A bioinformatics platform for managing biospecimens

The Lewin-Cameron laboratory at the Peter Doherty Institute for Infection and Immunity recently commissioned and installed OpenSpecimen, a bioinformatics platform for managing biospecimens inventories. The system was developed by Krishagni Solutions in conjunction with the US National Cancer Institute and is distributed in Australia and New Zealand by AXT.

The main focus of the Lewin-Cameron laboratory is to understand why HIV infection persists on antiretroviral therapy, to develop new strategies to cure HIV and to define the factors that drive liver disease in HIV-hepatitis B virus co-infection. The laboratory collaborates extensively with researchers across Australia as well as the US, Europe, Asia and South Africa.

With a geographically diverse user group and a library of over 100,000 specimens, the choice of a robust platform capable of dealing with the vast amounts of metadata was imperative. OpenSpecimen was found to be the most suitable solution for the lab’s requirements, enabling its researchers to concentrate more on research and spend less time on administration and record keeping.

“OpenSpecimen is web based, which allows for easy access from multiple sites, meaning that data can be entered [in] real time by nurses at clinical sites and by researchers in the laboratories,” said Lewin-Cameron lab member Dr Judy Chang. “This improves workflow and reduces transcriptional error by reducing paper records that need to be subsequently converted to digital records. There is also no limit on specimen capacity, which is ideal for clinical research labs that have high throughput demands.”

One of the features that was particularly attractive to the laboratory was the ability to customise the open-access OpenSpecimen software platform. “This meant we could quickly adapt to different study protocols, which can have varied collection and storage requirements,” Dr Chang said.

The laboratory chose to directly involve Krishagni Solutions in this work and the data migration, with Dr Chang saying the developer was “very easy to work with”.

“There is an online forum and user guide available for getting general support from the OpenSpecimen user community and Krishagni staff,” she noted. “In addition to this, Krishagni have provided fast responses to email requests and questions. We did not implement a large number of customisations, as we used the customisable capabilities already build into OpenSpecimen. Furthermore, Krishagni updates the software regularly and new capabilities are continually been made available.”

Photo credit: Peter Casamento.