Types of calculations to know for a research lab

[Violagirl]

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Starting this week, I will be involved with volunteering as an undergraduate student in a biomedical research facility. I will be helping out the postdoc around the lab on a project that he is currently working on and I will be primarily involved with helping out with basic tasks around the lab (making reagents, taking care of the mice in the lab, etc.) I have not done research before outside of the classroom and am nervous about what to expect, especially with making reagents. I don't much confidence when it comes to working in the lab as I had a few not so great moments in taking biology and O Chem lab last year.

For anyone that's done research, I had a question about making reagents or any other types of calculations that would be good to know. I know dilution calculations are important. Are there any other types of common calculations used that would be good to review? Thanks to anyone that reads through this.

 

[kami333]

(C1) X (V1) = (C2) X (V2)

Mass molarity calculator

Primer calculator

RCF calculator

Most reagent/stock solution recipes are easily found via google.

 

[Praefectus]

If you're writing a paper based on this research, knowing how to do stat tests (p<0.05) can help.

 

[sankri92]

Pretty much C1V1 = C2V2. Anything else you can look up online. What's more important than memorizing equations is having presence of mind. Try not go to work sleep deprived and grumpy. You will make alot of mistakes. Come well prepared and try to run the whole experiment in your head before beginning.
I work in a Pharmacology lab.

 

[DAPI]

Figure out how to accurately plate the number of cells you want if you're doing TC. There are several ways to calculate this, but ask your post doc how he does it and just follow that probably.

 

[benzonase]

Know how to interconvert between metric units and calculate dilutions in your head inside out and backwards and youll be set

probably the one thing you definitely do multiple times every day for forever 😛

 

[OCDOCDOCD]

This differs wildly depending on the project you do. If you do electrophysiology expect to get well acquainted with the Nernst equation. If you do population modeling you better be comfortable with Eigenvectors. If you work in a typical bio lab though it's unlikely you need to know much more than how to make dilutions.

 

[MonkeyDRuffy]

It varies depending on your duties in the lab. Basic statistics (t-test, correlations) can be useful. I'd say equations and calculations you learned in first year Chemistry are probably going to be used. I would suggest asking your Postdoc for types of calculations that would be useful to know for this lab.

 

[Guero]

For trouble shooting, keep in mind that many alternate protocols (e.g., blots, staining, and for you, protein purifications) are available on the web, even in Wikipedia, and can often resolve problems by answering the same question from an alternate route.

All stoichiometric calculations are helpful, but only those relevant to your project and protocols are essential to know by heart.

Always be kind to your lab mates, clean up after yourself, return your equipment when you're done, and offer to help others during some of your downtime. You'd be amazed at how that help will be reciprocated when you're watching a zombie blot crawl out of the developer at 10pm on a 12 hour Saturday. That is, they'll be much more likely to go out of their way to help you (and buy you beers at get togethers) if you're generous. 🙂

I've spent nearly 3 years volunteering in a molecular neurotrafficking lab and have made life-long friends and landed authorship. I'll always have contacts, colleagues, and collaborators here, even in other labs. Granted, not every lab is as welcoming and tight knit as the one I fell into, but it's worth the effort to see if you can make those lasting relationships and connections.

Feel free to PM me w/specific questions. I love teaching and offering advice. Good luck!

 

[FirstAndFinal]

Don't worry about knowing everything before you start. What you should do is take notes while in lab and really focus when someone is teaching you something. If anything is confusing ask right then and there. Be clear on what is expected of you. Really, someone who seems very focused is what labs appreciate. They know you will not know everything and can make a mistake sometimes but if they see you are earnest in doing your best they are much more forgiving and will look upon you favorably.

Things to avoid: coming in late, not cleaning up after yourself, not taking notes, being a klutz, obviously prioritizing everything in your schedule ahead of the research, talking about how you don't really like their project, asking for an explanation of the same task every time you are assigned it because you have no notes, etc.

Also, if you know you need to write a paper about the research at the end of the semester get a lot of your questions answered as you go. You will look really foolish if after 3 -4months of being there you're preparing to write your paper and you're asking questions like, "So what's the main goal of this experiment? What is the liquid that I've been injecting in the mice? What's the control that I've been injecting? Why did I do XYZ task?"

 

[Violagirl]

Thanks so much to everyone that responded! It was really helpful for reviewing some of the calculations you mentioned before starting on Tuesday! It's looking like I'll just need to be able to convert between units and calculating dilutions for now. Otherwise, thanks a lot for the advise as well, it helps a lot to know that they don't typically expect you to know what you're doing right off the bat.

 

[chillaxbro]

No offense but you seem like a really ditzy girl. Try not to screw up the poor guy's experiments.

 

[Guero]

No offense but you seem like a really ditzy girl. Try not to screw up the poor guy's experiments.

