Printing the human genome on punched tape

blog.mattbierner.com...

For the past week, I’ve been holed up nights in a warehouse attempting to print the human genome on punched tape. Punched tape is an old data storage medium that encodes binary data by punching holes into paper tape that is typically rolled up like a reel of film. The reference human genome weighs in at some 3.2 billion base pairs and 3.2 billion is a big number. Really big. After a week of off-and-on printing with two punch machines, I’ve used up around 50 rolls of paper and the the work area is already starting to fill up but I’m not even 5% through one measly little chromosome yet.

This project uses a pair of tabletop paper tape reader+punch combo units made by GNT in the early 80s, although even back then punched tape was pretty dated. These machines use eight holes per row of data, with each hole encoding one bit of information (so one byte per row). At ten rows of holes per inch, storing 1MB requires about 2.5km of tape.

Here’s how the four bases we all know and love are encoded

A very simple python script reads the genetic data line by line, encodes it into a bit pattern for printing, and sends the binary data to punch machines over a serial connection.

No one manufactures real punched tape any more, so I had some rolls custom made and shipped across the country on a pallet (thanks Papertec!) The ten inch diameter reels I am using hold around 2000 feet or so of tape, and take about one hour and ten minutes to print. This means that printing the entire human genome—with its decadent 3.2 billion base pairs—would require approximately 13,300 reels of paper tape with a cumulative length of some 5000 miles. Printing would also take two years running two punches 24/7.

The time between tape changes is pretty damn close to one hour and eight minutes too…) Sadly though, as I only have 500 reels of tape to work with, the best I can hope for is under 4% of the genome. More realistically, I may make it through 200 rolls in my month of printing.

Came across this and thought i'd share it. I gotta say it seems like a pretty, Hmmm, ambitious project. There doesn't seem to be a ton of value to doing this and it seems pretty wasteful in some ways but I guess it would be kinda cool to see the entire human genome printed out in a human readable encoding on paper...I guess.

The cheapest paper I could find was Russian and costs $10.00 per roll. The need is for 13,000 rolls, so $130,000.00 worth of paper rolls. Assuming a bulk order could be had for cheaper, that's still tens of thousands of dollars worth of paper. The perptrator's answer for "Why?" seems to be nothing more than "Why not?"

As far as storage, an eyeball approach would suggest you could get 10 reels in a cubic foot. So that's 1,300 cubic feet, which is not quite 50 cubic yards, which is about five dump truck's full, assuming a typical standard 10 wheel dump truck. Huge dump trucks can, of course haul larger loads. If the reels were packed very tightly they would fit in a typical single-car garage floor to ceiling.

Of course, once punched they would have to be re-rolled and cataloged very carefully, not the mess you see on his warehouse floor. Paper is not an especially durable storage mechanism. Even if protected against the environment paper tends to get brittle very easily due to the acid content of the paper. So even in a sealed environment where the air was pumped out in favor of pure nitrogen, for example, it would not last more than a few hundred years.

God I hated that stuff.

That, and punch cards. Had a WATFIV project with a couple of hundred cards. Rubber band broke on the way to the computer center and I had to reorganize the whole pile. Missed that day's batch run.

8-bit bodot teletype, ah, those were the days on ship trying to type as you slide by in heavy waves, Fun stuff trying to keep up with 30 wpm..

Flash Z message, get it to to the Captin ASAP

"We have gone to war sir"

RIMPAC 82...

His face went white........

a reply to: thedigirati

CR LF Letters

Loved the sound of an IBM card punch spitting out cards.

Threw my last card deck away a few years ago. Kind of wish I hadn't. We'd paint pictures in marks-a-lot pens on the edges so we could identify them in the cubicles where they were returned by the white lab coated guys.

a reply to: schuyler

Good for flip animations too.

I’d hate to be the poor sod that has to untangle and roll that all back up.

a reply to: Phage

God I hated that stuff.

DNA? Agreed!

Pesky stuff that causes every misery in the world.

a reply to: Baddogma

That.

And punch tape.

originally posted by: Phage
a reply to: schuyler

Good for flip animations too.

We used to make “poinsettias” out of used punch cards, sprayed red (or metallic gold for the chi-chi) they made cool Christmas decorations back in the ‘60’s.

Hanging chad didn't seem to be an issue with punch cards like it is in elections. Voters should use key punch machines instead of voting machines.

originally posted by: thedigirati
8-bit bodot teletype, ah, those were the days on ship trying to type as you slide by in heavy waves, Fun stuff trying to keep up with 30 wpm..

Flash Z message, get it to to the Captin ASAP

"We have gone to war sir"

RIMPAC 82...

His face went white........

So you didn't show him the Exercise Exercise Exercise Line?

Seven level tone mod RATT and the teletypes never stopped. R 390 and R 1051. KW 26 and the KL-7. The KL-7 could read paper tape.