Array Re-shuffling in Perl

This dependency-free array randomiser will return a re-shuffled array or a slice of random $iL array elements.

Directories and File Structure

The Progenetix Jekyll template modifies the standard Jekyll file structure.

Format of the YAML Header

The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.

Genome editions and liftover

Since the first release in 2000, the human reference genome is continuously being worked on. While the most recent major release (GRCh38) dates back to 2013, minor releases (GRCh38.pX) are issued more frequently and can be downloaded from the official NCBI Genome Reference Consortium website.

Local Jekyll based website generation

In an ideal scenario, your Github served website could be build locally, with the same output structure and layout.

Keras with GPU on Mac using PlaidML

Since Apple and nVidia broke up harshly a few years ago, the official support of all nVidia GPUs were stopped. Shortly after, all deep learning frameworks stopped their support of GPU acceleration on Mac. Now, there is finally a simple and productive solution: using Keras with PlaidML.

PlaidML provides backends for Keras without requiring CUDA and nVidia hardware. It event supports Metal on Mac to provide a great improvement of performance. Now we can utilize our AMD GPU on Mac to drive Keras!

MongoDB Cheat Sheet

Setting up a standard installation of MongoDB on OS X

Ontology Term Contributions

Progenetix data as custom tracks to UCSC genome browser

Displaying copy number data in UCSC genome browser

To visualize genomic segments based data data (e.g. CNV calls), there are two kinds of plots we can produce in the UCSC genome browser.

Simple Map Plotting Utility

This utility allows the plotting of Google maps with included proportional markers, based on a file accessible through an URL (e.g. a Dropbox share link).

Some Regular Expressions and more…

This page contains some regular expressions which have come in handy during our work. Code is in Perl style syntax.

pgxdb_biosamples_extract_biocharacteristics_mappings.pl Perl Code Documentation

pgxdb_generate_collections.pl Perl Code Documentation

pgxdb_get_geo_metadata.pl Perl Code Documentation