I recently blogged about protein folding here [LINK]. Protein folding basically is a type of analysis that can help researchers better understand how certain diseases like Cancer, Parkinson’s, Alzheimer’s and so on develop and how they can be cured.

Last month a version of the protein folding software was released for PS3s. Since the last month, 250,000 users have downloaded it and are running it. The resulting computing power is equivalent to 400 teraflops. That’s 400 trillion floating point operations per second.

The program overall achieves 700 teraflops so PS3s are contributing quite a bit of processing power. The hope is that in the next year the program can break the petaflop (a thousand trillion flops/sec) limit, a feat that has never been achieved in the history of the world.

Based on this news Xbox 360 is contemplating participating in the program [LINK].
You can contribute to the program with your desktop or laptop computer here [LINK], it’s free.

There are things you can do and distributed computing can help. I have known about Stanford University’s Protein Folding program [LINK] for many years now but never felt compelled to set it up. With cancer hitting so close to home it’s time to rectify that.

"What is protein folding and how is folding linked to disease? Proteins are biology’s workhorses — its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery.

Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer’s, Mad Cow (BSE), CJD, ALS, Huntington’s, Parkinson’s disease, and many Cancers and cancer-related syndromes."

"Folding@Home is a distributed computing project — people from through out the world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals.

Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved."

If you have a computer at home or have access to one at work I encourage you to download and install Folding@Home [LINK].

This past Saturday was above 75 degrees and I got really hot. So the next day I walked into the barber’s and asked for a shave. #2 on the side and #3 on top. After a few mins of uncontrollable laughter they got down to business. I walked out half a pound lighter, decidedly itchy and looking mean as all get-out. In Ireland they’d call me a skinner, worn only by the toughest of inner-city rabble. I’d be expected to have a tattoo somewhere saying "I Love Mum", drink 14 pints of lager and shout for my team on a Saturday.

In the US it’s just another haircut. Fun stuff.

The Emergency Room
During the course of that Saturday she underwent a series of blood tests and scans including a CT scan and an MRI. The results indicated numerous large lesions in her right liver and left lobe. By 9pm I was on the way to the hospital. "Under Pressure" was playing on the radio. Whilst I was driving to the hospital my wife was told by the doctor on call (Dr. Michael Gould of Somerset Medical Center) that she had colon cancer which they believed had spread to her liver.

He should not have done that without a biopsy. No one can tell you you have cancer without a biopsy.

Monday saw a series of phone calls and triage. We scheduled an appointment with a GI doctor (Dr Marvin Lipsky) on Wednesday the 11th of April 2007. That appointment came and went. He was thorough, spoke very fast with little elocution. The diagnosis was that she did not have a blockage in her colon and that they would do a liver biopsy to determine whether the liver lesions are benign or malignant indicating cancer. The earliest we could schedule the biopsy for was the following Tuesday (17th). Karen’s sister was getting married the following Saturday (21st) in Dallas and Karen would not be cleared to fly after the procedure. This was a difficult decision but the need to diagnose the problem outweighed the wedding and on Thursday the 12th we decided to cancel the trip to Dallas. That week I worked Tuesday, Thursday and Friday.

The First Biopsy

The biopsy was done on the 17th and we got the results on Thursday the 19th. They were negative meaning the biopsy indicated normal tissue. We were elated at this news but I should’ve known to ask more questions. With the wind in my sails I booked my wife and daughter on the first flight to Dallas the next day and they were able to attend the wedding. Unfortunately my daughter was sick the entire trip and in hindsight should’ve stayed home.

The Second Biopsy
The following Monday (the 23rd) a second biopsy was done to confirm the first result. The radiologist(Dr Sneickus) was frustrated that we had not gotten a result from the first procedure and it was then that we learned it was possible the first result was a false-negative. He promised the results to us the next day. Unfortunately these results took longer and we didn’t get them until Friday the 27th of April over the phone from Dr Lipksy.  He told us that Karen had cancer, that it was an advanced stage (stage IV) and that it would require chemo and most likely surgery. He could not give a prognosis until further tests were done. He recommended we hang up the phone, schedule a colonoscopy through his office and setup appointments with an oncologist, Doctor Moriarity in Overlook hospital, Summit.

The Colonoscopy

Yesterday (May 2nd) my wife had a colonoscopy. The found a small tumor about 30cm into her colon. All other parts of the colon are within normal limits. The rectum is normal (thank God). So this was a good outcome. The tumor is not the size of a bowling ball or anything. It’s about half the diameter of her colon.  I guess she just was unlucky that it grew so quickly through the wall and went to the liver.  They biopsied the mass and marked it with dye.

Last night she had a fever of 101.5 and after calling the doctor, took some tylenol and it went down.

The Oncologist

We met with our first oncologist, Doctor Dan Moriarity today in Summit Overlook hospital. They are pretty good reputation-wise and closer than Robert Wood. We’ll use RW for a second opinion but we were encouraged by the consultation this afternoon. It’s about 20mins from our house if you race. 30mins if you take it easy.  He’s a nice guy, soft spoken but calm with easy demeanour.

Basically he’s scheduling a PET scan for sometime soon but starting treatment in the mean-time.

A port will be inserted next Tuesday the 8th of May. This is a rubber-plug designed to make the drugs easier on your veins. It sits under the skin near your collar bone.

Then starting 2 months of chemo, with Avastin and 5-FU administered with a take-home pump. Chemo will be every two weeks starting on the 14th of May.

After a bunch of research on the web I have learned this is the standard chemo protocol for colon cancer it seems regardless of the stage. I’ve also heard that this is an "aggressive" treatment of chemo. The Avastin alone costs $10,000 per treatment. One person has estimated a single chemo appointment to run into $14,000 and my wife will receive them for the next 2 months. Thank God for insurance.

I did record everything with my MP3 player and I’ll review everything tonight. I’m also starting to believe the Chemo will be the same at Robert Wood Johnson so why go out of your way to get to a doctor that’s further away??? Overlook will be far more convenient travel-wise. Let’s see what the 2nd opinion reveals. Definitely if surgery is considered in a few months we’ll go to RobertWood as I think they have the best surgeons.

After two months they will re-scan and expect everything to shrink and shrivel away into nothing. That’s what I’m visualizing in my spare moments.

Friday May 2nd:

Got results of the colon biopsy, confirmed the mets in the liver came from that tumor. No surprises but I’m learning to take everything that’s not BAD news as good news. Also got Karen’s CEA, it’s 237. I was alarmed at this at first as normal ranges are between 0 and 10. From research on the web I am told the typical CEA for a stage IV patient is between 700 and 1000. The key is that this number goes down once chemo starts. It’ll eventually reach 0 once all cancer is out of her body.

Make no mistake, this is the beginning of a long journey. We have a strong marriage and two beautiful children. I feel like we are really just starting our life as together as a family. We appreciate everyone’s support thus far and recognize that we’ll be leaning that much harder on people as time goes by.

Karen and I are up-beat and determined to kick some cancer ass.
 

Didn’t work today though so I turned to coding. 

Tonight I spent some time working up a small utility to collect movie trailers and convert them into Windows Media Format (WMV) something that’s sorely lacking on the net. I’m sure I’ll get a cease and desist soon but for now I’ll leave this link up [TRAILERS].

This was a fun project as it was quick to do and involved multi-threading. Always great fun.

Please spare a thought or better yet a prayer for us tomorrow.