Who Uses eCAT

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Dr Alex Swarbrick, Group leader, Cancer research program, Garvan Institute of Research, Sydney, Australia

Posted by admin on August 10th, 2010 @ 1:01 pm


“One of the best features I like about eCAT is it’s ability to bring together disparate bits of information that occur in different places as well as different times and to have all that in one place that gets archived and backed up centrally.”

About the Swarbrick lab

The Swarbrick lab investigates the protein coding genes and microRNAs controlling the self renewal, differentiation and metastasis of cancer cells. Alex aims to expand the basic understanding of cancer progression to allow the development of better therapeutic strategies for hard-to-treat cancers. His lab uses a range of model systems, including 2D and 3D cell culture, animal models and human tissues. They also collaborate closely with  colleagues in the Cancer Research Program who bring expertise in signal transduction, anatomical pathology, tissue banking and developmental biology.


“Many of our projects are collaborative projects between several people, some of them all in the same lab, some in other parts of the building or the Institutute.  So, finding a way to combine data, combine experimental ideas, and put that all in one place has always been a real challenge.

Another major challenge has been sharing of reagents. We have a large database of cell lines, mouse tissues, and other biological resources as well as protocols that it’s always been very hard to manage using paper-based records.


We use eCAT as an experimental labbook for all the people in the lab.  They enter all the key information, everything from background through to methods, protocols and results and discussion into eCAT.

The other fantastic feature of eCAT that we use a lot is this ability to include metadata and links within records, so when it comes to managing biological samples this is really important.  So when we have transgenic mice we can track the mouse, the tissues that were made from the mouse, the extracts from the tissues, then the analyses on those extracts and keep them all linked through eCAT.


The way that eCAT helps us is manyfold.  With eCAT we can link to established protocols — instead of having to write out detailed protocols every time someone does an experiment they can link to established protocols as well as putting in some relevant modifications.  By putting in primary data it brings all these disparate data types together so electronic data as well as text and so on into one place and we don’t have to go digging through a server trying to find the relevant Excel file or image or Affymetrix transgenic profiling data set.  That can all live in one place and it’s very easy to find.

When we are managing biological samples we can easily track data — for example in the case of transgenic mice the mouse, the tissues that were made from the mouse, the extracts from the tissues, then the analyses on those extracts — through an experiment whereas doing it with a paper-based approach would be extremely difficult.

The great thing is that people who are working on the project, including myself, can access that and be up to date with what”s happening, make annotations, make changes and suggestions, so it really makes it a much better collaborative situation.”

Professor Mike Shipston, Director of The University of Edinburgh’s Centre for Integrative Physiology

Posted by Rory on June 30th, 2010 @ 6:40 pm

“It was a major surprise; transferring to an electronic lab notebook is actually very easy.”

About the Shipston lab

“We’re interested in ion channel physiology.  We look at post transcriptional and post translational mechanisms of ion channel regulation. That goes from the regulation of alternative splicing to regulation of simple ion channel proteins through to the behavior of ion channel intact organisms such as transgenic mice.  So our work spans the remit of molecular biology, protein biochemistry, high resolution cell imaging, electro physiology, right up to behaviorial studies in animals.


We generate a wide variety of types of data sets, for example data from molecular analysis, quantitative analysis, for example quantitative RTPCR, gene cloning, through to electrophysiological analysis, for example from confocal images and total internal reflective microscopy right up to to behaviorial assays in animals.  So it’s really about coordinating those types of data sets that fit together, keeping them contained within projects, because the data sets are derived from different people within the lab.  Also we have a very big extended network both in the UK and across Europe and the US.  Its about keeping that information together.

We have a large number of people coming in and out of the lab, the challenge is keeping track of that data and integrating it in with data from existing projects.


We use eCAT as a cataloging and information retrieval system.  We can keep catalogs of resources  and protocols up to date and exchange that very effectively between lab members.

We also use eCAT as an eELN.  The great thing about eCAT is its incredibly flexible in terms of how you can set it up.  For example each member of the lab has their own folders and put their own experiments within that, but its every easy to put that information together.


It was a major surprise; transferring to an electronic lab notebook is actually very easy.

The other thing is because eCAT is web-based you can access it from anywhere

Having everything tied together under one resource, so results, protocols, constructs, where things are physically, having everything together under one system has just been perfect.”