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Case studies from Team Hosted and Install users of the electronic lab notebook eCAT.

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Paul Plummer, Assistant Professor Veterinary Diagnostic and Production Animal Medicine and Veterinary Microbiology and Prev. Medicine, College of Veterinary Medicine, Iowa State University

Posted by admin on June 8th, 2011 @ 9:37 am

Tell us about your work

My faculty position at the College of Veterinary Medicine has two primary components. Roughly 60% of my time is spent doing research with the remainder being focused on clinical medicine and teaching veterinary students. My clinical practice focuses on Large Animal Internal Medicine and more specifically internal medicine of ruminants. I am particularly interested in infectious disease and food safety issues associated with cattle, sheep and goats. My primary research focus is Campylobacter jejuni molecular microbiology. C. jejuni is the number one cause of food borne bacterial enteritis in the United States and abroad. We work on the environmental adaptation, antimicrobial resistance and pathogenicity of this organism. I also have active research projects in Papillomatous Digital Dermatitis of cattle,Coxiella infection of ruminants, metagenomics of culture negative mastitis and functional genomics of Bibersteinia trehalosi, a respiratory pathogen in ruminants.

How do you use eCAT?

My lab has used eCAT since the start of the lab – about 1 year ago.  Everyone in the lab uses eCAT as their exclusive laboratory notebook.  That includes one research associate/lab manager, 3 graduate students, 2 undergrad students, 3 collaborators and myself.  We recently upgraded from 10 to 25 licenses to accommodate growth in the lab.

The lab members have adapted well to eCAT.  Most of them have not every known anything different, so this is their only experience with a lab notebook.  Obviously some have used paper notebooks before starting in the lab and for them it is a little more of a transition.  That being said all of us appreciate the search option functions, the linking to files and the consistent collection of data.

How are you finding eCAT?

As a PI I like the ability to monitor experiments and make sure that the students are keeping up to date with their bookkeeping.  Using the dashboard I can see what has been added every day by each student.  I can easily access that information and provide ready input back to the students even mid-stream.  This has in some cases saved me a significant amount of money in terms of following “red herrings” and in other cases has saved me significant time by stopping or modifying an experiment in progress that was destined for failure.  It also helps me minimize the pile of “paper towel notes” that the students have buried on their desk and note put into a proper record.

I like to be able to have real-time access to any of my data – worldwide.  Last fall I was in Japan to give a talk, wanted a picture I had not brought but could easily retrieve it and the data off eCAT.

The search function is a life-saver.  It might be nice to have an auto-fill for “field name” in the advanced search but that is the primary thing I would modify.  It also has a function called “record table” in the advanced search that gives you a very nice summary of particular data (i.e. sample data or strain data etc).

I like being able to modify fields in given templates to what I desire to collect for information.  By doing this I can tell the students to fill in every field and make sure I have a complete record.

I run eCAT on my own server and have the data backed up at two remote sites.  A colleague that had a lab fire lost 4 lab notebooks of data – not a fear that I have with eCAT and backups (beyond obvious desire not to have a fire).

I like the ability to have collaborators have access to the data while not downloading it to their computer.  I had considered dropbox as a file sharing system – but don’t want all of my data in a given folder downloaded onto the students’ hard drives.  Admittedly they can print it off eCAT or download it if desired which is not a concern since they are a collaborator.  I am more concerned about “eating up their hard drive space” with dropbox downloads of unneeded material.

How do you find the people at Axiope?

The group at Axiope is great to work with and very helpful.  They respond quickly when there are questions regarding the use or management of eCAT.

What else would you like to see in eCAT?

We do a lot of field sampling – by using eCAT and iPADs we can access data through remote servers and input data quickly.  Axiope I believe is working on an iPAD app specific for eCAT AND I CANNOT WAIT TO SEE IT!

 

 

Kevin Cauchi, Systems Administrator, College of Literature, Science and the Arts, University of Michigan

Posted by admin on May 20th, 2011 @ 5:02 pm

About the University of Michigan

“We’ve been investigating electronic lab notebooks, and have looked at 6 – 10 different products.  I’ve been working with the system administrators and the PIs in each department.  We’re looking at an initial deployment in our Physics and BioPhysics departments.  The goal is to have the majority of users in the College of Literature, Science and the Arts using an ELN solution.”

Challenges

“One of the biggest challenges we find is getting people to adopt.  A lot of the time it has nothing to do with the technical limitations or aspects of the system.  It has to do with a cultural issue.  People have been used to using pen and paper notebooks for years.  Moving to an electronic lab notebook is a major change in the way they work.”

Attractions of eCAT

Affordable

“One of the things that stands our in terms of eCAT is that it is affordable.  A good 99% of the solutions we’ve looked at are very, very expensive, and coming from an educational perspective we don’t have the money of a pharmaceutical company to spend on licensing.”

Web based

“Also the fact that it’s web-based is a major advantage.  The client platforms in the university are very heterogeneous, so you have people running macs, you have people running Windows machines and you have Linux clients, and a lot of the software out there is built to run on Windows – it’s client-server based.”

Flexible

“One of the other things I like about eCAT is that it is very flexible.  It’s not tied down to any special area of research.  The ability to create templates, and structure your data the way you want to structure it, is a major advantage as well.”

Let’s you work the way you are used to working

“Some of the other solutions we looked at had similar functionality, but in lots of ways these solutions are built in a way tht you have to modify the way that you work, to work with the solution, whereas eCAT is a solution that will work with the way you are already working, just in electronic format.”

Straightforward technically

“From a technical standpoint eCAT is a pretty straightforward application.  We’re looking at an onsite installation so we can mange the data.  eCAT is very easy to set up and backup and everything else, so it’s a good choice for what we intend to do.”

 

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.”

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.”