Djeen (Database for Joomla!’s Extensible Engine): a research information management system for flexible multi-technology project administration

BackgroundWith the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today.FindingsWe developed Djeen (Database for Joomla!’s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance.ConclusionDjeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group.Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material.

[1]  David DiGiusto,et al.  Implementation of a configurable laboratory information management system for use in cellular process development and manufacturing. , 2012, Cytotherapy.

[2]  Avraham Leff,et al.  Web-application development using the Model/View/Controller design pattern , 2001, Proceedings Fifth IEEE International Enterprise Distributed Object Computing Conference.

[3]  Chris F. Taylor,et al.  Guidelines for reporting the use of mass spectrometry informatics in proteomics , 2008, Nature Biotechnology.

[4]  Sean D. Mooney,et al.  Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group , 2007, Briefings Bioinform..

[5]  Christian J. Stoeckert,et al.  Characterization of Unknown Adult Stem Cell Samples by Large Scale Data Integration and Artificial Neural Networks , 2009, Pacific Symposium on Biocomputing.

[6]  David Tai,et al.  K-Screen: a free application for high throughput screening data analysis, visualization, and laboratory information management. , 2011, Combinatorial chemistry & high throughput screening.

[7]  Sahiti Myneni,et al.  Organization of biomedical data for collaborative scientific research: A research information management system , 2010, Int. J. Inf. Manag..

[8]  Shannon McWeeney,et al.  MIFlowCyt: The minimum information about a flow cytometry experiment , 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[9]  Alexandre Melo,et al.  SIGLa: an adaptable LIMS for multiple laboratories , 2010, BMC Genomics.

[10]  Jari Häkkinen,et al.  BASE - 2nd generation software for microarray data management and analysis , 2009, BMC Bioinformatics.

[11]  Gianluca Bontempi,et al.  Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes , 2008, Clinical Cancer Research.

[12]  Feng Cheng,et al.  MADMAX - Management and analysis database for multiple ~omics experiments , 2011, J. Integr. Bioinform..

[13]  Patrick J. Killion,et al.  Microarray data visualization and analysis with the Longhorn Array Database (LAD). , 2004, Current protocols in bioinformatics.

[14]  Lennart Martens,et al.  ms_lims, a simple yet powerful open source laboratory information management system for MS‐driven proteomics , 2010, Proteomics.

[15]  Daniel J. Crowther,et al.  LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine , 2010, Source Code for Biology and Medicine.

[16]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.