Protein folding and docking on the Playstation

Folding@home, as most people in the field would know, is the massively distributed protein folding simulation. As far as I remember, users around the globe can download a screen saver and contribute their idle computer processors to aid explicit (and recently implicit) solvent simulations of proteins folding and/or misfolding. Understanding this process is therapeutically important, as I have pointed out in an earlier post.Recently, a friend of mine mentioned that people had begun using Playstation consoles as a more than adequate substitute for expensive, and cumbersome nodes which are commonly used in computer clusters. The reason for this is that modern games require such heavy graphics and processor power, that the Playstations are computationally very efficient. Moreover, due to their popularity, the cost of a single Playstation is quite cheap, and the technology is very well developed. It makes sense that scientists involved in biological simulations have caught on. Folding@home and Sony have recently got together, making even idle Playstations useful.

It's not just protein folding, but the powerful playstations can be used for other computationally demanding assignments such as ligand docking. I just read that Simbiosys has released a version of their docking software for the PS3.

To lower the cost and power consumption typically associated with compound-library-screening programs, SimBioSys has also released eHiTS Lightning. This package combines the 2009 eHiTS software with IBM's Cell/B.E. chip multiprocessor, found in the Sony PlayStation 3, to achieve a 10-fold increase in computational speed. The PlayStation 3 hardware (shown) replaces some of the expensive computer infrastructure required for virtual screening programs, opening up computer-aided drug design to smaller companies previously unable to afford it.

Pretty damn cool!

Roku rocks! Netflix streaming video, right to my television!

When Netflix launched their video streaming service, I was ecstatic. Being able to watch a movie on my computer anytime I wanted to, was spectacular convenient. And having been part of a generation, who are more than used to watching movies on our tiny laptops, this form of media delivery, with its smaller screens, overheating laptops on our laps, and terrible sound, did not bother me at all. (On a side note, I still remember how shocked I was to see commercials while watching Family Guy for the first time on TV. The reason being, I was part of the vast number of people who had only seen Family Guy and other shows like it via P2P networks.) Of course the convenience of instantly watching needs to be offset by something, and that something is a reduced library of movies and shows which can be watched instantly. So Netflix doesn't offer its full range of media, but it still lets you watch about 50,000+ things. And it's unlimited viewing via streaming for $8.99 a month.

Sp recently my brother told me about his latest purchase, the Roku player.This player streams the available Netflix movies and shows via the Internet right to your television. It can use your wireless Internet as well, is sometimes in high definition depending on the movie, and moreover, it requires no subscription, just a one time cost of $99, plus of course a monthly Netflix subscription. However, I would buy the HDMI cable from Amazon or something, as its about 10 times cheaper than buying it from the Roku website.

Anyway, I love this device. It's so much better to watch stuff on my television than on my laptop. Plus some movies are in HD, so the picture is a lot better. And the amount of shows available are more than enough for someone like me, who is always about 5 seasons behind everything. Plus I'm into independent and art house movies, and recently I've been obsessed with re-watching the classics, so I'm more than happy with the variety that Netflix and Roku provide. The Roku player for streaming Netflix movies is one of the most affordable and useful pieces of tech out there right now. I can't see myself ever living without one.

I'm temporarily deactivating myself from facebook

I love facebook, but I'm addicted to it. I literally log on to it first thing in the morning and it's always the last thing I check before sleeping. Even while procrastinating during work or day dreaming or while watching tv, I subconsciously log on and start browsing the facebook profiles, notes and pictures of people, most of whom I don't really care about, nor will I ever meet...ever again in life. Its really sad.

I really need to focus in the next few months, so I'm going to do a little experiment here and deactivate myself temporarily from facebook. (Interesting to note that I think its not possible to delete ones account, which is kind of wierd and a little dangerous.)

Anyway, so let's see how long this experiment lasts and how productive I am. I certainly hope I'm a lot more productive. I'll still keep on blogging though, so the 3 people who follow my blog are still entertained. Woo hoo!

