Saving your Research Ca$h in the Lab

Cost and benefit analysis. 

Its very simple. In biochemical and biomedical research labs we have space, equipment (pH Meters, centrifuges, PCR machines, pipettors and more), shelf chemicals (dry and liquids), biochemicals (proteins, enzymes, metabolites, DNA, RNA), bacteria, mammalian cells, culture media, and people (students, staff, research assistants).

In the academic research environment, as a Primary Investigator  (PI) and a Professor, we have to write grant applications to government agencies (NIH, CDC, NSF) and private foundations to get the cash that will buy everything listed above and also to pay our assistants and payed student research assistants, and sometimes to pay a large hunk of our own academic year salary. (Most professors at Universities get paid based on 8 months, Sept to May, which is the “academic salary”. Any pay for working during the summer usually has to be obtained from a research grant, and if there is not enough cash for that then we work during the summer too, for free.)

The ability to collect results, solve research questions, train students to be the next generation of scientists and physicians, is directly impacted by how far we can stretch our funds. In the end it all comes from the same pot of money we have managed to convince an agency to give to us. So its important, especially if you are a new assistant professor, to spend your money wisely. Wisely does not necessarily mean purchase the cheapest option on its face value. That can be a mistake that leaves your research dead in the water too.

My advice: spreadsheets. Use them. Everything you do in the lab involves five things usually:

  1. space.
  2. person power (hours and wages/hr)
  3. equipment
  4. chemicals
  5. labwares (tubes, pipettes, tips, dishes etc)

Each of those five items in the list has a cost associated with it. So use a spread sheet to compare alternative methods and processes. Sometimes you will be able to consider doing a process in-house or out of house.

Need a new antibody that you want made to a specific amino acid sequence from a protein? You do that in the 2000’s by having a company make it for you. They make the epitope, inject the rabbits, collects the serum and purify the IgG antibody to your target of interest all for about $1200. If you do that yourself, you will spend several thousands of $$ in time and reagents and rabbits to make the same product. So, antibodies you make with a commercial provider. That is an obvious example of a cost benefit analysis in your research.

Sometimes the cost benefit is not that obvious.

Real time PCR is an example. My lab is expert at gene expression analysis, very accurately, using real time PCR. Investigators at my University and from other universities, have asked me to guide them as they started to measure expression of their gene of interest in their systems of study. These days I would recommend using Taqman probe chemistry and an endogenous control probe set. What that means is not important for this discussion, but suffice to say that it is true that Taqman chemistry appears to look a bit more costly than the method just based on Sybr-Green. Sybr-green just adds a dye to almost any PCR reaction, and technically one can get some cheaper PCR reagents to do this method. Seems cheaper, and many labs will go for the Sybr-green option regardless of my advice. I know that in the end the Taqman probe method saves money compared to Sybr-Green. Why? Simple. While each individual reaction is a bit more costly in Taqman chemistry versus Sybr-Green, Taqman chemistry allows running an endogenous normalizer control in the SAME reaction tube. Thus we can set up half as many tubes as using the Sybr-Green method. In the later, a separate reaction must be done for the gene of interest and the normalizer gene. Futhermore, there are data quality issues to consider. Sybr-green will pick up undesired PCR products, “false positive signals”, and the reaction conditions will then have to be adjusted and the experiment repeated entirely. Taqman chemistry does not suffer that problem, and the chemistry is also very specific to specific mRNAs expression from genes. Thus we rarely need to repeat an analysis for failure reasons. That saves money.

“Garbage in, garbage out” is important.

You can save lots of money by spending less of it on an experiment, but if you get garbage out for data, you just have garbage. No results. Eventually you can burn through your pile of research cash, processing a lot of garbage while thinking you are saving money. So for experiments, think about the quality of data you need in the end. Better quality data is better data to publish, period. Its easier for reviewers to evaluate for conclusions.

Another place to save money is software for data processing.

Most computational tools available start out free, from academic researchers and professors. Then companies make programs with the same programming methods, add more graphical user interface and sell it back to researchers for hundreds or thousands of dollars. Graphing and curve fitting software for one example. However, if you take a little time here and there and experiment, you can actually find many software solutions that are free and shared. For dose curve fitting, as an example, you can get a very powerful stats environment called “R”. There is a dose curve fitting package you get which runs in the R system, called “drc”.