That was uncalled for.

 

[BlueLabel]

That was uncalled for.

Agree. What a jerk.

 

[Bodysurfer]

M1V1 = M2V2 or similar such as [conc 1]*V1 = [conc 2]*V2 as mentioned below is used so much in the lab:

Also in western blotting, a lot of the time you'll have to dilute the stock antibody solution. For example, 1:2000 was used a lot in my lab and the stock solution is assigned a concentration of 1

Ex

(1) * X microliters = (1/2000) * 9 microliters

 

[Violagirl]

No offense but you seem like a really ditzy girl. Try not to screw up the poor guy's experiments.

I found this comment to be rude. I have not been involved with research before and wanted to post this thread to be as best prepared as possible.

 

[Violagirl]

M1V1 = M2V2 or similar such as [conc 1]*V1 = [conc 2]*V2 as mentioned below is used so much in the lab:

Also in western blotting, a lot of the time you'll have to dilute the stock antibody solution. For example, 1:2000 was used a lot in my lab and the stock solution is assigned a concentration of 1

Ex

(1) * X microliters = (1/2000) * 9 microliters

That is really nice to know actually and one of the techniques used in my lab. Thanks! 🙂

 

[Benedictus123]

nthing the "C1V1=C2V2." It's amazing how many times people claim they understand this, but then need a lot of help with calculating concentrations as soon as they have to do it by themselves. Also understand how to calculate averages, standard deviations, standard errors, and how to do a t-test and interpret the results. More complicated statistics (like ANOVA) are probably something you can leave to your mentor.

But honestly, it's sort of silly to ask. There are thousands of 'equations' that represent various physical phenomena, not to mention statistical techniques and other mathematical functions (like the aforementioned eigenvectos/values) that may or may not be relevant to your research.

 

[Violagirl]

nthing the "C1V1=C2V2." It's amazing how many times people claim they understand this, but then need a lot of help with calculating concentrations as soon as they have to do it by themselves. Also understand how to calculate averages, standard deviations, standard errors, and how to do a t-test and interpret the results. More complicated statistics (like ANOVA) are probably something you can leave to your mentor.

But honestly, it's sort of silly to ask. There are thousands of 'equations' that represent various physical phenomena, not to mention statistical techniques and other mathematical functions (like the aforementioned eigenvectos/values) that may or may not be relevant to your research.

Yeah, I figured it would probably seem silly to ask but I felt it would be relevant to get some sort of perspective on what equations/calculations are normally used in research from what you learn in your typical chemistry and biology courses.

Thanks for the information on the statistical calculations, I will definitely keep those in mind. 🙂

 

[Ruminate]

Can you be more specific on what that lab does? Protein?RNA?DNA?Any cell line work or bioinformatics? If you want to get some more out of the lab, then I'd try and get a feel for it. You can help out with the maintenance, but I'd suggest you try and work on a main project. Don't use up all your volunteering time by just answering to someone.

Main things to know for maintenance:
1. Dilutions/Serial Dilutions (esp. for making stocks and aliquots, protein work, running gels)
2. Percentages (eg 2% secondary antibody)
3. Logarithms... (Data analysis, pH)

Essentially, basic algebra is super important for all labs. Then, depending on what work your lab does, you can add some more skills. If you go into a kinetics lab, then maybe some basic calculus would be helpful (ie integrals). If it's a physiology lab, then physics would be helpful (ie electricity manipulation, force dynamics, fluid dynamics). etc

Really useful:
1. Microsoft Office (not just the basics. Be proficient.) If you take care of the mice, there probably will be a running tally of mice used/available. Use Microsoft Access and not Excel..
2. 1 program to do data analysis which is not Excel...Don't waste 50 hours going through cell by cell making calculations like many people in science do... If you do this, you will receive all sorts of goodies because you will blow people away (esp in a non-computer oriented lab). For example, SASS, SigmaPlot. The BEST thing would be to learn Matlab and you can do everything on there.
3. 1 computer programming language. For example, Pearl or python. These are helpful since you can write a few lines of code to give you much faster and more output. A script in pearl can running through your Excel file and give you some computational data (mean, etc) by just running the program... rather you sitting there doing =average() and whatnot. Matlab is powerful to do all these things as well.

 

[Benedictus123]

For example, SASS, SigmaPlot. The BEST thing would be to learn Matlab and you can do everything on there.
3. 1 computer programming

Prism is my program of choice for modeling or stats. MATLAB is baller too, ODE45 has saved me many times.

 

[chillaxbro]

I found this comment to be rude. I have not been involved with research before and wanted to post this thread to be as best prepared as possible.

Making dilutions? Really? That's literally high school level stuff. Have you taken intro bio or chemistry labs? I can't imagine anyone taking in an undergraduate who hasn't at least done intro lab courses. 😕

It's good to know that you're trying to be prepared though, keep it up.

