DIYbio is

an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.

DIYbio also has a google group, where a wide range of questions – from bio-patents to DIY gel electrophoresis shopping list and model organisms is dicussed. There is also a DIYbio/biohacking FAQ.

Today for me is the day of discoveries. I learned about the International Open Space Initiative (to give robotics enthusiasts a way to send their tele-controlled and/or intelligent robots to the Moon and Mars), about the DIYbio and biohackers, about OpenManufacturing (which doesn’t seem to have produced enough content to link to), Open Source Medicine (ouch!), BioBrick Assembly Kit (with an assembly manual), OpenWetWare, and a whole bunch of other awesome and inspiring community efforts, which do not belong here.

Do you feel the wind of change?

Stumbled upon SciVee.TV – an open video upload service for research-related videos.

I believe it is highly useful. Compare: watching an 8-10 minute video of someone’s research to reading their article on that same subject. For me, those 8-10 minutes make video option a clear winner.

One of the envisioned uses of SciVee is to upload videos describing peer-reviewed published articles. This has two benefits for the reader: quickly getting acquainted with the essence of the article, and having that article as a complete reference for any questions not discussed in the video. For the author, this gives an additional bonus of higher visibility of his research.

Personally, I’ve immediately found 3 videos pertinent to my topic. Of those, one was accompayning an article in PloS Biology, one was an hour-long lecture, and one was a poor quality audio recording of someone’s intended research.

SciVee is young, and that is currently the largest drawback: not much could be found in a narrow research field. But I’m sure it will grow.

If you ever need to glimpse at the properties of the Poisson distribution with lambda=0.16, or find the factorial of 6163338 (as a gamma function), then Wolfram|Alpha is a perfect tool for you (unless you have some math package at hand).

The motto of Wolfram|Alpha is Making the world’s knowledge computable. Basically, it is like Mathematica plus a growing corpus of factual numeric data, plus a system to interpret user’s input. This is a nice online reference and computation platform.

Recently, I have come across an excellent piece of advice called Ten simple rules for getting published. The only thing I have to add is that final rule #10 should be kept in mind while checking through all the previous rules – e.g. when editing someone’s submission, make sure that you are in position to be the editor for that article, and make sure your decision will influence chief editor’s decision – otherwise there’s no use reviewing.

PLoS Computational Biology, where the “simple rules” were published, has a Ten simple rules collection, which includes a handful of other useful advice articles, like 10 simple rules for selecting a postdoctoral position.

Found here.

Recursively set directories only to drwx-rx-rx (755):

find . -type d -exec chmod 755 {} \;

Recursively set files only to rwx-r-r (644):

find . -type f -exec chmod 644 {} \;

Recursively remove carriage returns (^M) from the end of all *.php files:

find . -type f -name “*.php” -exec /home/user/dos2unix.sh {} \;

In all these cases, {} is replaced with the filename/directory find has found matching your parameters; \; at the end just stops exec processing.

Stimulated by a bug in a complex and unfamiliar web PHP application with heaps of custom tweaks by other programmers, I decided to try a more professional approach to PHP programming and debugging than the standard var_dump() and family.

As a result, I’m now using Eclipse PDT with Xdebug and Xdebug Helper (Firefox extension). Now I don’t understand how I used to debug my PHP programs before!

After proper configuration (I’m using local Apache, but it is also possible to debug remotely), my work flow is rather simple:

• use my web-app as usual, e.g. tweaking and testing here and there
• if something server-side goes wrong: click the XDebug helper icon in Firefox, and perform some server-request action (e.g. load a page)
• debugging is started in Eclipse PDT, where I can step through the code, set breakpoints, and examine all variables
• as soon as the problem is fixed – click the XDebug helper icon again to continue using the site normally (w/o invoking the debugger)

It takes some time to get used to, but then it’s a breeze.

Some advice:

• don’t use apt-get/aptitude to install Eclipse; it will be much easier both in the short and long run to use some all-in-one package from the Eclipse PDT site; all you need to do – download, extract, run!
• before actually starting to do anything, tweak the eclipse.ini file by increasing heap size from 40 MiB (default) to some larger value (I used 128MiB). If you don’t do this, then at some point your debugging will become painfully sloooow, and then you’ll start getting tons of “out of heap memory” errors, each one suggesting that you quit Eclipse immediately
• install XDebug with apt-get/aptitude – worked perfectly, and there’s /etc/php5/conf.d/xdebug.ini not to mess with php.ini
• do read XDebug guide for PDT 2.x (I’m assuming you got the 2.x version); it should be the only document you will really need to configure everything

I only wish Eclipse was faster – that is, written not in Java but e.g. C or C++.

Giovanni Dall’olio has recently posted a presentation on using make.

Although it has “bioinformatics” on the title page, this is a good and very easy to understand make intro.

Original post is here.