Category: Laboratory Organization

DoctorAl Digest 17

Some great pieces from around the Internet this week!

As scientists we often don’t think about data management until it’s too late and we end up losing data due to a computer crash or catastrophe! Don’t let this happen to you! Excellent advice from Melanie Nelson over at the Beyond Managing Blog on data management.

An honest and frank appraisal of the challenges faced by working moms. Funny and heartbreaking at the same time. (Not for the squeamish!)

An excellent piece by Hope Jahren that needs to be read by all scientists. Lots of people have been talking about it on Twitter and blogs this week.

The excuse that all male panels at conferences “just happen” has been busted by a mathematical analysis.

Enjoy!

 

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Lab Freezer Organization

My freezers at home are fairly well organized. The one in my fridge is pretty full, but we have a good sense of what is in there. The chest freezer in the basement is very well organized after we did a purge last year and decided to organize by main ingredient. We can tell quickly when we are running out of something and need to buy more.

I’m in the process of doing the same for my lab freezers. We have a -20°C chest freezer in the lab that we use for storing various biological samples. I recently purchased 2 additional vertical racks and a bunch of 2 inch tall freezer boxes since the samples from my students’ projects have massively increased in the 5 years that I’ve been working here. These boxes work great for samples that fit in 1.5-2 mL tubes, but aren’t so super for biochemicals that I need to store at this temperature. I’m currently experimenting with various plastic containers in order to find a system that works for us.

We currently store our more sensitive/long-term storage samples in a rack in a shared -80°C freezer. A fellow faculty member has been very kind in letting us squat in the freezer for the past 5 years. Last week I was able to purchase a freezer of my own (oh, happy day!) and am proactively planning how we will store our samples. Our current set up is a rack that holds 16 2 inch boxes which has worked well for samples, but isn’t so great for several molecular biology kits that we regularly use. I’m happy to be getting our own freezer as I’ve been dismayed by the storage behaviours of other researchers who share the freezer. Pro tip: unlabelled baggies are not an effective storage tool! I’m also quite territorial when it comes to my freezer rack. I’ve been really angry when others have taken my boxes out of my rack and replaced them with their own boxes. Not cool!!

We will also be switching over to a labelling system that actually uses freezer safe labels. Previously we had been writing on our tubes with extra-fine Sharpie markers, but this is difficult. I’ve recently purchased various labels from GA International and I’ve been impressed with the quality and performance so far. The colour dots in particular will save us lots of time when locating DNA vs. RNA vs. protein samples in our storage boxes.

A logical freezer organization system will save you valuable time. I think that we’ve all had that experience where we got lazy or sloppy and are then cursing ourselves later when we can’t find that important sample in the freezer. It can sometimes take hours, days, or weeks to generate a biological sample depending on your experiments. It makes sense to store the sample so that it maintains integrity and you know where to find it when you need it.

What approaches have other PIs taken to storing your biological samples in freezers?

 

Midichlorians, agar, and manuscript titles

In light of the recent release of “The Force Awakens”, I enjoyed this neat blog post by Dr. Cameron Webb just before the holidays: Could a mosquito bite make you a Jedi?

We use quite a bit of agar in my lab to make DNA gels. I also like chocolate milk, largely due the texture provided by carrageenan. Both of these products come from algae and Morocco has started to limit the amount of algae that can be harvested on its shores. Some labs are starting to stockpile agar before the price goes up. An interesting blog post over at Nature.

A super blog post that talks about and provides examples of the types of titles that you could give your scientific manuscript. Some great ideas here over at The Thesis Whisperer blog!

