PolITiGenomics

The Genome Center’s new Data Center Building won the prestigious (I’m told) Keystone Award for Project of the Year from the St. Louis Association of General Contractors. This award is given to construction projects in the St. Louis area for building excellence in the fields of safety, constructibility, speed, budget, etc.

You can see more pictures of the data center on flickr. Now that we have moved in, I will post some more pictures as soon as I can.

Tomorrow, 30 October 2008, at 12:30 EDT, Douglas Holtz-Eakin, representing Sen. McCain, and former FCC Chairman Reed Hundt, representing Sen. Obama, will participate in a Technology Policy Smackdown hosted by the New America Foundation and Wired Magazine. It is a pretty lame name for a discussion of the candidates’ tech agendas, but it should be interesting. The debate will be webcast live starting at 12:25 EDT (see above link for more details).

About a year ago Tim Cutts from Sanger suggested I modify (he was being nice, improve is more accurate) lsgmake-gap to use LSF’s job arrays rather than spawning a separate job for each per-lane step in the GAPipeline. A year is too long to for a good suggestion like that not to be implemented, nonetheless it has taken me about that long to get around to doing it. But, hey, it’s done now and you can download the new version: lsgmake-gap-0.9.tar.gz. Next on the list is modifying lsgmake-gap to be able to handle the auto-calibration lane in GERALD (available in GAPipeline-1.0, although the Pipeline parallelisation documentation has not been updated). Hopefully it won’t take me a year to get around to implementing that. You can also get any older version of lsgmake-gap.

Update: I have released lsgmake-gap-0.10.tar.gz that changes the default number of make jobs from two to one.

Here is some more information on each candidate’s stance on technology issues, what’s new is Gov. Palin’s stances derived from her record. You can review the stances of Sen. McCain, Sen. Obama, and Sen. Biden. The articles only cover a few topics, but it is clear that Sens. Obama and Biden need to reconcile their stances on a few issues.

I’ve been getting a lot of spam comments on the blog so I added a CAPTCHA to comment posting. Specifically, I have added CAPTCHA’s from the reCAPTCHA project which uses CAPTCHA’s to help digitize old books. Adding the CAPTCHA’s was greatly facilitated by the WordPress reCAPTCHA plugin. So rest assured, every time you post a comment, you are helping to enlarge the freely available intellectual commons.

Sen. McCain has recently released his technology platform. Sen. Obama has had his technology platform available for while. Sadly, Sen. McCain’s proposals seem to favor moneyed, entrenched interests by opposing common sense patent reform and net neutrality.

Update: Lawrence Lessig has posted his response to Sen. McCain’s technology platform.

One warning, it is nearly 17 minutes long.

Researchers in Japan have created the first DNA molecule made from entirely artificially created bases. While some are trying to manufacture artificial life by creating DNA molecules in the lab, the aim of this research is to take advantage of, and in this case expand on, DNA’s high information density to create a very dense data storage platform. Natural DNA has four different bases (A, G, C, and T) it can use to encode information. To expand DNA’s ability to encode information, these researchers created four new bases and integrated them in to a DNA molecule.

There has been a lot of studies recently that indicate that multitasking is harmful to productivity. In other words, there are significant switching costs when you mentally move from one topic to another. There is a New Atlantis article summarizing the findings entitled The Myth of Multitasking. Ironically, this story was picked up by Slashdot, one of the larger disrupters of concentration in IT. My high school algebra teacher knew all this a long time ago as he would always tell us, “age quod agis”: do what you are doing.

The next upgrade of the 454 FLX platform is called Titanium. The previous name gave a better indication of what the upgrade entails: XLR-HD which is short for eXtra Long Reads-High Density. The XLR is due to the run having twice the number of cycles so the average read length will increase from 250 to 400 bases (the average read length is not exactly double due to nucleotide flow order, mononucleotide runs, degraded signal as the number of cycles increase, etc.). The HD is due to smaller, more densely packed wells on the picotiter plate which increases the number of DNA fragments sequenced per run. Putting these together, 454 FLX Titanium runs will quintuple their data output from 100 Mb to about 500 Mb (or more).

This increase in data does not come without a price. Up until now, the primary analysis (image processing and base calling) of 454 data was able to be performed in a few hours on a moderately powerful computer. With the increased data output, primary analysis requires a small cluster: 20 cores with 1 GiB RAM per core having shared access to 1-2 TB of disk space. While those are the minimal requirements, 10 cores per run region seem to be the sweet spot for best performance. The initial production release will support Red Hat-compatible GNU/Linux distributions (RHEL, CentOS, and Fedora). Previous releases also only officially supported Red Hat-like operating systems but we have not had a problem running them on Debian GNU/Linux (454 also indicated they are pushing toward LSB3 compliance). Fortunately, 454 is eliminating the hard-coded dependence that the software be installed and the analysis processes have write access to /usr/local/rig. This will make installation across a cluster much easier. They are also abandoning their custom IPC implementation in favor of the “standard” MPI, specifically OpenMPI or MPICH2. While it is good that they are using a standard IPC implementation, it is unfortunate that MPI implementations are so fragmented and often incompatible, i.e., if one vendor uses MPICH2 and another uses LAM, you need to set up different systems to support each because they cannot coexist on the same system without problems.

I know this is unrelated to informatics, but if you will allow me to journey back to my transport phenomena days as a chemical engineer, the new picotiter plate requires much smaller beads, about 1 micron in diameter. At these length scales, transport phenomena, specifically boundary affects and polymer diffusion, may become important during the emulsion PCR and sequencing. Someone needs to calculate a Reynolds number.

Oh, one more thing, there is talk of paired-end reads with 20 kb inserts.

Similar to Ars Technica’s list a couple weeks ago, PC Magazine is running a story about each presidential candidate’s position on net neutrality, broadband availability, H-1B visas, intellectual property protection, and privacy.