The Race to the Publish Line – Keeping Track of your Stats

August 28, 2013 | Posted by Fraser Tan in Grad School Help |

We scientists are awfully good at generating data. Organizing and retrieving it, though – that’s harder. In college, we were taught to use a sewn paper notebook and a pen to record all our data – take that idea and throw it out! The modern lab notebook needs to be flexible, scalable, searchable, browsable, share-able and secure.

There are many different ways to organize your data; play around until you find a system that works for you. I divided my work into domains and figured out a system for each domain. Using a disparate set of programs, I cobbled together my own version of an electronic notebook, coupled with a few instances of paper notes. If I had to do it all over again, I would make a much more efficient system, but I wasn’t that smart nine years ago.

Tracking experiments

An example of an immunostaining experiment

An example of an immunostaining experiment

First, I created a standardized method of naming all my experiments. For example, to study multiciliated cells, I used a primary cell culture system called MTECs. Thus, each time I started an MTEC, I would generate an ID number, which was usually the date (ex: MTEC20060823). Then all further experiments, like immunostaining, would be labeled with that ID; if I stained the MTEC, the resulting images would be labeled MTEC20060823_1_01_63X_488_555. This refers to the MTEC that was created on August 23, 2006, the first filter of the culture (whose identity I would know based on my MTEC template), the first picture of that filter, the magnification used, and the two channels in the image. Thus, for every picture, I find the matching experiment and know what exactly was going on.

For each of my experiment types, I made protocol templates in Word. For each immunostain, I filled in details like the tissue, the purpose, what antibodies I was using, and any modifications to the protocol. For mouse genotyping, I tracked the parental genotypes, the expected genotypes of the pups, the PCR primers and conditions, expected band sizes and the gel image. Using templates saved me time and gave me a clear place to keep critical information about each experiment.

Tracking metadata

My system above was still rather stilted. I found myself scrambling through multiple ring binders to find the exact printout for the immunostain, then the exact printout for the mouse or MTEC, then trying to find the image on my computer. I could have saved myself a whole bunch of time if I’d used a database.

A database is an incredibly powerful tool for managing vast quantities of data by storing information about that data. Say you take a picture of a stained mouse lung. A database can store the picture, the genotype and age of the tissue, the antibodies and their channels, what hypothesis the experiment was designed to address, and what the results said about that hypothesis. Years later, you can find all E14 mouse lungs stained with e-cadherin and Foxa2, and pick the nicest one for your figures.

There are many database programs that can help. Personally, I like FileMaker Pro. It’s relatively easy to learn, and since it’s a relational database, I could link various types of experiments together easily. My labmate Hernán Espinoza designed a database to manage his mouse colony (and he was kind enough to share it with me – it was a lifesaver!). FileMaker helped me implement and run an in situ hybridization screen; I tracked all my target genes, which ones had probes, and all the resulting images. You could even use FileMaker to track experiments – a step I never got around to. And, for the life of me, I wish I had set it up from the beginning to file all my pictures!

There are other databases out there besides FileMaker. iPhoto and Aperture work well as image repositories. Evernote can help keep track of projects, seminar notes, lab meeting summaries or general ideas. Many of these can be synced with an iPad/iPhone app, making them portable as well as powerful. You can try an electronic lab notebook (ELN). These weren’t in widespread use during my graduate career, so I don’t know much about them, but they are gaining popularity. ELNs embody the crucial idea of harnessing technology to help track, store and retrieve your precious data. (For more information, check out this great post by The Postdoc Experience.)

Tracking papers

There are a plethora of apps designed to help you avoid stacking your desk three feet high with piles of PDF printouts (and killing all those trees). Almost all citation management software these days can ogranize documents into folders (similar to iTunes playlists), annotate PDFs, support collaborating and sharing documents and can insert citations into manuscripts. I was an early convert of Papers, an award-winning document repository database. Papers is a desktop app that has a lovely intuitive interface and web connectivity; you can search all major paper repositories (such as PubMed, Google Scholar, arXiv, etc) directly within Papers itself, which makes importing the PDFs a snap. The downside? Papers is $79, but there are student discounts available, and my labmates and I got our professor to pay the cost for us. Zotero is a free all-inclusive package that allows you to store PDFs, annotate them and cite them. Zotero allows you to share folders with collaborators, and syncs your data to their servers so you can access it from multiple locations. (Papers doesn’t directly support this, but you can easily set up a hack via DropBox or another cloud storage system.) Mendeley is a popular online PDF annotation system that also lets you connect with other researchers and discuss your papers. Endnote is the canonical citation manager and has added PDF storage and organization function. Lastly, before Papers had annotation tools, I used a great program called Skim to highlight and take notes on my PDFs. For a lovely comparison of citation managers (more than I’ve mentioned here), check out the University of Washington Library’s chart.

What works for you? Share your tips, tricks and insights in the comments below!

About the author

Fraser supports our customers on Science Exchange. She completed her graduate and postdoctoral studies at Stanford University and served on the Marketing and Development Team for BenchWise.org before joining Science Exchange..

 

 

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