The R-project can replace SPSS, very expensive statistical tools software, and is now used in all fields of research from sociology to genome-wide association studies to dose curve fitting. You have to install a few packages yourself (on a Mac, we use Macs), but the installer packages do the work, and you have to get used to typing some terminal command line instructions. But what you get out is advanced high quality data fitting. You have the benefit of saving funds, to pay more students, who need tuition money badly and everyone is a winner. Even your granting agency enjoys seeing you get more bang for their buck.

MyCurveFit.com  is a nice tool, web interface with an excell plug in optional, for free occasional fitting of your dose response data. However, they limit how many fits and much data points you can fit in their free version. Taking off those limits requires a monthly subscription.

Better Curve Fitting , more options, free, but you need to type more:

R-project https://www.r-project.org/ and drc package

If you are a biology lab and want to just fit dose response curves, email me, I can point you to the packages to download and install and how to fit your own data from an excel spread sheet.  mitton@oakland.edu

 

Listen to Hour 1 of Science Friday: News Roundup, Plastic Clothing, Canine Communication, Lucy

Hr1: News Roundup, Plastic Clothing, Canine Communication, Lucy
Science Friday

http://www.sciencefriday.com/podcast-download/34747/hr1-news-roundup-plastic-clothing-canine-communication-lucy.mp3

How anthropologists peer inside scarce, ancient fossil bones to find clues about our evolutionary history. Plus, how dogs pick up on our tones, gestures, and moods.

Subscribe the podcast http://www.npr.org/rss/podcast.php?id=510221

—-
I use this Ap on Android to listen to podcasts like Science Friday:

Public Radio & Podcast 2.14.3

https://play.google.com/store/apps/details?id=com.nprpodcastplayer.app

Its science Friday every Friday in the Mitton lab.

Predatory Publisher Exploits Einstein, Debases Science

Another weekly informative post on another predatory junk publisher. From the Scholarly Open Access blog.

Scholarly Open Access

Relatively awful Relatively awful

A new, India-based predatory publisher has emerged — Einstein International Journal Organization. The publisher gratuitously uses the name of one of one of history’s greatest scientists to attract manuscripts and author fees from unwary researchers for its nine anti-journals.

View original post 380 more words

Info Sports Navigator #Rio2016 and more.

Want a tiny #sports info App that does NOT have banner Ads? #Rio2016 & more. World Sports Navigator on Google Play! https://t.co/UrI4mb14IO

Share this post with more networks:
http://ow.ly/5JFp100hCtw

Made by Dr Mitton. Its free. #Android

OU students focus on eye diseases during summer research program

Our SUPER program is getting lots of kind coverage in the media this summer for which we are thankful.
To:

Automation Alley
Rochester Patch
Rochester Media

Thank YOU…

Good stuff is happening here in Michigan in an Eye Research Institute that is one of the few and oldest doing NIH-funded basic science outside of a faculty of medicine. In addition to the National Eye Institute (NEI) at the NIH, we also benefit from support of a Michigan based private foundation: Vision Research ROPARD Foundation.

Our faculty have to write excellent grant applications that convince peer reviewers to give us money from the same funding pie being snacked on by much larger universities, even though we are a smaller university without the core support facilities that enable research at larger schools.

That makes a good faculty mentor to teach students ,future colleagues, in biomedical research.

Our students will not pay us back, just as we never had to pay back our mentors. They will do what we do now, paying forward to teach a next generation and we expect them to mentor at least seven students in their future careers no matter what their future jobs are.

That is how academic scholarship goes. That is ultimately the most important thing our faculty do here at Oakland University, which is congruent with the philosophy of the American Association of University Professors. We teach students to become lifelong independent problem solvers, self taught students and teachers of the future. That is how things are gradually changed for the better.

http://www.automationalley.com/News/PressReleases/Release-Detail.aspx?releaseid=24171

http://patch.com/michigan/rochester/6-oakland-university-students-spent-summer-saving-your-eyesight

http://www.rochestermedia.com/ou-to-host-student-symposium-on-eye-research-july-29/

Watch “Solar Impulse – Best of First Round-the-World Solar Flight, Crossing the USA” on YouTube

I am an educator of future scientists and researchers while we carry out biomedical research. So…

Our laboratory has sponsored a wing solar-cell on this aircraft. The sponsorship funding fuels an educational foundation at the SolarImpulse group that has already produced written and video resources for teachers around the world. Topics include: energy, solar energy, zero emissions concepts, battery chemistry and the use of advanced engineering technologies.

You can sponsor a solar cell too at solarimpulse.com

Watch a video on the Atlantic crossing here:

Https://youtu.be/E_POEC6PXEA