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crontab

What you need to know: Either use the minute hour day month day-of-week format, or shortcuts like @daily . The script should be placed in /etc/cron with permission to be executable, i.e. 755.

Setting up remote git repository

On your remote machine, create a new directory and start a new git repository. On your local machine, or wherever you have the files, start a git repository, add the files you need, and commit them. Now you have your files under revision control, but only locally, which is bad if your hard drive breaks or if you work from more than one machine. So add the repository on the remote machine as another remote directory and push to it. To get the files on another machine, do

converting files to .ps

You can use Preview -> print -> Save as PostScript to turn a pdf or jpg into ps. Only problem is, that the new image is the size of the paper you printed to, not the original image size. As on the picuture below, there's extra space added at top and bottom of the picture.

The edges of understanding, Arthur D Lander

"A culture’s icons are a window onto its soul. Few would disagree that, in the culture of molecular biology that dominated much of the life sciences for the last third of the 20th century, the dominant icon was the double helix. In the present, post-modern, 'systems biology' era, however, it is, arguably, the hairball ." -- doi:10.1186/1741-7007-8-40

A study of scientific publication ethics

Just went to a great talk about publication ethics. The next time you review a paper, use this easy tool ( eTBLAST ) to check for plagiarism. Just copy and paste the abstract to it. "Identification of duplicate citations in the bio-medical literature The project aims at identified highly similar citations (based on their abstract) to flag potential cases of unethical publications, using a text comparator algorithm named eTBLAST." Right now it only searches medical databases (Medline, Pubmed, NASA, ...) but it will search the arXiv soon!

Can a Systems Biologist Fix a Tamagotchi?

Here 's a great paper that humorously lays out the challenges of reverse engineering. "Another common inspection tool in biology is gene perturbation experiments. As already mentioned, this technique can provide useful information, but it is also used more blindly, e.g., by deleting in turn every single gene in an organism to see what happens. In software engineering, no one has ever seriously proposed to remove each instruction in a program in turn to see what breaks. One might have a slightly better chance of acquiring useful knowledge by removing all pairs or triplets of instructions, but this immediately becomes unfeasible."