Monthly Archives: June 2014

fig-k11

New Publication: State-Dependent Network Connectivity Determines Gating in a K+ Channel

publication, research

In we showed that the closed state of Kir1.1, a important potassium ion channel found in the kidneys, was stabilised by a single hydrogen bond. builds on that work by looking for any interactions that stabilise either the open or closed state of the channel by systematically mutating the majority of the residues to alanine. We were surprised to find that 47 mutations destabilised the open state but only 2 destabilised the closed state, one of which was the one we’d found before. Modelling suggests that this is because open conformations of the channel are more optimised and compact hence mutations tend to be more disruptive. The work was partly funded by the Wellcome Trust and hence is free to download.

fig-k11-2

2014-06-25 at 15-38-27

Getting an ext3 Drobo 5D to play nicely with Ubuntu 12.04

geek

Our lab has recently bought two to give us some large storage. They work out of the box with Macs but getting them to play nicely with Linux, specifically Ubuntu 12.04, has been a bit more work so I thought I’d share the recipe that, for us at least, appears to work. Much of this has been cobbled together from the page and also from a very helpful earlier . One thing I could not get to work, unfortunately, is USB3. There appeared to be problems with USB3 and Linux when I was trying this out. Finally I should mention that the Drobo here was setup on a Mac, so was formatted HFS+ to begin with and, of course, follow these commands at your own risk. They worked for me, but they might not work for you..

 

First plug the Drobo into the power and connect with the USB lead to your Ubuntu machine. Don’t use any blue USB ports – these are USB3 and I couldn’t get them to work with the Drobo. After a while the Drobo should appear as a USB disk drive in a window. You can check what Ubuntu is doing by looking at this log

$ dmesg | tail

It will show something like

[250886.772714] usb 1-1.1: new high-speed USB device number 10 using ehci_hcd
[250887.331458] scsi19 : usb-storage 1-1.1:1.0
[250888.328628] scsi 19:0:0:0: Direct-Access Drobo 5D 5.00 PQ: 0 ANSI: 0
[250888.329605] sd 19:0:0:0: Attached scsi generic sg3 type 0
[250888.330168] sd 19:0:0:0: [sdb] Very big device. Trying to use READ CAPACITY(16).

First we need to intall the latest version of the linux Drobo tools, so we will probably need git and let’s get QT as well so we can check the GUI.

$ sudo apt-get install git
$ sudo apt-get install python-qt4

Now cd to somewhere where you put packages etc and run

$ git clone git://drobo-utils.git.sourceforge.net/gitroot/drobo-utils/drobo-utils

This will download all the files and binaries you need

$ cd drobo-utils/

Just check it is all up to date

$ git pull

Check it is all working by seeing if this works (warning: this can take about a minute)

$ sudo ./drobom status

In theory, we can bring up the GUI as below, but on my machine I just got python errors about KeyError: 'UseStaticIPAddress'. Check it if you want.

$ sudo ./drobom view

Next we need to know which device the Drobo is currently plugged into. This will probably change everytime you plug the Drobo in.

$ ls -lrt /dev/disk/by-uuid/

There should be a long alphanumeric list that I will call foo that is pointing to something like /dev/sdb. The foo should match the foo when I type

$ ls /media/

If so, then we know that the Drobo is connected to /dev/sdb. Next we need to set the Logical Unit Size (LUNS). This is the largest volume the Drobo will appear as, and if we run a df it will show this as the physical size of the Drobo even if there are not enough disks inside to make it this size. Since the Drobo 5D has five slots and we are using 4TB disks at present, then if we run with single disk redundancy the maximum size is 16 TB. You could make this smaller but then you would have multiple “drobo partitions�? mounted all pointing to the same machine. The disadvantage with a large LUNS is it means the startup time is long, as is any disk checking time. The units in the line below are TB! Caution these commands can take a while to run and I’ve not pasted in the usual “are you sure?�? prompts.

$ sudo ./drobom set lunsize 16 PleaseEraseMyData

Now we need to setup a partition for the disk using parted which should be already installed. This has its own command line. Although we are setting up an ext3 disk, it seems ext3 is just ext2 with journalling, so we ask parted for an ext2 disk.

$ sudo parted /dev/sdb
GNU Parted 1.8.9
Using /dev/sdd
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) mklabel
New disk label type? gpt
(parted) mkpart ext2 0 100%
(parted) quit
Information: You may need to update /etc/fstab.

Now we need to format the disk. Again remember to use the right device. Also note it is sdb1 since we are formatting the first and only partition, not the disk itself. Also note again we are formatting as ext2 but with the -j flag for journalling, hence ext3. Again, this will ask whether you are sure etc and could take a few hours.

$ sudo mke2fs -j -i 262144 -L Drobo -m 0 -O sparse_super,^resize_inode /dev/sdb1

Nearly there. If you remount the Drobo it should appear in /Media/Drobo (or whatever name you gave it above) Now we need to make sure you have permissions to write to the disk. For this we need to know your user and group numeric ids.

$ id
uid=9009(fowler) gid=100 groups=100

So my user id is 9009 and my group id is 100. Hence

$ sudo chown -R 9009:100 /media/Drobo/

If we want to mount the Drobo somewhere else, we need to edit /etc/fstab. First we need to know the UUID of the disk (this was the foo).

$ ls -lrt /dev/disk/by-uuid/

Copy the foo into the clipboard and open

$ sudo emacs /etc/fstab

Add a line at the end that looks like

# mount the ext3 Drobo
UUID=b278aff6-db1a-436b-995b-8808c2c82f9e /drobo1 ext3 defaults 0 2

make sure the mount point exists!

$ sudo mkdir /drobo1

Now remount the disk, either by rebooting or by issuing

$ sudo mount -a

and voila, you should find the disk by

$ ls /drobo1/

Check you can make a file

$ touch /drobo1/hello-world.txt

Check it appears in your list of disks using df etc. I’ve checked you can be a bit rough with it e.g. just pulling out the USB cable and then reconnecting to a different port. Seemed ok but I did need to remount it using

$ sudo mount -a

and then I could add and edit files as normal and there was no complaining in dmesg about write-only filesystems or anything like before with HFS+.

fig-bilayer-05-highres-layer-1-coords2-f000001

New Publication: NRas slows the rate at which a model lipid bilayer phase separates

publication

 

Here we examine by computer simulation what effect adding a small cell-signalling protein does to a model ternary lipid mixture that has been shown before to phase separate. was presented at the in Nottingham in May 2014, the theme of which was Molecular simulations and visualization. We followed the progress of the phase separation of the lipid bilayer by measuring the length of the interface using an edge detection algorithm from image processing. An example python script can be downloaded .

post

We found that the protein, NRas, indeed slows down the rate at which the bilayer phase separates. The protein also tends to localise to the interface between the domains which is consistent with it acting to reduce the line tension between the phases.

The questions asked during the discussion (and my answers) will be posted on the journal’s website soon. I’ll update this post when that happens. This paper is open access so is free to download.