Category Archives: Tools

Validate DNA FASTA file with a javascript function

gitlogoI couldn’t find a quick function that validates a single DNA FASTA file in javascript, so here a setup (it uses the same structure as this protein FASTA validator from the Oxford Protein Informatics Group).

function validateDNA (seq)	{
	//Based on: http://www.blopig.com/blog/2013/03/a-javascript-function-to-validate-fasta-sequences/

	// immediately remove trailing spaces
	seq = seq.trim();

	// split on newlines... 
	var lines = seq.split('\n');

	// check for header
	if (seq[0] == '>') {
		// remove one line, starting at the first position	
		lines.splice(0, 1);
	
	}

	// join the array back into a single string without newlines and 
	// trailing or leading spaces
	seq = lines.join('').trim();
	
	//Search for charaters that are not G, A, T or C.
	if (seq.search(/[^gatc\s]/i) != -1) {	
		//The seq string contains non-DNA characters
		return false;
		/// The next line can be used to return a cleaned version of the DNA
		/// return seq.replace(/[^gatcGATC]/g, "");
	}
	else
	{
		//The seq string contains only GATC
		return true;
	}
	
}

Have fun

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Measuring light intensity with the TSL-235 and a Raspberry Pi

picThere are many ways to measure the light intensity using a Raspberry Pi and one of them (that doesn’t require an ADC) is the TSL-235. It is a photodiode connected to a small circuit that generates a pulse of which the frequency depends on the light intensity. This frequency can be directly read out using a Raspberry Pi as explained below.
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Setting up Syncthing for Raspberry Pi

Nowadays everything is apparently in the cloud. However the cloud comes in many different sizes and shapes. In my case primarily¬†in the form of dropbox. However there are always downsides of “out sourcing” your data to an undefined cloud. Some popular¬†alternatives include BitTorrent Sync (not open source and your data is still touched by a third party), ownCloud (an open source dropbox clone, however the performance on a Raspberry Pi is not very smooth) and since December 2013 Syncthing. The last one is a kind of open source implementation of BitTorrent Sync, so in contrast to Dropbox your data is distributed over your own computers and not at a distant server. In my setup I use a headless Raspberry Pi that is tucked a way in a cupboard as a node in the network, so this client is always online. Continue reading

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Git for Scientists in 2 minutes

gitlogoSince the introduction of Git the world of version control went through a revelation. Currently Github is the biggest player in the field, offering a free place to host and collaborate on your open-source code. However Git is also very useful for a scientist to keep track of in silico experiments and it does not require any sophisticated or complicated tools. In this post a small tutorial on how to set Git up for your experiments. Continue reading

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