Who Uses eCAT


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Alex Swarbrick’s lab at the Garvan Institute uses eCAT to allow everyone in the team to manage shared facilities, reagents, results and ideas in its work investigating the molecular pathways that are mutated or deregulated in cancer.

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

“eCAT is absolutely essential to the running of my lab. Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments. This allows us, for example, to connect an experimental mouse with the tube containing its tissues in the freezer, to the 6 different experiments (conducted over a year) that analysed those tissues in different ways. Managing this kind of ‘metadata’ is absolutely essential to our work, and very difficult to do without tools like eCAT.

I think eCAT will be become more important as the group grows, since it becomes harder to keep in touch with everyone’s work. For example, I can use eCAT to remind myself of recent experimental results without hassling someone in the lab. It also facilitates collaboration within and outside of the lab. I also know that data is being properly catalogued and experiments are being written up and that all this is backed up every night. Since everyone uses the same interface, it is easier for new people to understand the way the lab works and to pick up on projects.”

The modENCODE (model organism ENCyclopedia of DNA Elements) Project, which includes collaborating labs at University of North Carolina, University of Cambridge, University of California, Berkeley, San Diego, NimbleGen, the Dana Farber Cancer Institute, and the Weizmann Institute, moved from spreadsheets to a wiki to eCAT

Posted by Rory on June 30th, 2010 @ 3:28 pm

“We initially stored our data on a wiki using embedded spreadsheets. We soon learned that this was not a feasible option due to the complex structure of the data, and we started shopping around for alternatives. When we were tasked with searching for an alternative to the wiki, or free web-based alternatives, we found that they were lacking in features and/or support. Initially, we were looking into LIMS, but those platforms were highly specialized, very complex, and expensive. eCAT is a better fit for us because of the fairly intuitive UI, the ability for the database structure to be modified by the end user, cost, and importantly, customer service. We have been highly impressed with the level of customer service offered from Axiope. It is clear that they take pride in their product, are concerned about the customer’s experience and are always receptive to suggestions for feature additions and/or changes.

Due to the thoughtful UI of eCAT, it took little effort to get all wet lab members trained to use eCAT to facilitate data entry. Members of our labs have also been starting to use the e-notebook feature of eCAT. They find it very easy to enter their experiments and organize their data. They are starting to realize the power of allowing them to more natively integrate electronic sources of data (documents, images, web links, etc.), which was something not readily accomplished with a paper notebook.”

Professor Larry Gonzalez at the University of Oklahoma talks about how he uses eCAT in his work, which involves using a variety of techniques, ranging from behavioral measurements to in vivo and in vitro electrophysiology, toinvestigate the effects of chronic drug exposure on brain function.

Posted by Rory on June 30th, 2010 @ 2:30 pm

“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. Because it’s accessible over the internet eCAT is easy to view, from 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.”

Matthew Nicotra, Research Instructer, Starzl Transplant Center, University of PIttsburgh Medical Center

Posted by Rory on June 30th, 2010 @ 1:00 pm

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

About Matt and his work

“We do transplant immunology using mouse models and comparative immunology using an inverabrate model for hista compatability and animals related to jelly fish and sea anenomes.

Challenge

Before using eCAT I would keep my data for experiments in various places.  I had my paper notebook at the bench with written notes and gel images and other pieces of data — printouts taped in various places.  And then on my computer I’d have folders for every experiment with Excel spreadsheet and data files and digital images and other data.”  It was really a challenge to go back a month later or so and try to remember how all those pieces of data related to each other.  So I’d open a folder and try to figure out which Excel spreadsheet had the data I wanted, where exactly did that image come from and when did I take it.

Solution

Using eCAT has helped with keeping all that stuff organized because I can have one page with all my notes on an experiment.  Imported into that are  my digital images.  I can link to Excel spreadsheets, I can link to other experiments, I can link to data files, and it’s all right there.  I don’t have to speand any time figuring out where anything is. “I use eCAT five to six times a day if not more to upload data images and keep track of my experiments, write notes,and  plan experiments for the future.

Results

The thing I like best about eCAT is its very simple to use.  I looked at some other electronic lab notebooks and they were complicated or overly designed.  eCAT has a very simple interface.  Its very flexible so I can just go in and immediately start writing my lab notebook the way I used to with a paper lab notebook.

If I want to I can make templates for different types of experiments, like PCR experiments, flow cytometry data, those sorts of things.

It’s simple, I don’t have to spend any time figuring it out.  And I can get to it from anywhere.  So if I’m home or in the lab or somewhere else I can get to my data at anytime.

Perhaps the most important thing is it’s on the web.  I don’t have to spend any time doing IT support.  They update it when they come out withnew updates to the software.  And its backed up, so I don’t have to worry about data disappearing or, heaven forbid, there is a fire in our lab.”