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.”

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.”

Andreas Johansson, Microbiological Laboratory, Campus Helsingborg, Lund University

Posted by Rory on June 30th, 2010 @ 4:22 pm

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

“I chose eCAT because it’s really easy to get started with and use.  With eCAT it’s actually fun to take notes!”

About  Andreas’ work

“We are mainly working with lactic acid bacteria and we try and isolate it from the common honeybee.  We do a lot of common lab experiments and we also do a lot of outdoor experiments.  We also work with a lot of groups around the world.

Challenge

The most important challenge was inconsistent or messy notes.   Another big thing is missing protocols.  They are all over the place.  You might have one tacked to the wall, others in a binder, and at the time you need it someone has borrowed the binder or you can’t find it.  Some things are in your head and some things are in the lab notebook.  Before there were experiments in three different lab notebooks and another one belonged to one of my colleagues.

Solution

I use eCAT for everything in the laboratory when I need to make a note of anything.  I use it for my experiments and my protocols.  But I also use it for things I didn’t use it for before I had an electronic lab notebook.  I use it for digital photos, so protein gels, screenshots of my HPC runs, screenshots of the small things I see during my experiment.  Before I would have just made a small note about it, now I have a photo of it.  And I also add time stamps during an experiment so I can easily see at what point I did a certain thing.

Results

The main result is very very large quality improvements.  It also brings structure to your experiments automatically.  Since you are working with project folders you have your own experiments, and you also add protocols, and you add the data and you add whatever electronic stuff you get during the experiments to that folder.  So everything gets sorted by date and time.  It’s much more structure, automatically.

Now when you’ve done an experiment and you want to share it with a colleague, it’s much easier.  It’s structured from the beginning and it looks good.  You can easily print it, or print it electronically and send it to colleagues by email.  And for me it’s actually fun to take notes nowadays!  I take notes on everything just because it looks good in eCAT.  Nowadays the first thing I do is to start a new experiment in eCAT, even before I start the small preparatory things.

Another big thing is that I am able to access my data from outside the laboratory. I’ts completely web-based so you don’t need to install any software on your computer.  This also means that as long as you have access to a browser you can access eCAT.  It doesn’t matter if you are on Linux or Apple or a Windows system.  That’s really important for the future.

The main reason I chose eCAT is because its really easy to get started with and use.  If something is hard to get started with and easy to use a lot of people will just have a look at it and never get around to starting the first experiment.  eCAT is easy to use; it also means I can ask my colleagues to use it as well.

It’s also easily configurable and its easy to customize your experiments.  You can make your experiments and your protocols look whatever way you want them to.”

Michael Shtutman, PhD, Assistant Professor, Department of Pharmaceutical and Biomedical Sciences, South Carolina College of Pharmacy University of South Carolina

Posted by Rory on June 30th, 2010 @ 4:06 pm

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

“The most interesting feature of eCAT is its flexibility.”

About the Shtutman lab

“My lab is doing functional genomics projects.   Our work involves many parallel projects with high throughput sequencing, analysis of results as well as wet biology assays.  In parallel, as the director of the functional genomics facility, we provide services for other labs.

Challenge

We run many different projects involving different people, so it was difficult to combine all the results together, and to trace the materials that appear as a result of the research projects.

Solution

We have project related-databases as well as materials-related databases.  eCAT allows us to enter all the project information and the materials information and location.

Results

With eCAT we were able to organize all our projects and materials, and create an integrated and searchable database of our work.

The most interesting feature of eCAT is its flexibility.  It allows us to add our own classes, and to add information in the manner most convenient for us.  The other features, including powerful search and the ability to add graphic data, are also advantageous.”

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.”

Andreas Johansson at Helsingborg Campus of Lund University talks about how easy it was to get started using eCAT.

Posted by Rory on June 30th, 2010 @ 1:32 pm

“I use eCAT for everything in the laboratory when I need to make a note of anything.  I use it for my experiments and my protocols.  But I also use it for things I didn’t use it for before I had an electronic lab notebook.  I use it for digital photos, so protein gels, screenshots of my HPC runs, screenshots of the small things I see during my experiment.  Before I would have just made a small note about it, now I have a photo of it.  And I also add time stamps during an experiment so I can easily see at what point I did a certain thing.  The main result is very very large quality improvements.  It also brings structure to your experiments automatically.  Since you are working with project folders you have your own experiments, and you also add protocols, and you add the data and you add whatever electronic stuff you get during the experiments to that folder.  So everything gets sorted by date and time.  It’s much more structure, automatically.

The main reason I chose eCAT is because its really easy to get started with and use.  If something is hard to get started with and easy to use a lot of people will just have a look at and never get around to starting the first experiment.  eCAT is easy to use; it also means I can ask my colleagues to use it as well.”

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.”