The BDSG have considerable experience building systems for  managing and storing clinical and biological data in line with current best-practices. 

Current projects

Chernobyl tissue bank

The Chernobyl Tissue Bank (CTB) is an international cooperation that collects, stores and disseminates biological samples from tumours and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The BDSG has developed the CTB Portal - a unified online interface for prospective and current users of samples from the tissue bank. It provides an intuitive interface for requesting samples and associated research data tailored to researchers' requirements. The portal also includes a administration module used by the CTB secretariat to manage details of the projects associated with the tissue bank.

PI: Prof. Geraldine Thomas

Funding body: National Cancer Institute

Grant reference: 5U24CA082102

Data repository: https://cisbic.bioinformatics.ic.ac.uk/ctb/html_ctb_public/

Public website: http://www.chernobyltissuebank.com/

BDSG Contact: Dr. Chris Tomlinson

Publication: Thomas, G. et al (2012) Communication: The Chernobyl Tissue Bank - A Repository for Biomaterial and Data Used in Integrative and Systems Biology Modeling the Human Response to Radiation Genes 2012, 3:278-290 doi:10.3390/genes3020278

Imperial College Healthcare tissue bank database

The BDSG has developed system that holds information on Human Tissue collections that are held at Imperial College.  There are currently around 200 collections which have information stored about them including the Imperial College Hospitals Tissue Bank (ICHTB). The system also has a sample tracking system where information about individual tissue samples and donors can be recorded. Several tissue collections use this facility to record information about the samples that they hold. For instance, the ICHTB has over 80,000 samples recorded in the system and these can be searched by researchers via a web interface.

PI: Prof. Geraldine Thomas

BDSG Contact: c.tomlinson@imperial.ac.uk

Completed projects

EuSCAPE.net

EuSCAPE.net is a system designed to track epidemiological samples in an EU study. Users from different EU countries can use an interface to input information about isolates and their antibiotic susceptibility. Information about the isolates and their location is displayed using google maps.

BDSG Contact: Dr. Chris Tomlinson

Evimalar

EVIMalaR was a 5 year joint research FP7 Network of Excellence, funded by the European Commission, with 42 partners from 34 institutes in Europe, Africa, India and Australia. It sought to integrate malaria research directed towards a better understanding of the basic knowledge of the parasite, its vector and of the biology of the interactions between the parasite and both its mammalian host and vectors. The BDSG assisted in providing a respository for datasets.

Data repositoryhttps://cisbic.bioinformatics.ic.ac.uk/evimalar-seek

Public website: http://www.evimalar.org/

Funding body: EU FP7

Grant reference: 242095

BDSG Contact: Dr. Sarah Butcher

Florinash

Florinash was a 5 year EC-funded FP7 project investigating the role of intestinal microflora in non-alcoholic fatty liver disease (NAFLD). It brings together 6 leading institutions from 4 countries for which the BSS is designing and implementing a centralized database to store data from human and mouse samples. The system is able to integrate metabolomic, transcriptomic and proteomic profiles with patient metadata to enable the exploration of clinical hypotheses.

The BDSG built a bespoke database and search interface for  the anonymised data arising from the project. The BDSG were also heavily involved in the analyses of whole human gut metagenomes arising from the project – and together with Dr Lesley Hoyles, have developed a pipeline (IMP) to support further whole metagenome analyses. 

PI: Marc Dumas

Funding body: EU Framework 7

Grant reference: Health-F2-2009-241913

Data repositoryhttps://cisbic.bioinformatics.ic.ac.uk/florinash/

Public websitehttp://www.florinash.org/

BDSG Contact: Dr. Chris TomlinsonDr. James Abbott

Neom database

Neom is a web based system for recording information about premature babies that have been involved in clinical research studies conducted by the Kroll group. Information about samples derived from those babies is also recorded using the system. A flexible database architecture allows new data items to be added to the system with ease. 

PI: Prof. Simon Kroll

BDSG Contact: Dr. Chris Tomlinson