How has it been thus far? Well, too early to tell as today is my first day without facebook. It hasn't even been 24 hours since I deactivated my account, and I'm already having withdrawal effects. There seriously must be some medical term for Internet addition. If not, it needs to be considered. So I've been to the site 3 times before realizing that I can't log on. Of those 3 times, I plugged in my user name and password once before realizing it. This is madness!

It's all about the numbers - landing an interview by pumping out your resume

A friend of mine recently commented about how she didn't land an interview for some internship that she applied to. It was disappointing, naturally, but what I couldn't figure out was why she applied to just a handful of internships. After all, from the human resources point of view, it really is all about the numbers, regardless of how well the economy is doing (Although obviously, in better economic times, you are more likely to get interviewed).

I think that one needs to apply to tens of hundreds of jobs in order to get your resume even looked at, and this is how I have chosen to explain this:

Let's assume that the probability of you landing an interview for one job application is p. Therefore the probability of you not landing an interview is 1-p. And if you apply to n jobs, then the probability of you not landing any interview is (1-p)^n. And the probability of you landing at least one interview is 1 - (1-p)^n. So if I would want my chances of getting an interview to be more than 50%, the equation I would need to solve is: 1 - (1-p)^n > 0.5.

Simple enough. So let's select some random probabilities of getting an interview for p.

If the probability of getting an interview is = 0.1, then you need to send out 7 resumes in order guarantee yourself at least 1 interview.

Obviously 0.1 is a really high probability, unless you are a genius, so let's work with some more realistic ones.

if p = 0.01, then n needs to be 69 job applications.
if p = 0.001, then n needs to be 693 job applications.

Well, you get the idea. In order to maximize the chance of you landing an interview, you really need to pump out that resume to as many places as possible. Obviously this model is extremely simple, with several non-realistic assumptions, but I feel that, generally speaking, this idea holds true.

Sadly, since its not at all possible these days, we have to wait for 693 jobs to open up. And after that, we still need to ace the interview. And I don't have an probabilistic scenarios or models for that. That's all on you!

Money saving tips from crazy people

In these harsh economic times, saving money is on everyone's mind. Google is now moderating a website called 'Tip Jar' where it gathers tips from users and various websites. Readers can rank these tips and the ones that are ranked highest, obviously pop up first. A lot of them are quite sensible, but some near the bottom of the page are just plain stupid. I'll share the ones I find most amusing.

"Breast feed your children for the health benefits (to mother and child) and take the cost savings of not buying formula and bottles as an added bonus. Even with the costs of a breast pump and storage supplies, you'll still come out way ahead."

Health: "Using a cotton ball, apply vodka to your face as an astringent to cleanse the skin and tighten pores"

Tech: "Use google maps to create a cultural/contextual map of your community"

Misc: "Take the extra time to spell things correctly - it shows you care about who's reading what you've written. Grammar, spelling and punctuation are often overlooked when communicating via the Internet."

Misc: "Do not eat yellow snow."

Video game review: Civilization Revolution for the Xbox 360

Being a strategy game enthusiast, I was a bit apprehensive when I heard that Civilization was going to be released for video game consoles. After all, these consoles are RPG territory for the most part. Would people have the patience to play for hours on end, build an empire, thrash your enemies and take over the world? Would the game play be quick enough? Would the game be as addictive as it's predecessors on the PC?
Well, it turns out that the game is pretty darn good. It's the only game I've been playing on my Xbox for the past month, and I'm still enjoying it. It's definitely addictive, enjoyable, and provides an attractive and fulfilling experience; the kind of experience that I routinely sought after while playing strategy games on the computer.

The pros are obvious to all but it's the cons that bother me and I'll gloss over those:

1. Why are the maps so small? Why can't I decide how big or small I want the world to be?
2. 5 civilizations every single time? Can't I choose the number and which ones?
3. I should be able to make my own maps.
   
4. I prefer longer games, saving it a few times throughout, and that's not possible here
5. Different civilizations should have unique weapons and tools. Why is everything the same?
   

