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Installing Nvidia Driver on CentOS 6 PDF Print
Written by Sarkis Dallakian   

This post explains how to install NVIDIA proprietary drivers on CentOS 6. By default, CentOS 6 comes with nouveau drivers, which for 3D (OpenGL) rendering, is order of magnitude slower that NVIDIA's proprietary drivers.  For instance, I had glxgear running at round 400 frames per second (FPS) before installing NVIDIA proprietary drivers and at around 1000 FPS after. So it pays to add this extra step to your CentOS 6 installation. Before we start, make sure you have all required packages installed:

yum groupinstall "Development Tools"
yum install kernel-devel kernel-headers dkms

The last package (dkms) is needed so that we don't have to reinstall NVIDIA drivers after each kernel updates. Now we are ready to download NVIDIA proprietary drivers - http://www.nvidia.com/Download/index.aspx

To find out your Video Card model number, click Main Menu → System Settings → Display or run:

lspci | grep VGA

I then run /sbin/init 3 and then chmod +x NVIDIA-Linux-x86-290.10.run followed by ./NVIDIA-Linux-x86-290.10.run. However, this gave me:
"ERROR: The Nouveau kernel driver is currently in use by your system. This driver is incompatible with the NVIDIA driver, and must be disabled before proceeding. Please consult the NVIDIA driver README and your Linux distribution's documentation for details on how to correctly disable the Nouveau kernel driver."

After trying many different options I have found a solution described at http://www.linuxquestions.org/questions/ubuntu-63/nouveau-kernel-driver-825432.

So I added the following line to /etc/modprobe.d/blacklist.conf file

blacklist nouveau

and then did:

$ mv /boot/initramfs-$(uname -r).img /boot/initramfs-$(uname -r).img.bak   
$ dracut -v /boot/initramfs-$(uname -r).img $(uname -r)

Reboot and run ./NVIDIA-Linux-x86-290.10.run to finish installing NVIDIA driver.

Another difference, between CentOS 6 and earlier versions of CentoOS is that system-config-packages (Add/remove applications) is now called gpk-application. You need to run yum install gnome-packagekit if gpk-application is not installed in your system. Also, if you are planning to do OpenGL development run (source: www.centos.org - Forums - CentOS 6 - Software Support - Help me ..):

yum install mesa-libGL-devel mesa-libGLU-devel


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Last Updated on Wednesday, 08 May 2013 20:30
iDEA Conference and NBCR Summer Institute PDF Print
Written by Sarkis Dallakian   

I'm very excited to participate in the iDEA Conference. I was bold enough to submit one of the 30 entries for the iDEA Challenge and was rewarded by having an opportunity to participate in this conference. Illumina is a leader in Next Generation Sequencing (NGS) technology and they have done a brilliant job organizing this event. In case you haven't heard, NGS is rapidly replacing DNA microarrays as a diagnostics (Dx) and scientific tool. In fact, many of the software companies that used to work on DNA microarrays are now working on NGS.

I was interesting to see all academic and commercial entries and I look forward to future iDEA challenges.

Also, I'll be presenting PyRx during 6th National Biomedical Computation Resource (NBCR) Summer Institute on Thursday August 4, 2011 as part of Virtual Screening and Computer Aided Drug Design track. Please visit http://www.nbcr.net/si/2011 to learn more about this event.

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Last Updated on Thursday, 29 September 2011 09:26
ConnectomeViewer and Spatio-Temporal Simulation Environment (STSE) PDF Print
Written by Sarkis Dallakian   

I was looking for a sample code and found Nullege search engine for Python source code to be very useful. There are other search engines that do similar work, such as Google Code Search and Koders.com, however, Nullege seems to be the best one for Python. I have found the following excellent projects that I would like to share. The first one is called ConnectomeViewer and it's an amazing tool for brain research. The second one is called STSE and it provides spatio-temporal simulation environment for biological systems. It's nice to see that they are both using Mayavi for 3D Visualization. Since PyRx is using Mayavi too, this means that our users will be able to transfer their skills seamlessly between these tools. I'm looking forward to seeing other uses of Mayavi and 3D Visualization in life sciences.

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Last Updated on Monday, 14 February 2011 13:43
PyRx 0.8 Release Announcement PDF Print
Written by Sarkis Dallakian   

I'm pleased to announce the release of PyRx 0.8. Here is what's new in this new release:

Version 0.8 - 30 December 2010

[84] Implemented Vina Web Services client and added remote executaition mode for Vina wizard.


[83] Changed web service URI from http://ws.nbcr.net to http://kryptonite.nbcr.net. Opal client distributed with PyRx is compatible with Opal2 services running on this new server.

[80] We now show ScrolledMessageDialog with TraceBack when PyRx fails to start.

[76] Exporting SDF in Analyze Results allows to specify the Number of Poses to Retain. This option is available through Edit -> Preferences. In the case of Vina results, we sort the result using Vina Binding Affinity before saving the result. For AutoDock 4, sorting is done using Binding Energy.


[75] Implemented update feature available through Help -> Check for Updates menu. This enables users to get the latest features and bug fixes more easily. http://pyrx.scripps.edu/images/75_update.png

[74] Made a number of important changes and bug fixes related to flexible residue generation and docking. In particular the names of flexible and rigid parts of a macromolecule now ends with '_flex.pdbqt' and '_rigid.pdbqt', respectively. http://pyrx.scripps.edu/images/flex_rigid_74.png

[71] Users can now save docked structures and binding energies as SDF (Structure Data Format). Thanks to Martin Indarte post in the forum: SDF with binding energies/scores


[69] Switched back to using wx.TextCtrl in Text editors. This widget can now handle large files (> 5MB - tested with wxPython-2.8.11).

[66] Included an option for exhaustiveness in the Vina Wizard thanks to Martin Indarte post in the forum: Can I change the exhaustiveness in VINA wizard?

See also: List of Changes in PyRx Version 0.7

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Last Updated on Monday, 10 January 2011 16:06
Open Discovery and PyRx PDF Print
Written by Sarkis Dallakian   

I'm pleased to announce that PyRx was included in Open Discovery which is an integrated bioinformatics Linux distribution. It's a real pleasure to see PyRx as a new addition to the most comprehensive Bioinformatics Linux distro on the planet.

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Last Updated on Thursday, 29 September 2011 09:28

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