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Toronto scientists develop open-source, web-based app that tracks reagent collections


Toronto, ON – Researchers at the Samuel Lunenfeld Research Institute of Mount Sinai Hospital, led by Dr Karen Colwill and Marina Olhovsky, have developed an open-source, web-based tool to track both large-scale datasets and individual reagents, allowing for easy access, sharing and management of data across various projects and research groups. The software is described in the August issue of Nature Methods.

Before now, scientists had limited affordable resources to track and manage the rapid growth of large-scale reagent collections.

“At the Lunenfeld, we have extensive DNA and RNAi collections that are shared among multiple laboratories,” said Dr Colwill, senior author of the study and a staff scientist in Dr Tony Pawson’s lab. “OpenFreezer efficiently manages these reagents and allows us to access them as needed. Designed by biologists and backed by powerful computer technologies, OpenFreezer offers other scientists an affordable and effective route to manage and archive their own reagents.”

Currently, the software is being used by more than 150 scientists at the Lunenfeld covering multiple expertise areas including cancer biology, systems biology and proteomics. Dr Colwill expects that scientists internationally will utilize OpenFreezer for research endeavours across multiple aspects of biomedical research.

The software offers scientists several advantages including:

  • Permanent storage and archiving at a single site, with simultaneous access for an unlimited number of users;
  • Ability to add new reagents and customize existing ones;
  • Three central modules that allow users to track information on an unlimited number of labs, users and projects; assess the properties of different reagents; and determine the locations of a reagent’s physical preparations.

“Computer processing power makes a great difference in its potential to expedite genetic research via sophisticated data warehousing and management tools, such as OpenFreezer,” says Marina Olhovsky, a software engineer in Dr Pawson’s lab and first author of the study. “OpenFreezer provides a foundation for the operation of a laboratory within an enterprise software application framework. We encourage biologists and computer scientists to assist us with the future development of OpenFreezer.”

On a personal note, Olhovsky has dedicated OpenFreezer to her mother, Larisa Olhovsky, who lost an untimely battle with cancer in 2006. “This is Mom’s legacy. I dedicate this work in her memory as a guiding light for biological researchers on their path towards winning the battle against cancer and other diseases,” she says.

The software is freely available for demonstration and download under the GNU General Public License on the OpenFreezer website at www.openfreezer.org.