Tracking flu outbreaks through Google

Google's philanthropic division has revealed a tool that predicts flu outbreaks across the United States using search trends. The idea is simple: When people get flu-like symptoms, they use search engines like Google to search for information and cures for these symptoms. They've proven, as it can be assumed, that there is a link between the actual number of people having the flu, and the sheer numbers of searches for flu-like symptoms. Turns out that search engine data can actually predict flu outbreaks up to 2 weeks before the Center for Disease Control and Prevention (CDC) reports it. The NY Times has a great picture showing this trend:
So what does 2 more weeks of knowing about an outbreak give us? Why is it important? From their blog:

For epidemiologists, this is an exciting development, because early detection of a disease outbreak can reduce the number of people affected. If a new strain of influenza virus emerges under certain conditions, a pandemic could emerge and cause millions of deaths (as happened, for example, in 1918). Our up-to-date influenza estimates may enable public health officials and health professionals to better respond to seasonal epidemics and — though we hope never to find out — pandemics.

Here is graph for New Jersey. Looks like we're getting closer to an outbreak... So currently this is limited to the United States, but obviously this can be expanded to other countries as well. It also doesn't have to be limited to the flu. Think of the possibilities: it can be used by health agencies worldwide to prepare for the worst. Apart from the privacy issues, I think its fantastic how collecting search engine data can be used in such a useful way.

What are the rocks and pebbles underneath train tracks for?

Besides the usual media sources, questions and thoughts from my friends occasionally serve as inspiration for my blog posts. Recently my father brought up a question which has remained on the table for a quite a while now, while I'll now address.

What is the purpose of all those tiny rocks and pebbles that one sees laid underneath railway tracks?

He brought up this question, while my family and I were spending the day in New Hope, PA and happened to come across the historic New Hope train station, shown in the picture below, as we were ambling about. So what are all those rocks for?
In that conversation, I surmised that those crushed rocks were probably there to prevent plants and trees from growing between the tracks, and possibly impeding the path of the train. My dad felt that it had something to do with vibrations, and dampening them while the train moves. The idea is that the vibrations and force from the train on the track, spread across the hundreds of pebbles, leading to less strain on the tracks themselves and thus a smoother ride.

Turns out we're both correct (though his explanation is obviously a lot more clever). A quick glance through the Internet reveals that those pebbles, rocks, etc are called track ballast and according to wikipedia, they are...

...used to facilitate drainage of water, to distribute the load from the railroad ties, and also to keep down vegetation that might interfere with the track structure. This also serves to hold the track in place as the trains roll by.

Some other interested soul on Yahoo Answer's gives a couple of additional advantages to using ballast...

1. It prevents the rails from moving sideways which would be the natural tendency around most curves - the train would normally push the lines outward and the ballast stops this happening for the most part.
2. It is an easy way to make a level running surface for trains - special track tamping machines are used to re-pack these ballast rocks around and underneath rails where they have been pushed out by the constant passing and vibration of trains. Much easier than trying to make a completely level track bed on the earth, and cheaper than using concrete beds all the way too.

Right. So now we know...

The latest Loch Ness monster video doesn't seem to be fake

Keywords in CNN headlines

My friend read my last post, which talked about how 'sex' is so unusually high up on the NY Times.com searched keywords list, and he referred me to an interesting blog post. This friend of my friend, made a script that captures CNN headline keywords and then outputs a tag cloud. So the text cloud "contains the headlines of the past 30 days and is updated daily" according to the author.

The output over the past 30 days is an interesting follow-up to my post. Strangely enough, 'Food' leads the list. 'Iran', expectantly, also tops the list while 'Iraq' is not far behind. The word 'sex' has a count of 4, which is also interesting, as one would never assume 'sex' to be a biggest news of the day.

This is a cool tool. But what would be cooler, is if it would be possible to compile the same text cloud for BBC, Fox, Reuters, and some other leading Internet news providers. Comparing headline keywords from various sources would be quite indicative of what different companies find newsworthy or not.

