Category Archives: Open Access

Learn Physics with Free Space Flight Simulator

The free, Orbiter Space Flight Simulator, is not a typical computer game.

The emphasis is firmly on realism, and the learning curve can be steep. Be prepared to invest some time and effort to brush up on your orbital mechanics background. Good starting points are JPL’s Basics of Space Flight, and R. Braeunig’s Rocket & Space Technology.
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Improved physics: Gravity-gradient torque effects are now implemented. Vessels in low orbit will now experience torques as a result of their mass distribution. Orbiter’s model of angular motion has also been extensively overhauled.

via: Space Simulator Related: So You Want to be a Computer Game Programmer – Physics Concepts in 60 Seconds – PhysicsQuest – Non-Newtonian Fluid Demo

Howard Hughes Medical Institute Takes Big Open Access Step

HHMI Announces New Policy for Publication of Research Articles that will require

its scientists to publish their original research articles in scientific journals that allow the articles and supplementary materials to be made freely accessible in a public repository within six months of publication.

Great news. Some, including me, would prefer a shorter time but this is the limit on the slowest time that will be acceptable not a goal. I don’t know but I wouldn’t be surprised if HHMI is the largest source of research funds outside of the federal government in the USA. This is one more sign the tactics of the old school journals are failing.

HHMI and Public Access Publishing policy

The Howard Hughes Medical Institute has long viewed the sharing of research materials and tools as a fundamental responsibility of scientific authorship. That principle also extends to ensuring that original, peer-reviewed research publications and supplemental materials are freely accessible within six months of publication

Well put; it is amazing how out of touch with the basic concepts of advancing scientific ideas the old style journals are.

Life-patents

New Life, New Patent by Carl Zimmer:

ETC is right in suggesting Venter might become “Microbesoft”–controlling operating system for anyone who wants to build an organism from scratch. Other researchers, such as Keasling, are promoting a different way of doing synthetic biology–what they call open source biology. Scientists and their students are amassing an open inventory of parts that anyone can use to design organisms of their own. And it’s open source biology, these researchers argue, that will provide the best protection against any evil uses of synthetic biology. Instead of being hidden behind patents, the information about these parts would be available to everyone, and collectively solutions could be found. As this debate starts to unfold, I think open source biology will keep it from becoming nothing but deja vu.

I support keeping science open. Patents are a tax on society that the government grants inventors for their efforts, in order to benefit society, by encouraging the inventors to innovate. The end is benefiting society. The means is granting a right of the patent holder (a right they do not have without patent law) that will encourage them to make the effort to innovate. I support the proper use of patents, but we have perverted the patent process into something that harms society. The system needs to be fixed. And the whole area of patents on life I find very questionable.

Researchers Create Molecule-Sized Test Tubes

The test tubes are actually bubble-like nanocontainers that are porous to small molecules. Researchers can easily feed needed ions and other chemicals into the ultra-tiny reaction chambers.

Many scientists say that more can be learned about the dynamics of chemical reactions that power biological processes by studying the behavior of individual molecules rather than observing the collective behavior of many molecules, as scientists do now. But techniques for single-molecule studies are limited and often highly specialized. The new nanocontainers, however, will make single-molecule techniques both more accessible and more powerful
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The researchers say their technique can be easily applied in other laboratories, to enable scientists to study individual molecular reactions free of the complications of analyzing reactions in bulk solution. The new approach also improves on other methods used for observing the behavior of single molecules. One of the most common methods required that single molecules be tethered to a surface. With nanocontainers, however, the vesicles themselves are attached to a surface, meaning the molecules inside do not have to be. This simplifies analysis, because the effects of the surface on the reaction do not have to be taken into account, the researchers said.

