FluxTransgenics: a flexible LIMS-based tool for management of plant transformation experimental data

Lucas Af Hanke,Sérgio Va Campos,Aurea V Folgueras-Flatschart,Cristiano S Botelho,Fernando Af Braz,Roberto W Noda,Paulo Hs Batista,Andrea A Carneiro,Alessandra C Faria-Campos

doi:10.1186/1746-4811-10-20

Abstract

BackgroundThe production and commercial release of Genetically Modified Organisms (GMOs) are currently the focus of important discussions. In order to guarantee the quality and reliability of their trials, companies and institutions working on this subject must adopt new approaches on management, organization and recording of laboratory conditions where field studies are performed. Computational systems for management and storage of laboratory data known as Laboratory Information Management Systems (LIMS) are essential tools to achieve this.ResultsIn this work, we have used the SIGLa system – a workflow based LIMS as a framework to develop the FluxTransgenics system for a GMOs laboratory of Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Maize and Sorghum (Sete Lagoas, MG - Brazil). A workflow representing all stages of the transgenic maize plants generation has been developed and uploaded in FluxTransgenics. This workflow models the activities involved in maize and sorghum transformation using the Agrobacterium tumefaciens method. By uploading this workflow in the SIGLa system we have created Fluxtransgenics, a complete LIMS for managing plant transformation data.ConclusionsFluxTransgenics presents a solution for the management of the data produced by a laboratory of genetically modified plants that is efficient and supports different kinds of information. Its adoption will contribute to guarantee the quality of activities and products in the process of transgenic production and enforce the use of Good Laboratory Practices (GLP).The adoption of the transformation protocol associated to the use of FluxTransgenics has made it possible to increase productivity by at least 300%, increasing the efficiency of the experiments from between 0.5 and 1 percent to about 3%. This has been achieved by an increase in the number of experiments performed and a more accurate choice of parameters, all of which have been made possible because it became easier to identify which were the most promising next steps of the experiments. The FluxTransgenics system is available for use by other laboratories, and the workflows that have been developed can be adapted to other contexts.

Highlights

The production and commercial release of Genetically Modified Organisms (GMOs) are currently the focus of important discussions
Stafford [1] has discussed the need of computational tools designed to manage all laboratory information — including, but not limited to, the data produced by these laboratories — highlighting the relevance of such systems
We propose the construction of workflows to be used in the SIGLa system for data management of a plant transformation facility and modifications in SIGLa to comply with the needs of these complex processes

Summary

Introduction

The production and commercial release of Genetically Modified Organisms (GMOs) are currently the focus of important discussions. Stafford [1] has discussed the need of computational tools designed to manage all laboratory information — including, but not limited to, the data produced by these laboratories — highlighting the relevance of such systems. These applications are referred to as Laboratory Information Management Systems (LIMS) and are characterized by data storage and tracking functionalities, management of the laboratory processes, quality assurance and integration with other systems and equipments. Some examples of these include SQL LIMS [2], LabSoft [3], LabWare [4], FreeLIMS [5] and the systems developed by Hendrick [6], Quo [7], Tharayil [8] and Sanchez [9]

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Conclusion