Abstract
BackgroundIn modern life science research it is very important to have an efficient management of high throughput primary lab data. To realise such an efficient management, four main aspects have to be handled: (I) long term storage, (II) security, (III) upload and (IV) retrieval.FindingsIn this paper we define central requirements for a primary lab data management and discuss aspects of best practices to realise these requirements. As a proof of concept, we introduce a pipeline that has been implemented in order to manage primary lab data at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). It comprises: (I) a data storage implementation including a Hierarchical Storage Management system, a relational Oracle Database Management System and a BFiler package to store primary lab data and their meta information, (II) the Virtual Private Database (VPD) implementation for the realisation of data security and the LIMS Light application to (III) upload and (IV) retrieve stored primary lab data.ConclusionsWith the LIMS Light system we have developed a primary data management system which provides an efficient storage system with a Hierarchical Storage Management System and an Oracle relational database. With our VPD Access Control Method we can guarantee the security of the stored primary data. Furthermore the system provides high performance upload and download and efficient retrieval of data.
Highlights
In modern life science research it is very important to have an efficient management of high throughput primary lab data
With our Virtual Private Database (VPD) Access Control Method we can guarantee the security of the stored primary data
The upload itself is performed by a Java web start application called Laboratory Information Management Systems (LIMS) Light Uploader
Summary
In modern life science research it is very important to have an efficient management of high throughput primary lab data. To realise such an efficient management, four main aspects have to be handled: (I) long term storage, (II) security, (III) upload and (IV) retrieval. The process of gaining knowledge is tightly coupled with the data producer, bioinformatics tools, the structured data storage and long term archiving. In this context, Laboratory Information Management Systems (LIMS) are getting an increased focus in life sciences. An important basis of all laboratory processes is the primary data. The data must be available for all kinds of subsequent analysis and result interpretation (see Figure 1)
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