told me the outcome I ordered Chinese for the people I was staying with. After good food and a good conversation, I opened my fortune cookie and broke a smile as it read:

“Your true wealth lies with your friends”.

 

Download Windows Vista RC1…

I got it through TechNet, but now MS has opened it to the general public to download. You can get a product key on the spot and it can be used on up to 10 computers. Although Vista RC1 is pretty nice, i’m wondering how this RC1/RTMness will play into the final version’s shipment. I’m guessing MS will ship Vista through Windows Update and have customers pay online. In terms of ease of use that would be great.. but it basically means that if you go for the “free” upgrade to RC1 now, you’re headed down the road of having to pay $400 when your RC1 version doesn’t work anymore (since it’s impossible to roll back to XP). Eh, Vista is pretty nice so.. oh well. It doesn’t really matter too much if you put your files on a different partition or hard drive, separate from the Windows installation. If you do have to do a new install of XP over Vista when the time comes it won’t hose anything.