Going open access and creative commons licensing

The SPIE journals are redefining their copyright and access policies:

As of January 2013, any article for which a voluntary page charge of $100 per published page is paid will be immediately open access. Authors of these articles will retain copyright under a Creative Commons license. This program will expand access to and readership for your articles and fulfill mandates from employers and funders, as well as helping to support JBO.

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Lab reports in (Multi)Markdown

I’ve been using Markdown for a couple of months now and I must say it has grown on me like anything has before. Markdown was conceived by John Gruber to write for the web, but it wasn’t long before someone (Fletcher Penney) thought it could serve as a means to generate PDFs, LaTeX documents, slides, and just about any type of document you can think of, and this is how Multimarkdown was born. Multimarkdown builds on top of markdown to add some features that were missing from markdown so that it could be used to generate documents that could include references, footnotes, and other features more akin to printed documents. Continue reading

Academia can benefit a lot from a more democratic funding system

On a recent post in the Survival blog for scientists an interesting analysis of the research funding system. As a PhD student one tends to get input from one’s advisor so as to continue one’s academic career. And it somehow seems that the bureaucracy, as opposed to the actual research, is a major thing. Some might even argue that attending conferences is more about meeting (the right) people[1], thus improving your chances to get funded, to publish, etc. Is this the right approach? A compromise is what is needed, but how much?[2] Be that as it may, it surely doesn’t seem ethical. So why don’t we just flip the conference.

Much more has been said about the failure of current grant system than that has actually changed. My favorite opinion piece is this one by Peter A. Lawrence. The single-sentence abstract says it all: “The granting system turns young scientists into bureaucrats and then betrays them.” There are a couple of suggestions for improving the funding distribution in that article but the title of a comment by Markus Noll says enough about why nothing is changing: “Scientists in power will never change their system unless forced.”

via Academia can benefit a lof from a more democratic funding system » Survival Blog for Scientists.


  1. Check this post Should editors of Science and Nature socialize with scientists?.  ↩

  2. Working in the Conference Halls, Ronald G. Driggers, Opt. Eng. 50, 110101 (2011), DOI:10.1117/1.3660765  ↩

Writing the PhD thesis: the tools Part I

I’m getting ready to write my PhD thesis, and for some time now I’ve been gathering information on tools that can help me get from here to there. This first post is an attempt to organize this material, to write down my thoughts on the approach I plan to take for tackling the beast. This might not be exactly what I end up doing, so I’ll try to update the post on the changes or difficulties I’ve found along the way, to keep this in a sort of live document. Continue reading

The Poster Conundrum

Say you’re going to a conference to present you’re work at a poster session. First, in what kind of material do you print your poster? Second, do you strictly follow the guidelines or do you have your own template? And third, how do you come about transporting it? One thing is for sure, doing things as they’ve alway been done in your research group is not necessarily the optimal way, and any slight change to this workflow can make the whole poster endeavor end up costing from as little as €20 to the incredible amount of €250 or more. So this is not something to be taken lightly. Continue reading

The scientist’s day-to-day work is about building models not testing hypothesis

I recently came by this topic by reading the post from the Computing Education Blog by Mark Guzdial. It struck me that this actually is true, regardless of what the formality of the scientific method states. I work in this way. Whether you’re writing a research proposal, or a PhD project, you’re suposed to write within the formality of the scientific method, i.e. you have to start your research with a given hypothesis and prove or disprove it, the you draw conclusions. However, the researcher Nancy Nersessian from Georgia Tech found out by investigating how bioengineering scientists think and work, that this hypothesis testing approach is nothing more that a “received view”, what scientists actually do is described in the following

In the real world of scientific investigation, she said, scientists usually rely on a model-based process rather than a hypothesis-driven one. They formulate models based on what they know from previous research and then derive testable hypotheses from those models. Data from experiments don’t validate or invalidate hypotheses as much as they feed back into the models to generate better research questions.

The research is primarily oriented at finding out how scientists really think and work, so as to translate these values to students so they can become successful scientists. This doesn’t seem like a an easy thing to measure, but it could prove useful to redesign curricula that seeks to teach the scientific method in a very orthodox and traditional way, whereas the day-to-day work of scientists is far from this ideal or hypothetical view. The article continues in this line of thought

Based on her findings, Nersessian and her colleagues have developed a series of classes for science and engineering students at Georgia Tech that attempts to instill the skills necessary for a model-based approach to investigation. For example, students tackle the thankfully hypothetical scenario of a zombie invasion on campus and how officials could control and contain it. The first thing they must do, Nersessian said, is develop a model that includes relevant information on disease-spreading patterns, quarantine methods, and campus escape routes. Eventually, the students’ models begin to resemble real quarantine plans based on real-world diseases. By the end of the classes, Nersessian said, students should be “spontaneous, model-based reasoners.”

via Why Science Needs Applied Philosophy – Science Careers Blog.