 

[Ruminate]

You'd be surprised how many don't know how to make a simple 1:20 serial dilution...and know the final concentration... or know what final concentration you have on a protein assay. Or making master mixes.

 

[Guero]

Prism is my program of choice for modeling or stats. MATLAB is baller too, ODE45 has saved me many times.

Yup, love me some PRISM and ImageJ. One of my main contributions to my lab was figuring out how to do a quick ImageJ-assisted count of DAT and NET terminals post-stain. It was awesome. There's nothing quite like doing a lab presentation to teach the entire lab your method. I was on cloud 9 that day.

 

[Violagirl]

Can you be more specific on what that lab does? Protein?RNA?DNA?Any cell line work or bioinformatics? If you want to get some more out of the lab, then I'd try and get a feel for it. You can help out with the maintenance, but I'd suggest you try and work on a main project. Don't use up all your volunteering time by just answering to someone.

Main things to know for maintenance:
1. Dilutions/Serial Dilutions (esp. for making stocks and aliquots, protein work, running gels)
2. Percentages (eg 2% secondary antibody)
3. Logarithms... (Data analysis, pH)

Essentially, basic algebra is super important for all labs. Then, depending on what work your lab does, you can add some more skills. If you go into a kinetics lab, then maybe some basic calculus would be helpful (ie integrals). If it's a physiology lab, then physics would be helpful (ie electricity manipulation, force dynamics, fluid dynamics). etc

Really useful:
1. Microsoft Office (not just the basics. Be proficient.) If you take care of the mice, there probably will be a running tally of mice used/available. Use Microsoft Access and not Excel..
2. 1 program to do data analysis which is not Excel...Don't waste 50 hours going through cell by cell making calculations like many people in science do... If you do this, you will receive all sorts of goodies because you will blow people away (esp in a non-computer oriented lab). For example, SASS, SigmaPlot. The BEST thing would be to learn Matlab and you can do everything on there.
3. 1 computer programming language. For example, Pearl or python. These are helpful since you can write a few lines of code to give you much faster and more output. A script in pearl can running through your Excel file and give you some computational data (mean, etc) by just running the program... rather you sitting there doing =average() and whatnot. Matlab is powerful to do all these things as well.

The lab involves studying the effects of Tcells and Bcells for different autoimmune diseases. From what I know so far, I'll be helping out the postdoc on a project that involves studying the effects of autoimmune diabetes in mice through a few different models that involve analyzing T cells containing more than one receptor to determine if/how that the additional receptor recognizes self antigens. I know a bunch of it will involve watching/taking care of the mice with the specific genomic features that they are breeding to eventually obtain the generation of mice needed to next analyze the T cells that they want to study.

Thanks for the information! Especially on making contributions to the software, that's something I'll keep in mind to ask about to see how/or if they use anything specific to keep track of data.

Making dilutions? Really? That's literally high school level stuff. Have you taken intro bio or chemistry labs? I can't imagine anyone taking in an undergraduate who hasn't at least done intro lab courses. 😕

It's good to know that you're trying to be prepared though, keep it up.

My first few intro bio and gen chem courses were taken at a community college so a lot of we did involved cook-book like labs and nothing involved with research. Upon transferring to a university, I think I was unaware of what specific research protocols were used in actually research facilities. I think I was primarily confused and nervous on how much of what we did in the intro science classes were done in a research lab and to what extent. Thanks a lot though!

 

[myronnie]

Hmm..how to convert using the metric system..and how to use a pipet..
I seriously have to give side eyes to undergrads who ask me if they can use a .5-1uL pipet to pipet 1000uL....
Just pay attention and try to learn the most you can! Do some outside research and try to ask intelligent questions.. and if you don't know what to do ALWAYS ask because you wouldn't want to hurt yourself or hurt someone else 🙂

 

[911 Turbo]

I'd have a basic understanding of vector calculus and orbital mechanics before I step into any biology/chemistry lab... I wouldn't want to embarrass myself!

 

[Violagirl]

Hmm..how to convert using the metric system..and how to use a pipet..
I seriously have to give side eyes to undergrads who ask me if they can use a .5-1uL pipet to pipet 1000uL....
Just pay attention and try to learn the most you can! Do some outside research and try to ask intelligent questions.. and if you don't know what to do ALWAYS ask because you wouldn't want to hurt yourself or hurt someone else 🙂

Haha, I actually did see other students in intro to bio labs have that issue, I know micropippettes can be confusing to others if they haven't had much experience with them. 😛 And thanks a lot, I think a big part it too is the transition into it and figuring where and how different things work but most definitely will.

I'd have a basic understanding of vector calculus and orbital mechanics before I step into any biology/chemistry lab... I wouldn't want to embarrass myself!

Haha, nooo, can't have that.