Problem:

You want to play some sounds in a webbrowser.

Solution:

Modern Browsers have a fancy integrated AudioContext that allows you to play sounds. Here is an example (JavaScript Code):

// get the AudioContext
window.AudioContext = window.AudioContext || window.webkitAudioContext;

// Initialize audio context
var context = new AudioContext();

// Create an oscillator ... via this oscillator we can then play different sounds
var oscillator = context.createOscillator();
oscillator.frequency.value = 440; // this is an "A"
oscillator.type = "square";

// attach the oscillator to the sound output
oscillator.connect(context.destination);

oscillator.start(0); // start the oscillator (0=now) ...
oscillator.stop(1);  // stop playing this sound after 1 second

Problem:

You want to display a Graph.

Solution:

Create a simple text file describing your graph and save it with a .dot file extension:

graph {
node1 -- node2;
node2 -- node3;
node3 -- node4;
node4 -- node1;
}

Afterwards you can use a program of the graphviz package (sudo apt-get install graphviz) in order to visualize the graph. This package contains different layouting programs like dot, neato, fdp (all from the GraphViz project) etc. Simply call one of these programs in order to visualize the graph:

neato -Tsvg yourFile.dot -o outputFile.svg

Output from this command:

Recently I’ve encountered a strange issue with the Broken Link Checker plugin for WordPress:

While all HTTP URLs work just fine, every single HTTPS URL yields an Unknown error without any log message or explanation. Continue reading →

Problem:

You want to write a thunderbird plugin function that runs/calls an external program and returns stdio.

Continue reading →

Problem:

When using Ruby 2.0/2.1 with the vpim gem (tested with version 0.695), you get an error message similar to this:

/usr/local/rvm/gems/ruby-2.1.0/gems/activesupport-3.2.13/lib/active_support/dependencies.rb:251:in `require': /usr/local/rvm/gems/ruby-2.1.0/gems/vpim-0.695/lib/vpim/vcard.rb:678: invalid multibyte escape: /^\xFE\xFF/ (SyntaxError)

Continue reading →

In a recent project, I needed to compare STRING records to other PPI databases. However, this is not always as easy as it sounds, because STRING uses KEGG protein identifiers. Fortunately, at the STRING download page, a list of alias mappings is freely downloadable.

There’s still one major problem left, though: I couldn’t find any documentation about the format. It seems to be somewhat easy once you’ve figured out the basics, but I created a reusable Python function that filters a given organism and outputs a STRING ID, UniProt ID CSV:

Continue reading →

Recently I needed to filter a STRING protein-view database dump (e.g. protein.links.full.v9.05.txt.gz) by taxonomy ID. The original dataset was way too large (it had more than 670 million records).

In order to filter with constant memory (After all, the full STRING dump is 47GB large), I created this script that allows to filter for binary PPIs both matching the given organism (NCBI taxonomy ID), but also allows to filter for binary PPIs with at least one interacting protein of the given organism. Usually this doesn’t really make a difference for STRING.

Continue reading →

There’re many problems nowadays, which could easier be solved through the internet. In this post I descripe how to address these problems by bash alone.

The standard way to connect to a server in the internet, is to embed the connection stream

exec 3<>/dev/tcp/$server/$ircPort || echo "Some text or doing, if connecting failed"

Continue reading →

Problem:

You’re using the KDE4 Konsole and you want to install the Solarized color scheme plugin. However, you are way too lazy to figure out how to do that manually.

Continue reading →

Recently we had to work with the gtf2gff.pl tool to convert CONTRAST and TwinScan GTF output to the GFF format which can be read by many annotation tools.

Working with that script was really hard, it did not report errors at all, plus it is not programmatically reusable at all. There are different versions of the perl script on the internet, but what we needed was a standardized, short, readable version that does proper command line parsing using a standard tool like argparse and a conversion function that is usable from other scripts.

Continue reading →

Problem:

You have a Java FXML file document with a TableView and want to set the columnResizePolicy of this TableView in the fxml document.

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Problem:

You want to use stat() from sys/stat.h POSIX header to check if a file with a given name exists.

Continue reading →

Problem:

You intend to install LevelDB, but you don’t want to manually install & compile it as described here.

Instead, you just want to use the debian packaging system and some reproducible method of creating a DEB package from LevelDB.

Reasons for preferring not to compile & install manually could be:

• You want to deploy LevelDB to one ore more environments that don’t have a complete build environment
• You prefer a clean install-uninstall-purge package lifetime management
• You need a reproducible process to deploy LevelDB

Continue reading →

You can list all codecs supported by libavconv (the library used by ffmpeg / avconv) by using this command:

ffmpeg -codecs

avconv -codecs

Problem:

Why trying to access your Android device using ADB, you encounter the following error:

error: insufficient permissions for device

Problem:

You want to use printf to print something to the stderr stream (instead of stdout)

Continue reading →

Problem:

You want to use the pmi tool from the powermanagement-interface package, e.g. to standby your Linux computer using the command line, but you get an error message like this:

Error org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.Hal was not provided by any .service files

Problem:

You own a Toshiba Notebook and want to set LCD backlight brightness using the commandline.

Continue reading →

Problem:

You want to get the IPv4 and/or IPv6 addresses of the local computer’s network interfaces using NodeJS in an OS-independent manner.

Continue reading →