To bad I can’t find the article online: I. Cisse, B. Okumus, C. Joo, T. Ha, “Fueling protein-DNA interactions inside porous nanocontainers”, PNAS. The Howard Hughes Medical Institute is doing great things: $600 Million for Basic Biomedical Research – $1 Million Each for 20 Science Educators

Freeware Math Programs

3 awesome free Math programs

Maxima – A general purpose CAS (Computer Algebra System) is a program that’s able to perform symbolic manipulation for the resolution of common problems. As a matter of fact, modern CAS covers an extremely wide range of functionalities
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Scilab – Matlab is the standard for numerical computing, but there are a few clones and valid alternatives that are entirely free. Scilab is the closest that you can get to Matlab without spending a penny. It’s very compatible with Matlab (albeit not 100%) but it’s really flexible, powerful and comes with a Matlab converter and Scicos which is a block diagram modeler and simulator.

R – For statistical computing and analysis in the Open Source world, it doesn’t get any better than R. It is a programming language and environment that enables you to do pretty much anything that the commercial software (S-Plus) does. It is so widely adopted that it can be considered a standard in the field.

lpsolve is another one that I like for linear (integer) programming. LaTeX is also a great tool – a typesetting system; it includes features designed for the production of technical and scientific documentation (many will already be familiar with it but if you are not, check it out).

Open Source Education Curricula

Curriki Global Education and Learning Community

Our mission is to improve education around the world by empowering teachers, students and parents with user-created, open source curricula, and it’s all free! We believe that access to knowledge and learning tools is a basic right of every child. Our goal is to make curricula and learning resources available to everyone.

Another promising looking effort, though they do need to improving the editing of content. They also need to add tools to make it easy to find the content others have found most beneficial. And they should improve the accessibility of the content – all of it should be available using a browser (now some content is presented only as zipped files, some are word documents…). 200 science and 150 math documents are available now including: Big Cats and Intro to Electricity . The site includes content hosted itself and links to content hosted on other sites.

Open Access and PLoS

In An Open Mouse, Carl Zimmer discusses the conflict between closed journals and those that support open access.

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it.

His post mentions the recent bad publicity Wiley received. It seems to me the Journals still don’t understand that their copyright of research results paid for by public funds are not going to continue. And that open access science is clearly the way of the future that their continued failure to deal with is increasing the odds monthly that they will find themselves on the outside of those practicing science in the 21st Century.

PLoS on the other hand recently hired Bora Zivkovic as PLoS ONE Online Community Manager. He will be great and continue to build PLoS into an organization supporting free and open science. I loved PLoS proactive action recounted by Bora, he posted that he was interested in the job:

Next morning, I woke up to a comment by the Managing Editor of PLoS ONE asking if my blog-post should be considered as a formal job application. My comment in response was a Yes.

Finding Open Scientific Papers

Sandra Porter has posted a series of posts on finding scientific papers for free: A day in the life of an English physician – What’s the best way to find free scientific publications? – My new favorite method – one more experiment

via: Finding scientific papers for free

Encyclopedia of Life

Our goal is to create a constantly evolving encyclopedia that lives on the Internet, with contributions from scientists and amateurs alike. To transform the science of biology, and inspire a new generation of scientists, by aggregating all known data about every living species. And ultimately, to increase our collective understanding of life on Earth, and safeguard the richest possible spectrum of biodiversity.

They are using wiki technology to create an encyclopedia of life as discussed by E.O. Wilson in his TED Prize Wish speech. It seems like a great idea to me.

When Fair Use Isn’t Fair

In her post, Antioxidants in Berries Increased by Ethanol (but Are Daiquiris Healthy?), Shelley Batts, commenting on a journal article which was written based on publicly funded research, used “ONE panel of ONE figure, and a chart, from over 10+ figures in the paper.” The for profit journal sent a threat of legal action. This is exactly the type of behavior that leads many (including me) to push for open access publication of publicly funded research.

When Fair Use Isn’t Fair:

Isn’t the point of publishing data to disseminate it, rather that lob threats at grad students who happen to be excited about it?

It should be but many of the for profit publishers seem to have mistaken their mission to promote science (which would then generate funds to sustain their organization) for a mission to make money with no concern for science.

One comment on that post includes a link to the Standford Fair Use Project which looks like a great resource. Also see: Intellectual Property Rights and Innovation