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

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/user/alex/alex.flv

“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.

Challenges

“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.

Solution

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.

Results

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.

Challenge

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.

Solution

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.

Results

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.”

Professor Larry Gonzalez, Director of Biological Psychology and the Center for Alcohol & Drug-Related Studies, University of Oklahoma Health Sciences Center

Posted by Rory on June 30th, 2010 @ 5:37 pm

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/user/larry/larry.flv

“eCAT helps keep me organized and it’s very good at increasing my efficiency in documenting my research.”

About the Gonzalez lab

We investigate the effects of chronic drug exposure on brain function. We use a variety of techniques, ranging from behavioural measurements to in vivo and in vitro electrophysiology.

Challenge

I was interested in an electronic lab notebook that would allow me to document research protocols we use and collect the date through data forms we generate in the notebook and also be able to link to external forms and external data files that were created with other programs, both raw data and images.

Solution

“Myself or a research technician or a post doctoral fellow can generate a protocol and store it in eCAT.  We can create the data forms that can be filled out manually and entered during an experiment, and we can link to external files.  And if someone would prefer to use another program like Excel to generate spreadsheets instead of entering data into eCAT they can create a spreadsheet and we can link to that file, and its all kept together and organized well in eCAT.  And then when an experiment is completed we’re able to export the data to an external statistical data program for subsequent analysis.

Results

Because its accessible over the internet eCAT is easy to view, form my office or my lab, or at home.  eCAT does most of the things I am interested in doing with an electronic lab notebook.  It helps keep me organized, and it’s very good at increasing my efficiency in documenting my research.”

Mike Shipston’s lab at the Centre for Integrative Physiology, Edinburgh University, benefits from eCAT’s flexibility and ease of use in research using post transcriptional and post translational mechanisms of ion channel regulation

Posted by Rory on June 30th, 2010 @ 5:28 pm

“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 behaviorial assays in animals.   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 ELN.  The great thing about eCAT is it’s incredibly flexible in terms of how you can set it up.  For example each member of the lab has their own folders and puts 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.”