Saturday, 20 October 2012

The joy of academic conference spam

Once you get your names on a few papers, the influx of  academic spam increases. I probably get at least two of these spams a day in my inbox (not counting the ones that are diverted by Google's spam filter). I suspect those academics higher up the chain get even more. The most common ones are requests for conference attendance, session chairing, and reviewing; closely followed by international students and graduates looking for jobs or Ph.D. placements. They are nearly always totally unrelated to what I work on (computational genomics).

I got a classic example today:

Dear Torsten Seeman: 

Umm, you spelled my surname incorrectly. Sorry for misleading you with the correct spelling in my email address, websites, blog, and Twitter account.

The four sponsoring societies of DDW invite you to submit an abstract for presentation at DDW 2013 Scientific Sessions, to be held Saturday, May 18-Tuesday, May 21, 2013 in Orlando, FL. The DDW 2013 online abstract submission site is now open and will close on Saturday, December 1, 2012 at 9 p.m. ET. 

So it's in "Orlando, FL". Because I am Australian, I do have some idea of what else is in the world, and can deduce it is in the USA. But you are ignorant if you think the whole of the world knows all your two-letter USPS state codes! eg. CA = California or Canada? And unlike you, I know Canada is a country and not just a French speaking state of the USA.

<snip>DDW 2013 Abstract Submission Site: 
Poster sessions and DDW programming will start on Saturday, May 18, 2013. If your abstract is accepted, it may be scheduled for presentation on Saturday, Sunday, Monday or Tuesday. 
DDW Administration

Hmm, you still haven't explained what the hell "DDW" is. Your email domain is giving me a hint, but that was the last line of the email. OK, I'll click on the link to find out - I can't help myself. "Digestive Disease Week" eh? Thanks for giving me the shits.

[Report Spam] clicked.

Monday, 8 October 2012

Building a bioinformatics server on a budget in 2012


As more labs get into the "next generation sequencing" game, they are finding themselves unwittingly entering into the "high performance computing" game too. Some lucky labs will be able to access a local or national HPC service, or collaborate with those who do, or pay for access to one like Amazon EC2. But ultimately any bioinformatician will want (and need) a "general server" to experiment, develop, and test on. This is particularly true in terms of large, fast storage which is usually in short supply or costly in HPC environments.


With the small lab in mind, here I outline how, for about A$2500/US$2600/2000), you can build your own server with 6/12 cores, 64GB RAM, and 12TB RAID storage from affordable commodity parts:

  • CPU
    • Intel CORE i7 3930K - LGA 2011 
    • $580
    • The Intel CPUs are about 40% faster for the same clock rate than the equivalent AMD. This is a 3.2 Ghz 6 core CPU (12 threads) and can go to 3.8 Ghz when only using some of the cores. It has good RAM bandwidth too.
  • CPU Cooler
  • Motherboard
    • Gigabyte GA-X79-UP4 Intel Mainboard - LGA 2011 
    • $269
    • This motherboard was chosen as it takes the new LGA2011 CPU, has 8 DIMM slots, and 8 SATA ports, including 6.0Gbsp SATA3 ones which we will want for the SSD boot disk described later. We will save money by using Linux software RAID.
  • RAM
  • Root disk
    • OCZ Agility 3 Series 120GB 2.5" SSD Sata 6Gbs 
    • $170 (2 drives)
    • For the boot/root disk, we will use 120GB SSD instead of mechanical hard disk, for speed. Two disks in RAID1 (mirror) configuration. This would store the operating system, and any important databases eg. BLAST indices, SQL etc.
  • Data disk
    • Seagate Barracuda 3TB 
    • $924 (6 drives)
    • In bioinformatics you can never have enough disk space! Here I suggest using six 3TB 7200rpm drives in RAID6 arrangement for a total of 12TB storage. Reading will be fast, but writing a bit slower. We need to compromise on a budget.
  • Case
    • Antec P280 
    • $135
    • To hold all this stuff, this case is great value. It has good ventilation, which is crucial for keeping all the disks and the CPU cool.
  • Power supply
    • Antec TruePower New Series 650W 
    • $120
    • The case doesn't come with a power supply. I've chosen this one because it has 9 SATA power connectors for the disks, and some unneeded cable sets can be removed in a modular fashion.
  • Operating system
    • Ubuntu Server
    • $0
    • Ubuntu Server edition is pre-tuned for server settings as opposed to interactive desktop use. Because it is Debian based, you have access to far more packaged bioinformatics applications than Centos, including those in the BioLinux project.
  • Miscellaneous
    • Extra 120mm cooling fans (for the hard disk zones)
    • Extra SATA3 cables (ones with locking clips)
    • CPU thermal paste (the grey stuff)
    • PCIe graphics card (for the screen, any old one will do)


For about A$2500/US$2600/2000 and a little bit of Linux know-how, you can build your own "high-end" server. It is missing some of the features of commercial servers from Dell etc (eg. hardware RAID controller, IPMI remote management, hot-swap disks) but it is much more affordable.