 

 

Solid Advice on “How to Choose a Good Research Problem”

Running a lab and doing science are hard. I owe thanks to the Twitterverse for directing me to a thoughtful piece written by Uri Alon in 2009 which is still relevant today. The title is “How to choose a good scientific problemand it’s a very quick read, but it articulates very clearly the challenge in selecting scientific problems for yourself and your trainees. He relates that any scientific problem can be mapped out on two axes which are feasibility and interest. He argues that you want to avoid spending time in the quadrant containing problems that are hard and yield a small gain in knowledge. The efforts that you’d have to rustle up in order to solve a problem in that quadrant won’t pay off much. In contrast, putting a new student with little experience on a problem in the quadrant where the project is easy and produces a small gain in knowledge is a smart choice. As trainees gain experience and confidence (e.g. senior graduate students and post-docs), you can move them into solving problems that are a bit more challenging and lead to larger gains in knowledge. I really liked this approach for selecting good problems to work on and how to assign them to particular trainees. I also like his idea of making his trainees “take time”. He makes his trainees wait for 3 months or more before they commit to a particular problem. During this time his trainees read, plan, and question and come up with a solid problem to solve before they dive into research. I also take this approach with my trainees when they first enter the lab and there are certainly times when we both feel that we are wasting time by not producing results immediately. I will make the argument that this initial investment in time pays off in terms of my trainees better understanding their research and being more motivated and engaged in solving their defined problem. The other powerful observation that he makes is contrasting two different schema when it comes to visualizing what the research process looks like. The Scientific Method is taught in classes as a series of linear steps, which I think is wrong. Perhaps because of this false structure, many scientists view research as a series of sequential steps (e.g. that you must go directly from A to B). This leads to a lot of frustration because in my experience research never directly goes from A to B, but meanders all over the place. Alon suggests that it is better to start with a nurturing schema for research that expects that meandering will occur and takes steps to nurture students while they are stuck in “the cloud” (i.e. when everything goes wrong and your assumptions prove to be false). This schema accepts and embraces the possibilities for new research directions and personal and professional growth.

I’m often guilty of biting off more than I can chew with my own research problems, but I try to protect my students as best I can from this tendency. Alon’s short essay has given me some new things to think about and has confirmed some of my conclusions about choosing a good scientific problem that I have made during my first 5 years as the head of a research lab. I recommend reading his piece and seeing if it influences how you choose your future research problems.

 

Doctor Al Digest 10

A wonderful essay on the emotional labour performed by many women in the academy by Margeaux Feldman.

Lecturing is getting a bad rap these days. Some great thoughts by Stephen Heard on the expectations that we should have of our students if we are using lectures in the classroom.

Jeremy Fox has an interesting post up at the Dynamic Ecology blog about the best movies about scientists . I’ve blogged in the past about my impressions of the portrayal of scientists in popular culture here and here.

A great post by Terry at Small Pond Science about the conditions at his institution and how they constrain the type of laboratory that he can run.

An insightful post from Acclamatrix on anger over at Tenure, She Wrote.

Project Management for Scientists

project management notesToday’s topic in my group lab meeting is project management. It took me a long time as a scientist to believe that research projects could actually be managed. I think that I felt this way given the uncertain nature of scientific research; you never know if an experiment will actually work and you often can’t predict in which direction the research will go next. I’ve always been an organized person and it turns out that managing a research project isn’t all that different from other projects that you do in your day to day life such as go grocery shopping, clean out the garage, and plant a vegetable garden. Once I started thinking about science in the same way it’s like a light bulb went on.

I don’t recall ever having explicit conversations with my research mentors and supervisors about project management. That may be because I was fairly productive and am a planner by nature, but these are skills that don’t naturally come to everyone and that can be learned and improved over time. As a purely ridiculous example, I explicitly tell students that they should do something else with their time while PCR is running or they are incubating a sample for an hour. I’d like to think that they know this, but I have heard stories from colleagues, of students who will literally sit there for the duration of the incubation thereby wasting precious time that they could have used doing anything else. It’s like the science equivalent of watching paint dry.

Here are some thoughts on how I approach project management in laboratory science:

1) My first step is to define the project clearly and to determine what success looks like. If you skip this step you’ll never know when the project is done, nor will you know if you did it well. You need to identify the full scope of the work, what resources you’ll need (reagents, people, literature, etc.), and the time that you have available to do it in. Thinking about these limitations up front will decrease the amount of frustration that you and others experience later. At the same time, there is room for flexibility, which I will talk about later.

