Max OS-X: Shrink PDF files in the Finder

Today I finally got around to use Automator, and make one of the command line scripts I have been running for ages a little easier to use.

The problem I have been trying to solve is the fact that the PDF files that a Mac creates are normally of very high quality and hence large. If you just want to send someone a document for reading on screen, a much smaller PDF file would do. The open source package “ghostscript” has a tool called ps2pdf that can be (ab)used to adjust the size of components for PDF files. I installed this in /opt/local/bin using the “macports” software.

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Very odd ratio

I was reading some news when I noticed a mathematical curiosity. The article on a physics result mentioned a chance of “one in ten to the minus 7”. Of course this is a mistake: a small chance is either one in ten to the 7” or “ten to the minus 7”. The combination of “one in” and “minus” is nonsense. Interesting enough, this mistake is really common….

#math #oops

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Fight or flight reactions to the cost of computing

Wolf chasing rabbitSome of the computing services at universities become paid services. And the primary reaction in the science groups often is a fight because the realistic costs of operating the existing infrastructure are high. And if the fight does not work, there is a flight towards running decentralized infrastructure. This can look cheaper but maintenance and incident control are rarely accounted for.

We will need good documentation to convince people of the true costs of the alternatives. It is such a waste if the rare time of good bioinformatics experts is spent on inefficient server management.

Photo: CC-BY-SA, Hollingsworth on

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Can a clock with Poisson counting statistics replace your watch?

Thinking about Poisson statistics I was wondering how much use a clock would be that would count the seconds with counting statistics or Poisson statistics. That is: it has the irregularity of radio-active decay. Some people put their watch a few minutes ahead of the true time to make sure that they are never too late, but the problem is that they can start counting on that after a while. A true random clock might be unreliable enough that you would need to always stay carefully ahead….

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Commodies are not free

Computer infrastructure used in universities is not part of a market, let alone of a "transparent market" in which everyone has a clear view on what alternatives exist and what their relative merits and costs are.

Nobody in a university research group finds it strange to pay for pens and paper.

Nobody in a research group finds it strange to pay for state-of-the art lab equipment.

But very often computer services have been offered for free. Like water, and electricity, they have been discounted into general costs of running the university.

This situation is unsustainable in a world in which life-science research becomes driven by big data. And it also becomes unsustainable in a world where large storage and computer infrastructure suitable for routine jobs can be rented commercially.

The sustainable way to the future is to properly budget for data handling and storage. Budgeting for computing needs means people are required to balance cost and value, like with every other aspect of a research project.

Photo: CC-BY-SA-NC on Flickr by John Flinchbaugh

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