My name is Chen Guttman and I am a PhD student at the Zarivach laboratory researching X-Ray crystallography of effector proteins secreted by pathogenic bacteria. I’ve recently started writing about my experiences in the lab at my new blog, bench wise. I’ve also started using BioData’s laboratory management tool, BioKM, to help increase my productivity and research capabilities, as well as improve my chances of publishing my research.
I first came across BioKM while searching for a laboratory tool that would help me get organized at the bench. It looked nice and slick, so I’ve decided to give it a go and write a blog about my experience with BioKM as their community liason.
How did I manage my research in the lab up until now? From the beginning of my research career, I’ve never really used the classical laboratory notebook and instead utilized MS Office Word - logging everything that was happening at the bench. Microsoft’s Word program is a very versatile tool but I found that I was missing the online capability and had to constantly backup my files and sync all kinds of data, documents, and images from the lab server to my laptop. Many times I forgot to sync gels images and chromatograms and thus could not work outside the lab. It was a real drag…
What about my freezer, refrigerator and deep freeze (-80c) stocks? Hell, don’t ask! Just to think of the mess over there…each time I needed a plasmid for a transformation assay, I wasted a good 10 minutes finding it. 10 minutes! I could have had a cup of coffee…
After I signed up for this lab management tool, I decided to start with the challenge of organizing the laboratory’s antibodies collection. Our lab specializes in protein purification and crystallization and we routinely find ourselves running to the 4 degrees fridge to fetch our beloved and commercial antibodies. With so many protein tags on the market, it is easy to purify and also detect whether your protein of choice has been expressed.
My former lab utilized flow cytometry to monitor lymphocytes cells; we had over 30 different monoclonal and polyclonal antibodies collections. These large antibody collections were stashed both in the deep freeze and in the cold room, from different preparation batches and animal sources. That’s quite a lot of antibodies! Back then, our assistant professor was the knowledgeable one, the one who knew where every tube was placed and at what month (!) the antibody was purified from the serum. She had a good list, but the problem was that she was the only one that actually knew where it was filed and how to decipher the specific location that was logged…definitely a problem.
With memories of my former lab in mind, I decided to map the location and specification of all our antibodies in my current lab. To do so, I logged into my laboratory account at BioKM and started to list them one by one. I was happy to see many important fields where I was able to list all the information about each antibody such as its origin (Rat, Mouse, Sheep and many others), type of clone (polyclonal or monoclonal), its source, and the recommended dilution (very important!). There is even a description field that enabled me to add remarks in regard to each specific antibody. BioKM’s option to link the antibody to a certain project and to a specific location is well embraced and will definitely aid me in improving my research management capabilities and improving my efficiency at the bench.
While the antibody module is very thorough, I found myself longing for additional functions such as the distinction between primary or secondary detection coupling and a more detailed summary of the different antibodies once I’ve finished listing the different specs of each antibody. A detailed summary would enable me to quickly glance at the screen while preparing the dilution of the antibody onto the milk solution for the western blotting protocol.
How do you manage your antibody collection? Please share with us how you keep all your antibodies organized.
Chen Guttman is a Graduate Student at the Zarivach lab in Ben Gurion University. Chen blogs at benchwise and serves as BioData's community liason.