2) My next step is to think about the major milestones that need to be completed in order for the project to be finished. For even the most basic science experiment this will include things like generation of hypotheses and predictions, experimental design, ordering of reagents, allocation of people, doing the experiments, data collection and analyses, data presentation and communication (i.e. making figures, tables, diagrams, etc.), and generating a manuscript, poster, or talk to communicate your findings. That’s a lot of stuff to complete in order to successfully finish your project! One of the major things that I struggle with is maintaining an interest in projects that span several years of work; I often get bored part way through and struggle with staying motivated to finish.

3) Up next is thinking about the flow of tasks and their relationships to one another in your project. I like to think of the major milestones in a project as parts of a puzzle that need to be put together. When I build puzzles, I always start with the edge pieces first, and then work my way in; this means that the connection of some pieces requires the presence of other pieces first. With your project you want to determine whether some of your milestones are interconnected and have to happen sequentially, or whether some of your milestones are independent and could be worked on in parallel at the same time. For example, if you wanted to clone a particular gene in your critter of interest, you would first want to obtain the DNA sequence from a molecular database, you’d then design and order gene specific primers, you’d then perform PCR with your primers, purify your amplified DNA via gel electrophoresis and a gel extraction kit, clone your DNA product into a plasmid, and sequence the plasmid to ensure that the DNA sequence matched the one in the database. These tasks are sequential and one needs to happen before you move on to the next. Other projects have milestones that could be completed at the same time because one doesn’t depend on the completion of the other. This is also the time to identify what could go wrong. Where might your project go off the rails? Can you come up with a back-up plan to get around the problem should it arise? Can you plan ahead to avoid the problem? Can you ask for help?

4) Now you need to break your project milestones into smaller mini-projects that contain a small number of discrete steps. Ideally, you’d aim to complete a few of the small tasks every day and one of the mini-projects each week in the lab. This will help to keep you motivated as you’ll be able to measure your progress on the project and you will build up lots of little wins and that will keep your mental and emotional state positive.

5) The final step is putting together a timeline for completion. I like to set a deadline that I think is realistic, but I usually add several extra weeks and expect that something will go wrong during the course of the project. I then work backwards from that date when planning my time. I schedule in my major project milestones, my mini-projects, and my smaller tasks at a level of detail that I’m comfortable with. Some projects are tricky and it will be difficult to easily identify all of the mini-projects and small tasks up front. Do your best and don’t get off target because that can lead to project creep where the scope of the project balloons out and doesn’t resemble the scope of what you originally set out to do. You need to be flexible because plans can sometimes change mid-project, but head back up to what you defined in Step 1 if you feel that your project is getting out of control. You’ll often find that you reimagined the scope of the project without really thinking things through because you got excited by a neat result or finding. Think extra hard about whether you really want to commit to expanding the scope or redefining the success of your project before you leap in! That being said, there will be times when you need to retool your plans and timeline due to the unpredictability of lab research, but hopefully because you’ve identified the possible trouble spots in advance (Step 3) this will be minimal.

6) Execute your project management plan. Enter specific tasks and mini-projects in your daily and weekly calendar and set deadlines for your project milestones.

Some great resources:

If you need help with bigger project management concepts, Melanie Nelson’s blog Beyond Managing is great!

If you find that scheduling, prioritizing, and keeping up with your to-do list is a challenge, I recommend reading David Allen’s book “Getting Things Done” . It will change your life – I kid you not!

What tips and resources do you give to your trainees in order to help them manage their research projects?

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!

Research Budgeting for Scientists

Prior to starting my job as an Assistant Professor, I had never managed a professional budget before. I’d certainly managed my personal finances previously, but I’d never before had total oversight of a research budget and been responsible for figuring out how to spend it effectively and ensure that I wasn’t going over budget. This is one of those myriad of skills that you aren’t always exposed to as a graduate student or post-doc, although I do know some colleagues who managed research budgets before starting their faculty positions.

