Applied Bimatics - An Informatics & eHealth Blog

I am a clinician with a passion for informatics. This blog is about my eHealth journey exploring interoperability in Electronic Medical Records (EMR/EHR), Patient Safety, Pharmacovigilance, Data Analytics, Clinical Research and Bioinformatics in a clinical context. Comparing Canadian, Indian and Middle Eastern healthcare systems and services. Join our open facebook group here: https://www.facebook.com/groups/clinical.bioinformaticians/


Vigyaan CD Part II [NX SERVER]


Running NX server & accessing it from windows machines.

To start NX server, click on KNOPPIX -> Services ->NX server.

The script is supposed to add a new user called nxuser. However this functionality is not working properly in Vigyaan 1.0. Hence you have to use the root account or the default knoppix account. But by default both these accounts do not have passwords. Hence you have to set a password for both these accounts.

Click on the terminal icon on status bar.
su
passwd
<change the password>
Close the terminal window
System ->kduser
Select knoppix
Uncheck Disable account’
Click Set password and set a new password.

Now on your windows machine download and install nx client from NOMACHINE.

Find the local IP of the vigyaan box by typing ifconfig in a terminal window. Now you can access vigyaan box from your windows machine.


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Coiled Coils

Coiled coils consist of two to five amphipathic alpha-helices that twist around one another to form a supercoil which can be left-handed or right-handed. Left handed ones show a seven-residue periodicity and the right handed one a 11 residue periodicity the stability of which is achieved by a knobs-into-holes packing of apolar side chains into a hydrophobic core.

By modulation of their polar interactions, many different properties like extreme thermo stability can be achieved. Coiled coils are involved in signal transduction or molecular recognition. They provide mechanical stability to cells and are involved in movement process. Charged residues are frequently found at coiled coil interfaces.

The building blocks of IF architecture is an elongated coiled coil region (which inturn contains monomeric 1A and dimeric 1B, 2A and 2B sub segments connected by short linkers) flanked by non helical end domains. The dimeric 2B contains a discontinuity in the heptad repeat pattern called a stutter that creates an undecad repeat which is important for its structural integrity. The highly conserved region within the C-terminus of 2B has an inter-helical and intra-helical salt bridge.

There are several software products to predict the coiled coil region of proteins based on the above structural peculiarities.

References:
Peter Burkhard et al. Coiled Coil: a highly versatile protein folding motif. Trends in Cell Biology 2001:11(2); 82-8


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VigyaanCD






Setting Up your own Bioinformatics workstation using VigyaanCD

VigyaanCD at
http://www.vigyaancd.org/
has a nice collection of bioinformatics software and is worth downloading. It will boot directly from the CD and needs very little linux expertise as the X-windows system is almost like windows. However I wanted to use it along with windows and I did not want to reboot every time I switch operating system. This is the story of how I set up VigyaanCD on a second hand PIII and use it from my win XP laptop.

I bought a second hand IBM PIII, 450 MHz, 10MB HDD and 128 MB RAM. I formatted the hard disk and added the following partitions
/boot 2GB (ext2), /knophome 6GB (ext2) /knopswap (vfat) /dos (vfat)
My video card supports only 800x600

I copied the CD image to the boot partition with the knoppix tohd =/dev/hda1 command. I created a persistent home directory in /knophome partition and a swap in /knopswap

I start with the following command.
Knoppix screen=800x600 fromhd home=scan noprompt noeject

I will write about how to set up the NX server and run the NX client from laptop to access it in my next post.



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About Me

As a Dermatologist and Informatician my research mainly involves application of bioinformatics techniques and tools in dermatological conditions. However my research interests are varied and I have publications in areas ranging from artificial intelligence, sequence analysis, systems biology, ontology development, microarray analysis, immunology, computational biology and clinical dermatology. I am also interested in eHealth, Health Informatics and Health Policy.

Address

Bell Raj Eapen
Hamilton, ON
Canada