NYTimes most popular search keywords

The NYTimes most popular articles page on their website also include a list of the most searched keywords by readers. I occasionally glance at the list and its usually a pretty good reflection of the news trends of that week. Iraq is usually there, and recently Iran has been topping the list. However week after week, sex is consistently the number one most searched term. Now I know the average New York Times reader isn't the usual porn addicted freak, so the result is even more amusing for me. From the NYTimes...

Keywords most frequently searched by NYTimes.com readers.

1. sex
2. pet food recall
3. iraq
4. immigration
5. china
6. india
7. health
8. iran
9. global warming
10. long term care

Renewable Energy in Pakistan

My friend wrote this excellent article entitled 'Adding fuel to fire' which recently got published in one of Pakistan's leading daily's. He presents arguments supporting ethanol as the next new renewable source of energy in the country. I was impressed to learn that Compressed Natural Gas (CNG) has been heavily encouraged in Pakistan and has been quite a success. I have included some excerpts from his article. I urge you to peruse the published version at your leisure.

By lifting import duties on CNG conversion kits, converting government vehicles, and liberally distributing licenses for CNG filling stations, the (Pakistani) government kick-started a cycle of CNG production that was then propelled by basic market forces and low CNG prices. As a result of these policies, CNG use has captured a large share of the petrol market over the last two years. There are over 1 million CNG-enabled vehicles in Pakistan today, constituting nearly 20 percent of all vehicles in the country. It is the third largest CNG fleet in the world.

That's great to know that Pakistan has the third largest CNG automobile fleet in the world. However, as my friend and author rightly points out, CNG, though clean, is not renewable. As a result of this, he proposes several measures whereby ethanol can be introduced as the source of renewable energy

According to the World Bank, the only potential renewable fuel anywhere in the world that can currently compete with petrol is ethanol from sugarcane. Pakistan produces the world’s 5th largest sugarcane crop, of which 20 percent is exported. In fact, until recently, Pakistan was the second largest exporter of sugarcane ethanol to the European Union — a preferential status we have since lost because of WTO obligations and dumping complaints. Several distilleries have planned to close down in light of this fact. Instead of curbing production of fuel ethanol, however, we should redirect it to the domestic market. Eventually, a domestic industry will grow, and the further development of sugarcane feed-stocks will accelerate rural infrastructure development and result in rural job creation from farms and processing facilities.

Experiences with fuel ethanol in Brazil and around the world suggest that government action is essential in the initiation of such programs to coax the market away from pre-existing technologies. A Pakistani fuel ethanol program, like its CNG predecessor, will need initial government support to develop an infrastructure in which the new industry can grow.

This entails providing incentives for both production and consumption of fuel ethanol. the fledgling industry will need fiscal support in the form of subsidies, tax incentives, and state-guaranteed credit, to ensure that it has a consumer base and a competitive price. As production increases, economies of scale will develop until ethanol production is cost-effective and self-sustainable.

This is an impressive article and quite eye-opening for me. I believe the ideas that he proposes are quite manageable. There is, after all, an infrastructure already laid down for CNG production. Thus the government is aware of the looming energy crisis. It's great that Pakistan is far ahead of other nations with regards to industrial and automotive CNG incorporation. It would be even more impressive if Pakistan can think to the future, utilize its renewable crop resources, and thus produce energy domestically.

World Of Warcraft expansion delayed

Screenshot of the game from the creator's website...


I was thinking of restarting the game and had heard about the expansion set. Let's see how it turns out...

From BBC...

Blizzard has announced the release of the Burning Crusade expansion pack is now being delayed until January 2007.

The expansion, which gives players new races, territories and more powerful characters, was scheduled to appear in late 2006.

But Blizzard said more time was needed to "further refine" the extras.

Since it launched in 2004, the massively-multiplayer online fantasy role-playing game has proved a huge hit. Now more than six million people have signed up to play the game and send their warriors, warlocks, rogues and other characters questing in Azeroth.

The Burning Crusade is the first big expansion of World of Warcraft that makes a variety of changes to the game.

