Karol Kozak - Articles and news items

Figure 1 openBIS is a software framework for organising and annotating data and metadata from biological experiments, providing query and display functionality, integrating it into data pipelines and sharing it with other researchers

Towards a comprehensive open source platform for management and analysis of High Content Screening data

Issue 4 2010, Screening / 19 August 2010 / Karol Kozak, Angela Bauch, Gabor Csucs,Tomasz Pylak & Bernd Rinn, ETH Zurich

As High Content Screening (HCS) has moved into the mainstream for biological and pharmaceutical investigations, a lag of well integrated pipelines for automated acquisition, management and analysis of HCS results turns out to be a bottleneck for fully leveraging the wealth of information contained in a screen and moving to higher throughput. For many applications, monolithic pipelines cannot deliver the flexibility and versatility needed. Laboratories and scientific service providers instead usually look into integrating components from both the open source world and the commercial software world into best-of-breed data pipelines. In this article, we will present two open source components that can be used as flexible and powerful building blocks for such a pipeline.

The handling and analysis of large scale high content screening data

Issue 3 2007 / 23 May 2007 / Karol Kozak and Benjamin Eshun, Data Handling in TDS, Max Planck Institute of MolecularCell Biology and Genetics, Germany. Jeff Oegema, CEO, Scionics Computer Innovation, GmbH

Data management has become one of the central issues in High Content Screening (HCS) as it has high potential within predictive toxicity assessments. In particular, HCS applying automated microscopy requires a technology and system which is capable of storing and analying vast amounts of image and numeric data. HCS data includes comprehensive information about the bioactive molecules, the targeted genes and images, as well as their extracted data matrices after acquisition. Here we describe a bioinformatics solution HCS LIMS (Laboratory Information Management System) for the management of data from different screening microscopes. Additionally, the data handling approaches used in HCS for image converting, compression and archiving of images are discussed.


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