My new eBook: "Genomics - easy as Pi" - DIY parallel cluster computers in big data genetic research

This book has been inspired by recent convergence of two sciences, both of which are my life-long passions, both of which for the first time this year are becoming affordable to a an average person: genomics and cluster computers.
The field of genomics has exploded in the last few years beyond belief, the original human genome sequencing project, finished in year 2000, took 13 years and $3 billion to complete. Today, the cost of sequencing of the whole genome is approaching $800 (in bulk) and can be done in couple of hours.
The genome research has been concentrated around the prestigious institutions with generous grants that could afford access to newest sequencing technology. The positive outcome of the research sponsored by the public funds is that the results are also public and anyone can have access to genetic sequence information from the Web base databases and FTP sites. With a quick search you can get sequences of many organisms ranging from common bacteria, yeast, corn, wheat, fruit flies, mice, rats, extinct mammals, monkeys, apes, Neanderthal and many humans. Sequencing the next genome takes hours and there are thousands of them being sequenced now, as you read it.
For couple of hundreds of dollars you can determine presence of some interesting sequences using companies like 23andMe, best of all you can download the raw data of your test and start comparing it against other genomes or databases of genes immediately.
At the same time the medical field is learning about hundreds of thousands of proteins and trying to figure out which genetic sequences code for them. Doctors are discovering the genetic association of many diseases and individual drug interactions.
Each human genome is composed of 3.3 billion letters (base-pairs), comparing it against multiple other genomes requires some serious processing power. There are other organisms such as loblolly pine (Pinus taeda) that have 23 billion base pairs in their DNA, that is 7 time more than human!  Due to the sheer amount of data being generated every day there is a vast opportunity for new software tools and new applications of that knowledge.

The field of genomics is growing faster than any other technological advance in human history and few would argue that with potentially the biggest impact on our future lives since we learned how to use fire.

You will be able to find it on Amazon, Barnes and Noble Nook and Google Books soon:

Pumpernickel bread

Flat out

Monday, the weekday alarm wake me up at 2:45 AM, damn, I forgot to change it from the Friday’s server deployment day. I quickly resumed the sleep broken by many thoughts, mostly about what time it is. At 6 AM the second alarm on my trusty Timex Triathlon woke me up, but very unusually for myself I ignored it and my wife took the advantage to go to the shower first. Fifteen minutes later was my turn, I went to the bathroom, brushed my my teeth and before jumping to the shower I felt the weird hungry dizziness from my stomach. I went downstairs to get a glass of milk. “Weird” - my wife thought, “he never does that”. I was thinking the liquid full of sugar, fats and proteins will rehydrate me and give me a little boost. I’ve poured the glass of cold milk, took a sip and sat down on the couch in the dining room. Or at least I thought I did, grandma woke up to a thud of my body hitting the ground in the middle of the floor and broken glass. I had no idea, I hit the “deck”. I terrified them, my body unresponsive, twitching, my wife Natalia and grandma screaming at me, trying to wake me up, pumping my chest. I did come to once, lifted myself on the hand and collapsed again, unconscious. I came to again just to see my wife trying to use my phone to call 911, the microphone does not work on my phone I told her with some clarity of what is going on, but in fact I lost sense of time and place. I am not sure what happened and when. I remember my year-and-a-half daughter Zoe leaning on my chest right above my face and I really loved that sight, my little angel, gently slapping me on the chest and face. The emergency guys came very fast, we live around the corner from the Fire Department, by then I was very conscious and despite being ghostly white on my face I was recovering. Over next 2 days doctors performed a full set of tests on me: CAT scan of my head, X-Ray of my chest and Echo Cardio Gram. I was released the following day after passing the stress test (treadmill run uphill) while connected to EKG and Tilt test. I did not have a heart failure. It was stress.

The previous week was a nightmare, constant software issues, constant feeling  of fight-or-flight, constant email chains from the management, long 12-14 hour days, 20 people to manage.  My heart was pins-and-needles hurting. Friday was the pinnacle, deployment in the early morning, hence getting up at 2:45 AM, status calls, more issues and a very long pep-talk from the big boss on what I did wrong and how I can improve. I came back home at 6 PM. On weekend I mostly slept, then had a good dinner out on Sunday and went sleep very early preparing for the next week. I took 2 Advil PM tablets to make sure I can fall asleep at 7 PM. Next morning my blood pressure was too low, heart too stressed, my body gave up — passing out is body’s natural reaction to protect the brain from lack of oxygen. I’ve totally wrecked my system to a point that 4 days of bed resting had no effect, at the moment of this writing my heart still hurts, I am still aware I might find myself on the floor at any moment, or worse.