It was due to appear before Christmas 2006, but Blizzard said it was delaying this launch date by a "few extra weeks".

In a statement, Mike Morhaime, president and co-founder of Blizzard, said: "We feel confident that the extra time spent polishing the game will result in the high-quality experience that our players expect and deserve."

In mid-October, Blizzard began a closed trial test of the Burning Crusade in which a few players got the chance to try out the new races, places and abilities in the expansion.

Blizzard said the few extra weeks would give those taking part in the test more time to "participate in the final stages of development and continue providing valuable feedback".

Blizzard has yet to give details of exact worldwide launch dates or how much the expansion will cost.

Virtual Reality gaming and chronic neck pain

I laughed for an hour when Rich sent this picture to me. This is hilarious. Be sure to check out the link and the description talking about this...

What a device...

That needs to get smaller really fast!

Firefox + Performancing -> Blogger

I am updating my blog straight from Firefox using Performancing. It's connectivity with Blogger is impressive....This does make it easier to blog while I am browsing at work

powered by performancing firefox

Testing Picasa and Blogger's functionality

 
 
 
 


I guess it works... 

Online Dating. Still taboo?

5 years ago..maybe. But not anymore. The internet has become such a crucial part of our lives, that meeting people online has become a certainty. I think we are at the stage where the majority of people are still hesitant about dating but are coming around to being receptive to it.

Standard networking sites are also being used for dating. Facebook, Friendster, Orkut certainly are not primarily dating sites. But my friend's who are girls routinely get 'poked' by random guys trying to become friends with them. Some accept some don't, but never do they reply or respond. If you're on facebook, you're not there to really meet people but stay in touch with people you already know...agreed, even if it means people you met once and will never see again...It's all about the number of friends anyway.

Friendster has a search tool for finding people based on location, interests and so on. Though I am not an active user on friendster, I have gotten random messages. Same rules apply here. Put in your search parameters, put in the age, the gender and maybe the location and hit search. Then start randomly messaging people who you think are interesting (or attractive).

Orkut is just weird. It seems really fobby. We all know the weird guys messaging girls begging for "frandship".

My point is that all networks on the internet are conducive to online dating. To different extents, and the populace that resides within these networks are open to
meeting people online according to different strengths.

Facebook is too open, and awkward to meet people. It's odd to poke someone and say what's happening. Recently 3 random girls poked me and I didn't poke back. I noticed we had friend's in common and stuff. But its just odd. If I haven't met you, then why should I respond on facebook? Odd but true. It felt cheap. If my profile was up on shadi, I might respond. Though its not.

I think the most interesting aspect of this has been the spawning of ethnic dating websites. At Brandeis, I was always aware of Jdate for Jewish dating. Naseeb, Shaadi.com and Shadi.com were the others I was aware of. Most abcd's are on Naseeb it seems.

I posted my profile on naseeb a while ago just to see who else is on it. I feel its a lot more PG than other dating networks. I think its heavily moderated. But its interesting to see what kinds of people are on it. America is certainly diverse and families are spreading far and wide. Shadi.com are is basically for parents putting up their kid's profiles, but Naseeb is for kids. It's a very comfortable environment for some reason and it allows you to randomly talk to people. But, here in the desi state of NJ, everyone knows everyone and desi's talk like no other, so I doubt I would ever do that.

In conclusion, online dating is here to stay. Ethnic online dating can only grow and I completely support the concept. I think it's cool to have profiles online, meet people with no strings attached (not sex) and just stay friends and see what happens. No harm done, no gain. So what's the problem?

