EOF - Open Access for Science
The Scientific community, especially in the area of bioinformatics, always has been a strong proponent of open-source technologies. Linux and related technologies, such as the Perl programming language, rapidly are becoming the de facto standards for conducting computational research in the biological sciences. In fact, openness and information sharing are some of the most fundamental tenets of the scientific world. Scientific progress is based on the ideal that information uncovered by one group should benefit the research and development efforts of other groups as well.
Information sharing is promulgated through the publication of scientific research in peer-reviewed journals. However, there is one kink in this system. Most scholarly journals do not pay authors, and many actually impose page charges on scientists who contribute. Journal editorial boards also are typically made up of scientists who serve without pay. Yet, despite the fact that scholarly journals have little or no costs for articles and editorial direction, many of them require the payment of prohibitively expensive subscription fees before researchers from an institution are able to access the research contained inside these journals.
The growth of the open-source revolution within the bioinformatics world is causing a reevaluation of this publishing model, however. Perhaps, in essence, these two campaigns are really striving for the same goal. The open-source software revolution seeks to promote freedom among software users, so they have the freedom to use the software in any way they see fit. Among these freedoms is the ability to examine the source code and study the inner workings of the software in order to learn how it operates. Users then are free to modify this source code and adapt it as they see fit. Users then can make these improvements available to the rest of the world.
Within the Open Source community, this is how software evolves. Someone has an idea and releases a program that makes this idea possible. Others then are able to take this functionality and apply it to new problem sets, perhaps even ones the original author never thought possible. As scientists, we currently are seeking the same kind of freedom for our research results.
The scientific world actually has made some strides in this direction, with several upstart publications, such as the Public Library of Science (PLOS), making all of the articles they publish open access. However, many established publications still insist that they must continue to charge high fees for subscriptions and for on-line access to archives in order to turn a profit.
The momentum of the open access movement is picking up, however, and has led to the development of a promising proposal by the National Institutes of Health (NIH), an organization that funds much of the biomedical research within the United States. According to this new proposal, publishers can keep exclusive subscription-based access to publications that result from NIH-funded research for a period of only six months. After that time, the papers must be made available to the public in an electronic format that has been archived in a scientific literature repository such as Pubmed. If this proposal passes, it will be a major stride toward achieving open access for research articles in the biological sciences. It is expected that many publishers will adapt their ways rather than risk losing large numbers of articles that help their journals sell in the first place.
As Linux and open-source enthusiasts, this issue holds more for us, however, than simply the freedom to access scientific discoveries. It represents a change toward openness in an environment that in many ways was trying to become more closed. We all have witnessed the development of copy restriction methods on audio files, videos, e-books and proprietary software. Industry groups such as the Recording Industry Association of America (RIAA) also seek to add additional restrictions to the way we can utilize our electronic media and software.
This current publication movement is a step in the other direction—a step toward promoting the same types of freedom and openness that we seek when we turn to an open-source solution. The open access issue is not only significant for the scientific advances it may help unleash, but also because it provides the Open Source community with an alternative means to enlighten society about the virtues of freedom and openness. This, in turn, may garner more support for the open-source cause. Thus, in the spirit of freedom and openness, we should rally behind this issue and demand the right to access openly the research that our tax and tuition dollars are supporting.
Christopher M. Frenz is a bioinformaticist with more than five years of experience using Linux. He also is the author of the book Visual Basic and Visual Basic .NET for Scientists and Engineers (Apress) and currently is writing a book about Perl programming.
Practical Task Scheduling Deployment
One of the best things about the UNIX environment (aside from being stable and efficient) is the vast array of software tools available to help you do your job. Traditionally, a UNIX tool does only one thing, but does that one thing very well. For example, grep is very easy to use and can search vast amounts of data quickly. The find tool can find a particular file or files based on all kinds of criteria. It's pretty easy to string these tools together to build even more powerful tools, such as a tool that finds all of the .log files in the /home directory and searches each one for a particular entry. This erector-set mentality allows UNIX system administrators to seem to always have the right tool for the job.
Cron traditionally has been considered another such a tool for job scheduling, but is it enough? This webinar considers that very question. The first part builds on a previous Geek Guide, Beyond Cron, and briefly describes how to know when it might be time to consider upgrading your job scheduling infrastructure. The second part presents an actual planning and implementation framework.
Join Linux Journal's Mike Diehl and Pat Cameron of Help Systems.
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With all the industry talk about the benefits of Linux on Power and all the performance advantages offered by its open architecture, you may be considering a move in that direction. If you are thinking about analytics, big data and cloud computing, you would be right to evaluate Power. The idea of using commodity x86 hardware and replacing it every three years is an outdated cost model. It doesn’t consider the total cost of ownership, and it doesn’t consider the advantage of real processing power, high-availability and multithreading like a demon.
This ebook takes a look at some of the practical applications of the Linux on Power platform and ways you might bring all the performance power of this open architecture to bear for your organization. There are no smoke and mirrors here—just hard, cold, empirical evidence provided by independent sources. I also consider some innovative ways Linux on Power will be used in the future.Get the Guide