Best products from r/labrats

I use 3:

• Zebra F701 I love this pen. It's $5, is near-100% steel, has a click that is very quiet, has an incredible pocket clip, has great filing near the tip for grip. The entire thing comes apart, and you can tinker with it or take it apart/rebuild it as much as you like. I like the way they write - not too heavy, not too light. They leave a very small mark on the other side of notebook pages, but compared to some gel pens like the Pilot G2, it's nowhere near as bad. The ink cartridges are disposable, but you can buy replacements online. They last a very long time. Over the past 4 years, I've carried and used this pen all day, 5 days of the week. So far, I've gone through 3 (Most still work, but have some aspect of them that is broken, such as the threading wearing from excessive fidgeting or something). It's also worth noting that I have a habit of spinning my pens and fidgeting with them, so there's a huge increase on the frequency that i drop/slam my pens into the ground and the amount of wear-and-tear the threading experiences compared to a regular user. The pen itself, by the way, feels incredible - not just as in how it feels physically (very smooth), but I like the weight distribution for spinning it.
  
  
• Pentel Graphgear 500: This is the pencil I use. It's about $6, and comes in 0.3mm, 0.5mm, 0.7mm, and 0.9mm versions. If you buy bulk (~8 pencils, I think?) you can save a couple dollars per pencil. I prefer pens to pencils, but when I need a pencil, I always go with this. It's pretty standard for mechanical pencils, but one neat feature is the eraser - the eraser is not exposed on the back, there's a cover that you must remove to access it. This is something I really like - it makes the pencil look nicer, and you aren't pressing on an eraser to get more lead out the front. You can buy replacement erasers, for when it runs out. Note that this pencil is a bit front-heavy (the front is metal, while the back/center is lightweight plastic), and that the tip is a tad bit sharp (comes in handy for opening plastic packages, but I've never had it stab me by mistake). My #1 issue with this pen is that the pocket clip tends to come loose and fall off after awhile - this is a big issue for me, because I carry my pens/pencils in my pocket. Because of this, I'm considering other pencils, or maybe finding some way to hot-glue the pocket clip on? It's a shame, because I otherwise love this pencil.
  
  
• Pilot G2. This is a pen, you can buy a dozen for $1 each. It's gel, and writes bold. I use this when I want to write in bold. I also use this when I write a full page of equations in regular pen, then have space on the sides that I want to use- the bold nature helps separate it from the other equations on the page. This is the pen that I keep as backup for if my main pen somehow fails, and it's the pen that I let other people borrow (since so often we both forget to return it / get the pen back).
  
  I also have a fisher space pen. It's cool, but I find it is kind of small and easy to lose, so I just keep it at home and only use it at my desk.

Like the other comment mentioned, I have a notebook that is “my thoughts” basically. It goes where I go. It has random calculations, notes from meetings, notes from seminars, notes of things I want to remember to come back to later, etc. It houses all the stuff that I know I want to have written down, but doesn’t belong in my lab notes or book/article notes.

Books and articles I have on the computer and in some notebooks. I am not too picky on that.

My lab notebook is a little more structured. I use this one and I used to use this one
I really enjoy both. I only stopped using the national brand one because it is not hardback and I am just too rough on it.

When in the lab I do take my lab notebook and my other notebook that is just my thoughts so I have somewhere to write down other stuff without clouding the lab notes.
I feel like clear lab notes are important in the event I ever need to hand an undergrad my notes and tell them to figure it out. I am fortunate to be in a lab with 6 super awesome undergrads that have their shit together better than any others I have seen, but still. Good clear notes go a long long way.

I don't think this is exactly what you're looking for, but At The Bench - A Laboratory Navigator has a 10-page chapter about keeping a lab notebook.

Here's a brief Google Books preview; unfortunately it does not cover the relevant chapter.

This presentation(PDF link) cites a book called Writing the Laboratory Notebook by Howard Kanare, which (based on the Amazon reviews) might be more geared towards industry labs but could still be pretty useful in a general sense. You can find out for yourself, since I managed to find a full text copy online(PDF link). I don't think I'm accessing this through any proxies, so it does seem like it's freely available.

For a more thorough investigation of what's out there, you should consult your institution's library; I'm sure someone will be happy to help track down the exact book you are thinking of, or something functionally equivalent.

edit - here's a PDF link to another presentation, just for fun

I have experience with MEGA to generate trees. I agree that it's a clunky software, but once you understand how to use it, it's not so bad.

I recommend the following book if you want to become a MEGA power-user: https://www.amazon.com/Phylogenetic-Trees-Made-Easy-Manual/dp/0878936068


Before you start... you say you are looking at the protein sequences. Are you starting with the amino acid sequence or the mRNA sequence? If mRNA, make sure all sequences are in the same orientation (ATG/start on the 5' end of the sequence). I find that if you have just one or two sequences that have been copied in the reverse direction, the alignment may not work. You can also save multiple alignments -- try some with seemingly more conserved sequences (less gaps) and try the entire set.

