Sample Information Management System (SIMS)
- Submission and retrieval of information about patients and biomedical samples
- Easy to customize for various needs of biomedical projects
- Secures patient confidentiality by separating de-identified information from private record
- Web-based with role-defined user access rights
- Successful in a large international collaborative projects: MolPAGE, ENGAGE
- To see SIMS demo versions and test them click SIMS_T2D for Types 2 Diabetes configuration, SIMS_MS for Metabolic Syndrome configuration or SIMS_AD for Autoimmune Disease configuration, to login use read-only account test/test
Overview of SIMS
SIMS is a web based system that allows researchers to track information related to sample collection, processing, location, transportation and storage conditions etc. The system can be easilly used either for Data submission – entering and editing the information on samples and individuals, or Data access – browsing and querying this information, and generating reports. The organization of data within SIMS is based on three main categories: First level (Persons), Second level (Samples) and Third level (Aliquots), where an arbitrary number of second level records (samples) can be associated with each record from the first level (person) and an arbitrary number of third level records (aliquots) can be associated with each the second level record (sample). It is possible to configure SIMS with other categories' titles and meta-data (for example, Persons, Vists and Samples or Persons, Characteristics and Samples).
The data about persons contained in SIMS is anonymous - to provide this it is designed to be used together with additional software component PMT installed locally (however, the use of PMT is not mandatory).
SIMS has been specifically developed for processing of data related with metabolic diseases, however the submission form is sufficiently concise and many of the parameters can be reused in a vast spectrum of studies. Many features of the SIMS are configurable, and its adaption for other types of person data and samples is likely to be easy.
Technically SIMS is implemented as a relational database (currently PostgreSQL is used for development, but system has also been tested on Oracle, MySQL and H2), which is accessible online through a web-based interface (using the Java Server Pages technology and the Apache Tomcat servlet container).
Person Management Tool (PMT) is intended for registering confidential information about the research subjects from whom samples have been taken. The system assigns a unique anonymous identifier to each individual, which is then used for the individual identification in SIMS. A separate PMT instance should be hosted at each site participating in sample collection. PMT is availabe only as a standalone Windows application. The use of PMT is optional and SIMS can be configured either to accept PMT generated patient identifiers, to accept any identifiers, or to generate identifiers automatically.
Assay Information Management System (AIMS)
- A web-based customizable system for experiment data entry and management
- Web-entry forms for collecting metadata from 7 high-throughput experimental platforms
- Effective for bringing the experiment data and metadata in compliance with the “Minimum information about…” requirements
- Functionality extends to batch submission, batch editing and filtering
- Interlinked with third level data of SIMS (for example aliquots) by a common system of identifiers
- Proved to be successful in the large international collaborative project
- Light-weight LIMS-like solution for projects in systems biology and translational medicine
- To see AIMS demo version and test it click here , to login use read-only account test/test
Overview of AIMS
AIMS is a web based system that serves as the central repository for experimental data produced by different experimental technologies (genomic, transcriptomic, proteomic, metabolomic data etc). The basic structure of AIMS resemples that of SIMS, with data organized around three main categories: Studies, Experiments and Assays. However the system is designed to be extremely flexible reagrding its configuration, since it is intended for one instance of AIMS system to be used for data obtained by several different technologies. AIMS could be used either in conjunction with SIMS (there is a promting option for referenced records at the third level of SIMS) or separately.
The basic design principles and software environment of AIMS are similar to those of the SIMS: AIMS is implemented as a relational database (currently PostgreSQL is used for development, but system has also been tested on Oracle, MySQL and H2), which is accessible online through a web-based interface (using the Java Server Pages technology and the Apache Tomcat servlet container).
Data model
Experimental parameters are assigned to Assays and to groups of assays – Experiments. In turn, different Experiments can be group together into Studies that represents summary for a group of experiments. The “Assay” term represents a measurement performed on a given aliquot (e.g. a single hybridization in microarray technology). Aliquots or samples captured within the Sample Information Management System (SIMS) can be used for creation of new assay entries. The content of a particular Assay, Experiment and Study is technology-specific and depends on the metadata parameters for this technology. Each Assay belongs to a Experiment - a number of acquisitions which according to the investigator should be stored and analyzed together due to the underlying experiment design. Experiments can be grouped into Studies.
A number of data files and supplimentary files can be assign with each level: Studies, Experiments and Assays.
A vast choice of options for the metadata submission and editing ensures that the time needed for the formatting and uploading the results and metadata is kept to a minimum. AIMS does not only provide the means for data collection but also facilitates some simple searches and report generation.
SIMS and AIMS central objects are shown in the Figure .
Sample avAILability system (SAIL)
Overview
Biomedical studies are growing rapidly in both size and complexity. In the search for genetic or environmental factors that affect our health, very large numbers of patient samples and data generated from assays on these are being collected and stored in biobanks and other repositories holding data or biomaterial. Collection sizes are approaching millions of samples from a variety of cohorts and studies, with thousands of phenotypes or other types of sample data collected in a variety of experimental conditions. Technical solutions are needed to browse, index, annotate and manage such complex content. We have developed a system addressing this need, SAIL (“Sample Availability System”). The system is designed to hold phenotype availability information and meta data about samples,experiments and phenotypes, submitted by data owners or databases that contain actual measurement data. By being geared towards a complexity level that focus on describing data and availability rather than the measurements themselves, SAIL provides a way to browse and summarise complex content across diverse resources. This can be used in many different scenarios from designing new studies, understanding previous studies, and finding data and biomaterial from different cohorts that can be combined in meta-analysis studies. SAIL also contains functionality to annotate collections, with tools to create new vocabularies or use terms from standard sample ontologies, and to combine and harmonise vocabularies. The system can handle real valued data as well as availability data, which is useful to match study samples from different cohorts and to find the availability of samples in certain ranges of study parameters or measurements. The SAIL system is an easy and flexible tool for researchers and co-ordinators of sample collections to browse, understand and update large and complex content across many diverse resources to maximize their scientific value and usability.
A demonstration SAIL instance can be seen here .
Basic use-cases
Flash tutorials:
Emanta
- A web-based system for user and project management
Overview of Emanta
As inter-Institutional collaboration is becoming more and more prevalent, managing such collaboration is also becoming more and more laborious. To ease the workload of managers and primary investigators, we have developed a web application that eases the user and authentication management, provides a central repository for project documentation and information and facilitates scheduling and reporting -- all the way from study design to publications.
The source code for the latest version of Emanta can be downloaded from git://git.simbioms.org/emanta.git
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Software modules
