Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments

Source Code for Biology and Medicine

Richard Marais¹  Crispin J Miller²  Tim Yates²  Simon J Furney¹  Mike Gavrielides¹ 

[1] Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK;Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK

关键词: Database;    Web application;    Grails;    Cancer;    Oncogenomic data;    LIMS;    Sample tracking;   

Others  :  1139279
DOI  :  10.1186/s13029-014-0025-z

 received in 2013-10-23, accepted in 2014-11-12,  发布年份 2014

【 摘 要 】

Background

Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centres, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments.

Results

The current work presents a sample tracking system for oncogenomic studies (Onco-STS) to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database. The web application development programming framework Grails was used for the development and implementation of the system.

Conclusions

The resulting Onco-STS solution is efficient, secure and easy to use and is intended to replace the manual data handling of text records. Onco-STS allows simultaneous remote access to the system making collaboration among researchers more effective. The system stores both information on the samples in oncogenomic studies and details of the analyses conducted on the resulting data. Onco-STS is based on open-source software, is easy to develop and can be modified according to a research group’s needs. Hence it is suitable for laboratories that do not require a commercial system.

【 授权许可】

   
2014 Gavrielides et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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