title: Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.
abstract: 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.
authors.affiliation: Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.
authors.forename: Mike
authors.initials: M
authors.lastname: Gavrielides
authors.affiliation: Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Furney
authors.affiliation: Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Yates
authors.affiliation: Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.
authors.forename: Crispin J
authors.initials: CJ
authors.lastname: Miller
authors.affiliation: Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Marais
keywords: Cancer; Database; Grails; LIMS; Oncogenomic data; Sample tracking; Web application