Document information
DNALinux Virtual Desktop Edition
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- Universidad Nacional de Quilmes
PDF (259 KB)
- Document Type:
- Manuscript
- Date:
- Received 09 August 2007 22:11 UTC; Posted 13 August 2007
- Subjects:
- Biotechnology, Bioinformatics
- Abstract:
The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is that a virtualized environment doesn’t affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning, using, developing and testing bioinformatics applications.
Discussion
- Votes:
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4 votes
- Comments:
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2 comments
It seems you are not understanding the target audience of VDE. This is not a standard Linux distro aimed to Linux users. For some biologists, installing scripting languages or cygwin, is out of the question.
Clustering is not intended to be done under a VM. The main idea behind VDE is for unexperienced users who need to use Linux programs but for several reason they can’t install it in their machine.
Some demonstration and test can run better in a VM since you can install programs, that you can’t do it in a livecd system.
Regarding the program selection, they were picked based on the needs of personnel in my lab and from request for users. Some of them were not included because of license limitations, like Autodock. I would look into your suggested programs.
I already know all distros you mention in your post, since most of them were released after the introduction of the first version of DNALinux (liveCD), and they all have their pro and cons. For example those liveCD don’t allow the user to save their settings and data in such a easy way as VDE (in most of them you have to mount a ext2/3 partition, something not available to many users), the VM allow you to revert changes, so you are free to experiment without messing with the VDE neither with the local machine.
Regarding if this is a rehash of things already done, yes, most software are based on other pieces of software, but the final product (VDE) is new, original and presents some aspects that are useful for novice users. I made VDE based on requests from people I know, or from people that email me asking for this. At least from a final user perspective, it has it uniqueness. I am aware that most features can be replicated by other software, but the idea here was to put up an integrated package with most used bioinformatic software and give a particular experience. - (Login to share with a colleague)
Additional information
- License:
- This document is licensed to the public under the Creative Commons Attribution 2.5 License
- How to cite this document:
-
Bassi, Sebastian and Gonzalez, Virginia. DNALinux Virtual Desktop Edition. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.670.1> (2007)
- Version info:
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Other versions of this document in Nature Precedings
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Other versions of this document elsewhere on the web
None known.
Josiah Zayner on 14 August 2007 15:43 UTC
Interesting idea but lots of those applications either have versions for multiple operating systems or can be run on multiple operating systems simply by installing PERL or python or cygwin, why use them in a VD? Also with bioinformatics, clustering is a big deal, using the VD makes this very unappealing.
It is not always possible to install applications on a computer used for demonstrations making the VD somewhat more hazardous than a Live CD. You fail to include such important programs as GROMACS, VMD, NAMD, AutoDock, which are probably some of the most commonly used non-web-based programs. VLinux is your distribution but even better, including more bioinformatics programs. also check out ROCKS cluster or Scientific Linux. There are also many Live CD linux clustering distributions as ParallelKnoppix, Thinux and openMOSIX, all of these would be far more useful in bioinformatics. Developing and testing is nothing new with VD and can be done with any Linux VD. It seems your idea is just a rehash of things already done. What makes your distribution different?