Pros:

1 - If you're busy. And it seems, we're getting increasingly busy.
2 - If you live in an area where there aren't many areas to socialize. Like Boohickey, Missouri perhaps?
3 - If you're of a certain ethnic sect, and prefer dating only within that
4 - If you're within some ethnicity and they are spare in your area
5 - If you're shy, but still confidant enough to post and seek someone online
6 - It's a lot slower. You can take your time.
7 - It may not be about looks initially. It's probably more about character and personality initially then meeting someone at a bar is. If you meet them later, then..good luck! haha

Cons:

1 - Still a bit taboo. You don't see too many people saying, "Oh, I met her on craigslist and we're getting married tomorrow!".
2 - There are creeps and paedophiles out there. One has to be careful.
3 - Some people just want sex. That can't be helped.
4 - It can be frustrating
5 - You may not want to pay for the services
6 - For every authentic site trying find a relationship (eHarmony, Match etc), there are tons of those trying to get you hook ups (AdultFriendFinder, True etc). Kinda puts us an unease
7 - Tons more guys are on these site, then girls!! Some inequality. Its a reflection of our social norms. Guys are usually the ones hitting on girls and asking them out. So girls find it a lot easier to date than guys....in my opinion! (I know some girls might want to throw rocks at me for saying that!) So therefore, girls, perhaps, don't really feel the need to put their profiles out there.
8 - And the most obvious one. You don't see the person you're talking to. Might be a pro too as well! Look at 7 above.

From the Beacon Journal. 08/28/2006

Ethnic dating sites increasing
Matchmaking online up as parents add profiles on specialized Web sites
By Eric Benderoff
Chicago Tribune
CHICAGO - Teena Verbit didn't think her daughter was dating anyone ``spectacular.''

So she wrote a personality profile for her daughter and posted it on Jdate.com, a Web site for Jewish singles.

``I didn't think she would do it,'' Linda Verbit, 23, said of her mom, ``but she did. She put me on Jdate.''

Teena Verbit now approves of the young man her daughter is dating. ``My mom has never been shy about telling me her opinion,'' said Linda Verbit, who lives outside Philadelphia.

Finding a companion on the Web is hardly new. But now parents are jumping into the online dating and matchmaking game, penning profiles of their children and paying to have them displayed on sites catering to specific religious or ethnic backgrounds.

``My parents signed me up'' for Shaadi.com, said 30-year-old Sejal Patel. Her dad even enlisted a Web-savvy friend to help him post her profile on the Indian singles' site.

``It seemed like everyone in the world knew about my Shaadi profile before I did,'' said Patel, who began getting up to 30 e-mails a day. Her parents wrote the profile -- saying she likes family picnics, cooking and helping out at home -- and paid for the service. The Web site costs $110 a year for a platinum membership, which includes a bold-faced listing and more personalized matchmaking services.

But not everyone buys into religious online dating sites.

``I prefer to meet them as a person, not a profile,'' said 29-year-old Ahmed Rehab, executive director of the Chicago Council of American-Islamic Relations.

While he has visited Naseeb.com, an increasingly popular site for Muslims, Rehab is not a member. Nor does he know of parents pushing such sites on their children, but that wouldn't surprise him.

Online dating is one of the Web's oldest businesses, with the most well-known sites experiencing flat to modest growth. But sites focusing on religion, race or ethnicity have soared. At Shaadi.com, for instance, traffic grew 73 percent from June 2005 to June 2006, according to ComScore Media Metrix, which measures Internet activity. Unique visitors to Jdate.com grew 43 percent during that period, and the site is so used to working with people like Teena Verbit that they even have a name for them: ``Jmoms.''

Other religious dating sites target Baptists, Catholics, Christians and Latter-day Saints, among others. There are also sites aimed at blacks, Greeks, Hispanics and practically every other slice of life one could imagine.

The number of dating sites jumped to 1,122 from 850 in July 2005, according to data from Web site tracking firm Hitwise.

Such sites are ``a great tool for targeting and filtering information,'' said Sara Stevens, director of industry solutions at ComScore.

Prices vary, from free sign-ups and trial memberships to costly plans, such as a $251 annual fee at eHarmony.com, which focuses on personality traits in trying to foster relationships.

Spark Networks, which operates Jdate and other specialty dating sites, is quite familiar with well-meaning parents. A survey recently posted on Jdate.com found that 22 percent of members' moms paid for their kid's Jdate membership.