Software platform virtualization in chemistry research and university teaching

Abstract

Background: Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories.

Results: Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs.

Conclusion: Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.

Figure 1

Number of scientific papers and citations about virtualization and virtual machines. Source ISI Web of Science January 2009.

Figure 2

The virtual machine software installed on a host operating system allows the use of different operating systems on a single computer system. A Macintosh system could run native Windows or LINUX software or even multiple instances of the same operating system. All virtual machines can communicate with each other and are allowed to use all hardware computer resources such as graphic cards, DVD drives and USB ports. (Logo sources: Wikipedia, TUX mascot: Larry Ewing).

Figure 3

A Windows Vista host using Sun's VirtualBox runs three UBUNTU Linuxes, one WIN XP, one Windows VISTA and one Windows Server guest operating system simultaneously. The hardware is an Intel Nehalem Core i7 950 quad core CPU (3 GHz) with 12 GByte RAM and 4 hard disks in RAID10. The system virtualizes a total number of 41 CPUs.

Figure 4

Server consolidation: A single powerful computer runs multiple virtual machines and serves as compute server, backup server and web server. Such a setup improves maintenance efficiency and reduces hardware costs. The right picture shows a production server with a XEN Virtual Machine Monitor and 17 independent running systems (Actual VM names were replaced; Picture source: Zhi-Wei Lu; UC Davis Genome Center Bioinformatics Core).

Figure 5

The Windows Vista Ultimate host with Sun's VirtualBox virtualizes an Ubuntu Linux system with 32 CPU threads (left side) and a Windows Server system with 10 CPU threads (right side). The guest hardware is a quad core Nehalem Core i7 950 CPU with only 8 threads. Both guest systems work without problem, but fully exhaust all underlying hardware resources when all parallel threads are in use.

Figure 6

Hands-on labs: Virtual machines are used for teaching cheminformatics and mass spectrometry software classes. The hands-on class provides everybody with the same software and setups hence avoids installation and settings problems. All required software is installed and tested on a single virtual machine and this software image is later deployed to all computers in the class room. Right picture: Screenshot of the teaching VM with WIN XP and the AMDIS and MarvinView software running.

Figure 7

Popularity of cheminformatics vs. bioinformatics based on site specific Google hit counts across 325 universities (US) with research chemistry faculty. For all 325 universities a site specific search on Google was performed and mapped on the graph, i.e. cheminformatics site:berkeley.edu returned 93 hits and bioinformatics site:berkeley.edu returned 3620 hits. Because UC Berkeley hosts more bioinformatics related material it is safe to assume that bioinformatics is more popular than cheminformatics at UC Berkeley. Around 100 universities had no occurrence of the words cheminformatics or chemoinformatics on their global university websites (scores combined); Search date: August 2009.