Tag: experiments

On-line Storage of Lab Protocols

In the labs I’ve been in previously, common lab protocols were stored in a binder in the lab for reference. Usually I’d make a photocopy for my own use as a place to start and as I optimized the protocol for my experiments I’d mark up this copy. Once I had a solid protocol worked out, I’d generate my own copy of the protocol so that it served my purposes. When I started my own lab I wanted to make sure that my students had a binder of protocols that they could refer to for their own experiments. At the same time I wanted to prevent protocol drift (i.e. the inadvertent changing of a protocol over time). I thought about the common protocols that we would use in the lab and generated several binders for these that are stored in the lab. This approach works, but it’s a bit clunky and limited the students to looking at the protocols only while in the lab. I recently decided that it would make sense to generate a central, on-line repository for our lab protocols.

A quick search of the web showed that researchers do this in different ways. Some labs make their own Wiki to hold this information, others use cloud storage or an online protocol repository, and others used a campus intranet or password protected website. I’m currently in the process of evaluating all of the possible options. How does your lab store and manage experimental protocols? I’d love to receive advice and hear about options in the comments below!

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Tips for designing experiments

One guarantee of being a scientist is that you perform many experiments in your career that do not work. I always warn trainees just joining my lab that this will happen and that they should expect it. This is an issue that I discuss in particular with undergraduate students because often the only lab experience they have is through undergrad labs run as part of a course and those experiments are designed to work and have already undergone extensive troubleshooting. I make sure to tell my students that they will run many failed experiments and that this is a normal part of doing science and is a cornerstone of the scientific method. I tell them that so far in my career I’ve only had a few experiments that worked out perfectly the first time and that a failed experiment can happen for reasons other than their abilities or talent for doing science.

That being said, there are things that you can do to decrease the chances that an experiment will fail right out of the gate. I offer some tips below:

1) The first thing that I suggest to students is that they do extensive reading of the literature and established protocols related to their experiment before starting to design it. I’ve heard the phase “one hour in the library can save you one month in the lab” and I absolutely believe it! It’s really important to understand the rationale behind a particular protocol and the nuts and bolts of why you are doing each step. In the days of commercial kits I think that many people forget this crucial step and it often causes issues later.

2) Make sure that you are including all reasonably possible positive and negative controls as part of your experiment. From talking with several of my colleagues recently it has become clear that many undergraduate and graduate students have not had explicit training in how to determine what the appropriate controls should be for an experiment or are simply not including them. By including controls in your experiment you allow yourself the capability of narrowing down where problems cropped up in your experiments. When an experiment fails, this step can save you a massive amount of time when it comes to troubleshooting and determining what went wrong. The presence of control and experimental groups also ensures that you will be able to conduct statistical analyses of your data in an attempt to demonstrate whether your results are significant.

3) Write up an extremely detailed step by step protocol for your experiment. Try to think about what might go wrong and where key steps are in the protocol. Attempt to troubleshoot the experiment before you even do it. The plans for your experiment should be written in your lab notebook and not on paper towels, scrap pieces of paper, etc. This will ensure that your experiment will be reproducible and will help you to identify potential issues before you get rolling. If someone in the lab has done the experiment or protocol before, go and talk to them. They may have tips or tricks that are not explicitly written down that are valuable. Write out the protocol in your own words with as much detail as you can. I tell my students that if they needed to perform the experiment without thinking about the steps, the protocol should be detailed enough that they could do this.

4) Ensure that all of the materials and reagents that you need for your experiment are available and ready to go before you start the experiment. There is nothing worse than getting part way through a long protocol only to realize that you’ve run out of Tris buffer and have to order more in from the supplier. Complete any prior steps that are needed before starting the experiment. Do you need to culture cells, wrangle critters, grow plants, etc.?

5) Conduct a small trial run of your experiment. Starting things off with a pilot experiment allows you to save money, time, and can allow you to discover problems with the design of your experiment before you fully commit large amounts of resources to it.

Designing good experiments is an art form that requires years of practice in order to get better at it. I am still working on designing the perfect experiment, but I have certainly improved this skill by extensive practice over the years. Due to the challenge of designing an effective experiment it is truly amazing when an experiment works beautifully on the first attempt. This is one of the eureka moments that scientists live for!

Weird Science

James O’Hanlon has a cool post up right now on his website about the strange things that scientists do for science. It made me think about some of the weird things that I’ve done in the course of doing some of my research projects.

The first funny experience comes from when I was doing my Ph.D. I had discovered the enzyme that I work on, alternative oxidase (AOX), in animals for the first time using bioinformatics. I wanted to do some wet lab experiments in order to confirm that AOX was actually present in the DNA of an animal and that it was transcribed. At that time, I had AOX sequences from three animals: the sea squirt Ciona intestinalis, the nematode Meliodogyne hapla, and the Pacific oyster Crassostrea gigas. The sea squirt is an invasive species on the east coast of Canada, so getting my hands on tissue would have been tricky. The nematode is very tiny and a plant parasite, so that would have been a difficult sample to obtain. Pacific oysters are commonly eaten by people and I figured that would be the way to go. I called a wholesale seafood supplier to confirm the availability of Pacific oysters and drove about 1 hour to go and pick some up. When I arrived there were no Pacific oysters in the store front, so the owner had to take me into the warehouse to get them. It was pretty intimidating as this involved walking through several large pieces of plastic sheeting that separated the store front from the warehouse. I felt like I was in an episode of the X-files or a murder mystery and that I was being led to my doom. We got to the bin that was housing the oysters and the owner asked me how many I wanted. I figured that 24 oysters would get the job done. He started putting the oysters into thick plastic bags and we started chatting. Was I running a restaurant? Nope. (I guess that it’s unusual for individuals to buy 24 oysters at a time). Was I having a large dinner party? Nope. Well, what was I going to do with these oysters then? I said that I was a scientific researcher and that’s when things got weird. The guy completely panicked and started going on and on about how the oysters were safe to eat and were o.k. for human consumption. It turns out that he thought that I was a government scientist who was doing an unannounced, random inspection for the Canadian Food Inspection Agency! In retrospect it’s a hilarious story, but at the time I paid for my oysters and ran! The project was awesome by the way.

The second funny story is from my time during my post-doc. The university where I was working had a great arboretum (collection of trees) and I’d obtained permission to take leaf samples for a project that I was working on regarding the taxonomic distribution of AOX in non-flowering plants. When I went out to sample I used an ice bucket, lots of little tubes, scissors, etc. It would certainly look weird to anyone walking by. A few times I had curious people come up and ask me what I was doing and I enjoyed talking to them about my science. It was a great and unexpected opportunity to do some public outreach.

Head on over to James’ blog or follow the #strangethingsforscience hashtag to hear about some great science adventures!