Headlights stay on on Astro while parked

I use my Astro van as camping vehicle, when it gets cold at night I often turn the engine on to warm up. By default the Daylight Driving Lights stay on while engine is running which is very annoying in the campground situation. I found out that pressing Dome Override button 4 times will turn them off.

2015 Spartan Race: training day 1

I signed up for Spartan, 
if you want run together, or cheer and take photos, 
I created a team: "Valeria Warriors" to honor our late grandma who brought this family together.

Seattle, WA, Saturday 11:15AM-4PM, run start time 1PM (IMPORTANT)

weight: 185 lbs (of flab)

I might consider Wisconsin Tough Mudder, too:

Previous run photo:

Toxic woods

8000 grit conditioning whetstone

This Nagura stone is very small, I will be using it to condition other sharpening whetstones.


方法双方共に水をたっぷりつけて名倉砥石で軽く円を画く様に砥面を, まんべんにこすりすぐ泥が出ますのでそのまま御使用下さい。

Keyed Scarf Join

Making complex scarf join using mostly Japanese hand tools

Here is an example how a person can make a complex join using everyday carpentry tools.

Project Planning

"Planning is a good preparation for inevitable change of direction that throws out any plans made." ~ Uki

Kennedy Meadow Campground, PCT

I started my hike from Kennedy Meadow Campground, I picked the spot because it looked promising on the Google sattlite map with Little Kern River running thru and nice mountains surrounding the area. I had no idea at the time that this campground is a long-desired goal and destination of hikers arriving from the southern, desert leg of PCT, or Pacific Crest Trail.

I arrived driving J41 road at night I thougt I ended on the end of the world, roads in Sierra Nevada, especially at night are quite an experience with narrow passes over black, abbyssal drops.

I have spent the night sleeping inside my Astro AWD van on my military cot, which is much more comfortable than pitching a tent. In the morning I hiked at first light, way before couple of families with kids, few hundred yards away would steer up.

The campgroud is big and unlike crowded midwestern camps it gives you plenty of space and privacy. The vegetation is deserty chapparal but there are plenty of trees thanks to the river nearby.
The Little Kern Rivers is a beauty, at this time of the year in the late fall it was quiet, with plenty of clean water, the edges of the river had ice at some points, but the weather and the athmosphere were a daydream.

I hiked several miles north following the PCT, but then I decided to explore the mountains to the east. The hikes up and down the mountains are very steep, but not impossible with the huge boulders and tall trees, to reach the tops there are no paths to follow, just hopping from a boulder to another, sometimes squizing between bushes and sometimes walking on dry sandbars with deer tracks. You have the feeling that the monntail lion will pounce upon you at any moment from the boulder overhanging above you, l was happy to have my rifle with me.

Reaching the peaks gives you the ultimate reward of seeing the large valley bellow, the tall trees along the river and the PCT, look small, the remote valleys between the mountains sporting not a single human path look inviting with untold stories of adventure awaiting.

I think it is important for hikers zipping along the well travelled PCT to take this extra time and explore the land to the sides. This region, although not as beloved as subalpine meadows, is one of the best places a person can choose to explore. The nature is absolutely pristine, maybe sans grizzly bears that used to roam California and are no longer. The weather especially in late summer and fall is perfect and the river allows you to refresh at the hike's end in its clear, cold water.

I hope to come back there again!

Public private thoughts

It is difficult to balance what to write in a blog to keep it real and at the same time not to wash one's dirty loudry in public. I really don't know what the recipe is, but I think I should write about things that move me forward and omit the "little" stuff like the work and all the politics. We have a choice every single day to dwell on the past (day), or build the better self. I think the later is the answer to a public journal.


I took Natalia to movies tonight to see a movie "Wild", a story by Cheryl Strayed - I have been reading a book by the same title. The story is about a woman walking the Pacific Crest Trail, PCT to find herself. The book is amazing and the movie is excellent as well, however the book has much more detail, I was hoping that Natalia will understand my longing for mountains and time in the nature.
Last year while doing a solo weekend in Sierras in California I actually hiked along the PCT, if only for few miles -- l Can envision being on this trail for weeks at the time and the protonnd effect it would have an my psychology. l miss Sierra Nevada.