Once you have all your sequences in one FASTA file or multiple FASTA files, import them into MEGA. From the 'Align' menu, choose to edit/build an alignment. Add your sequences. Select all sequences for alignment and then align selected (you can get into some advanced settings here, change the alignment algorithm, etc.) Save the alignment as a .mas file and export as a .meg file.

Now, open your .meg file in MEGA's main window. From the phylogeny menu, select to build a neighbor joining tree. Based on the alignment, the program will auto-build a tree for you. Again, lots of functionality exists in the program, but it's not an intuitive UI.

Happy to help if you have other questions!

I've worked with gelatin (Also 300 bloom Type A)! I've mostly worked with transglutaminase crosslinked gelatin though, because normal gelatin liquefies at 37C and I used the gelatin for mammalian cell culture.

To make my gelatin solutions (without transglutaminase) I dissolved the gelatin at 65C in PBS, but water/cell culture media should work fine. I noticed that I had to keep the solvent quite hot for the gelatin to dissolve well. My lab notebook notes say that going below 65C made the gelatin dissolve a lot slower, but YMMV.

I've gone up to 25% w/v gelatin. However, the max I'd be comfortable working with is 15% w/v. Even at 20% the gelatin is quite viscous and hard to work with, it gels fairly quickly once you take it out from a 37C environment into room temperature. (My room can get a bit cold though) Note: Higher w/v = faster gel time and more solid gel (i.e higher compressive modulus)

The actual w/v you should use depends on your application I guess. Do you want to set it on the fabric and not have any go through? If so maybe a higher w/v might be better (15-20%?). You could also just let whatever w/v gelatin solution you have cool and pour it right before it gets cold enough to gel though.

With regards to your last point: Well you said that the technique involves setting gelatin on the fabric... so I'm guessing you should let the gelatin set first?

Tip: I bought a cheap coffee cup warmer and set it to 37-40C to keep my gelatin from solidifying in the cell culture hood, until I needed it to.

What is your budget? You can sometimes find these at outlet prices, and they of course work great as safety glasses and fit incredibly well:

https://www.amazon.com/Oakley-Mens-M-Frame-Sunglasses/dp/B002EL3122

>Tested and qualified as true safety glasses, this lens/frame combination meets all ANSI Z87.1 standards for clarity and impact resistance, as well as the protection criteria of Canada’s CSA Z94.3-02 standards.

I have a pair on right now that are very similar to these and I think it would be pretty doable to dress them up with dress pants. I have another pair of shoes that are nice to dress up that looks like these.

The pair I have that look like the first shoes I got from Rack Room (brand is Xappeal), and the second pair I got at Payless (brand American Eagle). I bought them ~5 years ago. I would suggest going to shoe stores and asking a worker if they have anything like that. It might pay off to go to a retail store like JCPenny or Macy's because they'll definitely have some more professional flat shoes too. I hope this helps a little!

Might I recommend the late Jim Pawley's excellent and comprehensive Handbook of Biological Confocal Microscopy?

Handbook of Biological Confocal Microscopy https://www.amazon.com/dp/038725921X/ref=cm_sw_r_cp_apa_i_odTYCbAS6N4TN

The Nikon microscopy U sites are good basic primers. I would also recommend getting to know the staff at your friendly local core facility who can help guide you on specific questions.

Good for you!

Here are some beginner tutorials written by students at my work
https://ourcodingclub.github.io/tutorials/

Also this book is excellent!

https://www.amazon.co.uk/Getting-Started-R-Introduction-Biologists/dp/0199601623

Try to learn ggplot2, it's easier than the standard graphics

ANOVA is built into R but I you'll need to run an ANOVA on a linear or generalised linear model. It's covered in the tutorials I linked.

For example (this won't run it's just an example of code)

Model1 = lm(height ~ sex, data = datafile)

Null.model = lm(height ~ 1, data = datafile)

Model.test = anova(Model1, Null.model, test = "Chisq")

Summary(Model.test)



For a graph it depends on how your data is laid out but you could feed it raw data and plot the means with error bars in ggplot2 with stat_summary like so

ggplot(data = datafile, aes(x=sex, y=height, colour=sex))+

stat_summary(geom="bar", fun.y=mean, position=position_dodge(width=0.95))+

stat_summary(fun.data=mean_se,position=position_dodge(0.95),geom="errorbar")

Hope that helps.