I’m pretty conservative with money and how I manage my funds is informed primarily by two things: I think that shopping around for the best price is a good idea and I like to know what the current balances of my accounts are so that I don’t ever run a deficit. These two approaches have served me well in the first five years of my position.

In my personal life I do not particularly enjoy shopping as an activity. The most frequent type of shopping that I do is grocery shopping and we have recently started to use the app Flipp in order to compare prices any given week and to price match items across different stores. I have transferred this idea to how I do the shopping of consumables and supplies for my lab. Usually several suppliers will offer the same or a comparable product; let’s use the example of 1.5 mL centrifuge tubes. In my lab I prefer the tubes to be clear, to seal well, and to withstand high centrifugation speeds. Taking these specifications into account, there are many suppliers and manufacturers who can provide me with a tube that will do the job. My next step is to figure out the price per unit and see who offers a good product at a reasonable price. For most items I’m willing to shop around and to try a new product, especially if the price point is cheaper than what I have previously been using. One thing to keep an eye on is whether there are shipping and handling charges in play. Often an item will seem less costly, but when you factor in the shipping costs that is no longer the case. I also have to make sure what customs charges apply if I’m importing an item from Europe or the U.S. since I’m in Canada as those charges can add a lot to the cost of an item.

In order to avoid running a deficit it’s important to plan ahead and estimate your future costs and also to have a really good idea of the current funds that you have available. Some costs are easier to project (e.g. student stipends, larger pieces of equipment) while some are more challenging to estimate (e.g. the price of agarose 3 months in the future). I’ve found that it’s been useful to go with higher than expected estimates in order to build a buffer into budgets.

I choose to run my research budget in this way because the vast majority if my research funding comes from Canadian taxpayers and they have a right to expect me to be responsible when it comes to spending those funds. I also refuse to put myself and my students in the position of running out of funds for their stipends as I feel that it is morally wrong and irresponsible. I won’t take on a student if I can’t pay for my portion of their financial support package.

I’d be interested to hear how other faculty do their financial budgeting for their research grants. Please leave your thoughts or advice in the comments!

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!

The Power of the Label maker

One characteristic that is very valuable to have as a tenure-track academic is excellent organizational skills. This job makes multiple demands on your time and is a real juggling act; keeping all of those balls up in the air at the same time is tricky business. I have found that it is very worth my while to discover and invest in tools that help me to maintain order in the face of chaos.

One tool that I have found to be indispensable is the label maker. I kid you not! Label makers have come a long way since the models of my youth. I remember vividly using archaic models with the alphabet dial on the top that worked by punching letter imprints into hard plastic. Very clunky- but strangely satisfying.

The current brand that I use is by Dymo and is their middle of the range model. I like it because you can purchase a wide variety of tape types (e.g. paper, plastic, etc.), and colours. I find the base model to be a bit clunky and the top of the line model has bells and whistles that I don’t need. Refill tapes are widely available and reasonably priced.

My colleagues seem puzzled by my love for the label maker and I’ve been the subject of gentle mocking for this proclivity. However, if you read any good productivity book or guide you will see that the label maker features prominently as a must have tool. On a day to day basis I use my label maker to label file folders. Although the bulk of my work occurs electronically, I still require paper file folders to keep track of invoices, budgets, project plans, notes from student meetings, teaching materials, grant applications, etc. A label maker allows me to label these files cleanly and professionally and makes them easy to find and identify in my filing cabinets. The label maker has also come in handy in the lab. When I first moved into the lab and organized it I labelled all the drawers with content labels. This helps me to remember where all of the gel electrophoresis equipment is stored, but has also helped to familiarize my students to the lab and has trained them to properly put away equipment. This saves time and money. If you don’t already have one, invest in a label maker; you’ll be glad that you did.