CASyM winter school of Systems Medicine took place between March 29th and April 1st 2017 in Ljubljana, Slovenia and is entitled »The 3rd SysBioMed hands-on tutorial: Systems Medicine Approaches in Personalized Medicine«
1Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia,2Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia,3Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
Introduction Suicide is one of the most common causes of death in the world. Slovenia, with approximately 500 suicide victims every year, ranks among the European countries with the highest suicide rates. Suicide is a very complex phenomenon, resulting from an interplay of wide spectrum of environmental and genetic factors. Genetic studies of suicide are very important as they help to identify the factors that contribute to suicidal behaviour and thus to find potential treatments. Suicidal behaviour is one of the research fields in the laboratory of the Institute of Biochemistry in Ljubljana. We collect human samples, such as blood, cerebrospinal fluid, liquor and brain tissue samples every week. Further DNA or RNA extraction and other kinds of sample treatment make the amount of data even larger. Standard ways of saving data (notebooks, Excel tables) are not efficient enough as they cannot provide orderliness, sufficient traceability and user-friendliness, which can cause loss of information. Therefore, the rapid advancement of information technology could offer new approaches that would enable easier and more efficient storage of data. Results We present a design and implementation of the information system which could be used for several purposes. It enables the storage of detailed information about collected and/or analysed samples, managing and editing the data, searching for suitable samples for an experiment, as well as statistical analyses and comparison between the samples. Furthermore, to achieve successful laboratory work, researchers need to keep a record of stored original samples, extracted DNA and RNA samples, as well as results of analyses they perform (such as analyses of gene expression – qPCR, DNA methylation). For this reason, the information system supports data import and export in CSV format, which also makes it compatible with the majority of commercial software products for data management and analysis. It was designed with open-source tools and platforms. It is easy to use and maintain and meets all users’ demands. Conclusion The storage of laboratory samples data can be a demanding task as a great amount of information needs to be stored in a systematic and reliable way. For this reason, we established a database, which enables efficient and organized storage of information about human samples obtained from suicide victims. A great advantage of the database in this form is its accessibility to a targeted group of authorised researchers. We believe that the system will contribute to better organized and more successful laboratory work also in other medical related research fields. Acknowledgements This work was co-financed by the Republic of Slovenia and the European Union under the European Social Fund (project ID 25-13-3), by Slovenian Research Agency grants P1-0390, P2-0359, J3-7132 and the infrastructure grant ELIXIR.
2006 - University of Ljubljana, Faculty of Medicine, Center for Functional Genomics and Bio-chips.