- Written by Daniel Cuevas
Recently, I've been faced with a problem where I feel my metagenome comparator program is running too slow. The main reason behind it is that it's performing operations that occur multiple times in a loop. These operations involve different tasks such as: reading lines from text, creating objects, inserting those objects into a data structure, retrieving those objects from the data structure, and writing the data structures to disk (just to name a few). So it would be natural to suggest to someone in my position to parallelize it all, and that's exactly what I want to do. However, I've never written any type of parallel applications, and thus, I need to do a little bit of learning and researching into parallel programming. (More of my ramblings after the Read More break)
- Written by Jeremy Frank
One of my friends from U of I sent me an interesting discussion of a recent paper with a potentially fatal error.....Note the article's editor...hehe. Anyway, the paper talks about a horizontally transferred gene from the human genome to the genome of the intracellular pathogen, Neisseria gonorrhoeae (http://mbio.asm.org/content/2/1/e00005-11.full).
The following blog has an interesting description of a more plausible reason for the published finding:
Reminds me of the story about Shewanella and Burkholderia being the clearly dominating organisms in one of the Sargasso Sea metagenomes...(http://www.nature.com/nrmicro/journal/v3/n6/pdf/nrmicro1158.pdf)
- Written by Robert
- Written by Ramy
An annoying thing that keeps occurring while I'm trying to update phage metadata is that I'm heavily relying on NCBI:Taxonomy. Well, obviously I know I can't blame them since they post a not-so-funny disclaimer at the end of any record
Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.
However, it is really annoying and it reflects everything else in NCBI: so static, unlike everything else on the web in the past 5 years... Now to update the record of each of about 55 phages described as "unclassified" in NCBI, I have to spend anything between 10 - 100 minutes, and I may end up without getting an answer. Just take for example, Gifsy-1 and Gifsy-2, two of the most famous prophages of Salmonella. They are lambdoid phages, i.e. tailed siphoviruses. Yet, their NCBI records say: unclassified!
ICTV doesn't seem to be doing any better with individual viruses (see their latest list).
This is not why I started this post anyway, I'm trying to document the "evidence" behind my taxonomy udpates to the metadata table, because it would be too messy if I include these data in each cell of the Google Doc. However, maybe later we will come up with a 'taxonomy evidence' record as we have an annotation evidence one in the SEED database (called 'Feature evidence').
- Gifsy: from Salmonella: Methods and Protocols @ Google Books
- Enterobacteria phage YYZ-2008: This one is tricky. BLASTN shows that its best matches are Enterobacteria phage 2851 (classified as Podoviridae) and Stx2-converting phage 1717 (classified as Siphoviridae)
- Written by Ramy
I have always taken (and used) for granted the 1031 number of phages in the planet. Normally, this is calculated from the estimation that there are 10 phages per prokaryotic cells, and the latter are estimated to be 1030. Usually the references to these numbers are: Jiang & Paul 1998, PMID 9687430 and Whitman 1998, PMID 9618454
Today I found what might be an older reference: Bergh et al. 1989, PMID 2755508, High abundance of viruses found in aquatic environments
Once I get access to the full-text paper ("thanks to" Nature's unwillingness to open even older articles), I can confirm the exact phage number as claimed in 1989.
If you know of a better (aka older) reference, feel free to share it.
This number (1031), by the way, can be read as: ten nonillions (by the US numbering system)
- Written by Rob Edwards
The Seed Servers are a newer way of accessing the SEED, but at the moment they are limited to the Argonne SEED. Rather than the SOAP based approach which is designed around a single call, the SEED servers are designed around sending larger chunks of data. If you are interested in using the SEED servers I have included a short demo in the read more.
- Written by Rob Edwards
The SDSU Seed (aka Phantome Seed, phage seed) is a complete local seed install. I mainly update the phages on this (because it is the phage seed), but can update microbial genomes if you need. If you want a more up to date site with microbial genomes check out the SEED servers (and my separate blog post about using those).
In the read more I detail how to access the local SEED if you are interested.
- Written by Rob Edwards
RTMg has been available a while, and we have done some pretty cool stuff with it [e.g. web, mobile, open social, and all publicly available metagenomes], but we need to enable others to play with it too. Now everyone can enjoy metagenome annotation in an instant. (Not the flavorless instant coffee type instant, but the rich and bountiful instant gratification type instant!). Don't believe me? Here is a video I made showing how to annotate a metagenome and create a pie chart of the data.
After the read more I'll show you how to do it too.
- Written by Brad Hull
So, I did this maybe a week or two weeks ago, but it was a great victory for science and metagenomics, and I figured I'd post it here. I finally got dropdown menus working in Joomla, guys! Yayyyyyyy. If you go to phantome.org and mouse over the tools menu bar, you'll get the condensed effort of my AWESOME work. Really, all it boils down to was I needed to click a single button.
Building dropdown menus, or "submenus" in Joomla is not terribly advanced. You make an item in whatever menu you're working on, in this case the main menu. But instead of its parent being "Top" you make the parent an already existing item in the menu, in this case "Tools".
However, unless you use my SECRET TRICK, the menu will only ever appear if you're on the "Tools" page already. Which is dumb. People don't want a menu for what they're already looking at. So after a few hours of googling, downloading extensions and modules I didn't need, and then a lot of clicking, I found the answer!
Edit the module for your menu, in my specific case I go to Extensions->Module Manager-> Main Menu in the administrator backend. Then you click the simple little box labeled "Always Show Sub-menu Items", and save your changes. Voila! Success, and awesome. You now have infinite dropdown power. You can have dropdown menus, you can have dropdown menus inside those dropdown menus. Those menus can then shack up and raise little menus of their own. You can have nothing but menus, if you wanted. Infinite menus, dropping down.
Joomla is pretty cool, provided you step into a ring and box with it for like, nine hours.
- Written by Brad Hull
As a few of you probably noticed, pipeline1, also known as seed.sdsu.edu, has been down at least since wednesday or thursday of last week. One of the drives was having "problems", we'll say, that were forcing pipe1 to be unable to boot. The actual boot drive wasn't the issue. The second drive was the issue. It was formatted with an lvm2 filesystem. Also known as "logical partitions". I guess it's one way to get multiple partitions onto one drive. The catch is that it makes it really difficult to fsck it if there's problems. After spending quite a while on it, here's what I've done to get it fixed.
1: Boot off of an ubuntu install disc. It gives me graphical windows, a terminal, and easy root access. Tools used: Applications->Accessories->Terminal
2: I had to install lvdisplay, part of the lvm2 package, to get a look at our logical partitions, but I'll tell you what they are so you don't have to do that. Our two logical partitions are /dev/VolGroup00/LogVol00 and /dev/VolGroup00/LogVol01.
3: Here is the SECRET TRICK. If you try to fsck either of those, it'll give you an error. First it will tell you that no such file exists, and second it will tell you that it tried anyways, and there's a bad super block. The second statement is misleading, concentrate on the first. So what I did was go to /dev/VolGroup00, and take a look at the two partitions. Both of them were symlinks! *gasp*
4: Those links pointed to the REAL partitions. /dev/mapper/VolGroup00-LogVol00 and /dev/mapper/VolGroup00-LogVol01.
5: I ran fsck on the problem volume (volume 00) and lo and behold, success! All the orphaned inodes and corrupt linked lists are finding their parents and...being trimmed? I don't know. Suffice to say fsck is currently running and hopefully pipe1 will be back up soon.