Don't be put off, learning r will make future stuff so much easier. I barely touch excel now

I personally own several aquariums and I love using these when I go on vacation. I have gone up to 2 weeks and came back with it having at least 20% full on a 75 gallon. Of course I wouldn't advise leaving research animals unattended that long!

https://www.amazon.com/Everyday-Feeder-Programmable-Automatic-Dispenser/dp/B001F2117I/ref=sr_1_1?ie=UTF8&qid=1483475753&sr=8-1&keywords=automatic+fish+feeder+eheim

Things I like about it,

1. Battery lasts forever, I mean I have never had to replace it and I've used it for up to 1 year with a 3 times a day feeding cycle.
   
   
2. The reservoir can hold tons of food. I use flakes as well.
   
   
3. It is highly programmable to how you want.
   
   Potential Issues,
   
   
4. I have ran issues where the hatch slowly opens as time goes on and can eventually dump too much food into the tank.
   a) I taped the hatch to the desired width and haven't had issues since.
   
   
5. I do not know if it will fit onto the type of containment you are using.
   
   
6. It may not the cost effective depending on the amount of tanks.
   
   
7. You cannot really control how much food it dispenses each time.
   
   
   Good luck!

EarlierIFU by leaving my entire rack of enzyme aliquots out on my benchtop for several hours. :/ THIS IS WHAT HAPPENS WHEN YOU GIVE ME TWENTY-ONE EXTRACTIONS AT ONCE, WAUGH. Why did I feel the need to take the whole rack out of the freezer while I did math??

Not gonna lie, I am going to try and reuse them anyway just to see what happens, which I know will be a big ol' nada. (And will make more so I can actually have ones that... you know... work. I'm not that irresponsible!)

I did get my totally legit lab notebook today, though. It's this one, and I love it, and even the documentation guy had to agree that it fulfills all the requirements he built into the record system. Yessssss.

Next week someone from Japan is coming to "help me out" in my lab. I can't decide if it's because they think I can't do my instrumentation, or if they're realizing that I am a bit overwhelmed when I am doing three peoples' jobs. Hopefully the latter... and hopefully we can figure out what the other is trying to do, since his English is iffy and my Japanese is non-existent.

Thanks for the reply!! I read this yesterday and it honestly helped me to get motivated. I bought these gloves from amazon: https://www.amazon.com/NoCry-Cut-Resistant-Gloves-Performance/dp/B00IVM1TKO/ref=sr_1_1?ie=UTF8&qid=1504298736&sr=8-1&keywords=cut+free+glove
and they worked amazing! I wore them today and the bites didn't hurt:)

https://www.amazon.com/gp/product/B005QRWEBK/ref=oh_aui_search_detailpage?ie=UTF8&psc=1

I like this one (use it in my kitchen). Super easy to clean, reliable, compact, and pretty cheap. I would buy one for lab work if I needed to. It is only accurate to 1 g measurements, though. Not sure if that will work for new/used cigarettes.

Good books:

Algorithms to Live By: The Computer Science of Human Decisions | Brian Christian and Tom Griffiths

Brand Perrimon 1993

Fire Mello 1998

Beautiful essay

Behave by Robert Sapolsky

https://www.amazon.com/Billion-Dollar-Molecule-Companys-Perfect/dp/0671510576

The Immortal Life of Henrietta Lacks

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Science fiction:

Asimmov:

I robot

The foundation trilogy

Dune | Hibbert

Flatworld

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Self help:

​

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Online resources:

bitesizebio.com

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Great articles:

http://www.pgbovine.net/PhD-memoir.htm

https://blog.regehr.org/archives/743

https://www.amazon.com/At-Bench-Laboratory-Navigator-Updated/dp/0879697083
Is a really good start - it also covers more "big picture" items about working in a lab, like etiquette and safety.

Very highly recommend https://www.amazon.com/At-Bench-Laboratory-Navigator-Updated/dp/0879697083. In grad school, we kept a copy in the lab and gave specific readings to new lab members. It's a super-friendly and pragmatic book, targeted to readers in exactly your situation.

But no book will resolve all the contradictory lab folklore, the field has lots of history and habitual behavior. Many researchers believe that if a particular protocol consistently works, then it's good because it eliminates a source of uncertainty. That doesn't make it the optimal protocol, but because so much of experimental science is eliminating sources of uncertainty, it's a perfectly reasonable opinion.

Plastic? Just use a Hole Saw like the ones plumbers and electricians use to cut holes in junction boxes etc.
Here's an example:

https://www.amazon.com/LENOX-Tools-Bi-Metal-Arbored-Technology/dp/B0052EC44Y


Lenox and Milwaukee are the best brands, but, if you don't need it for "production" levels, other outfits sell far cheaper ones, like Harbor Freight.

Love your cupcakes! My husband got me the cookie cutters. He either found them on Amazon (https://www.amazon.com/ComputerGear-Science-Lab-Cookie-Cutter/dp/B00F0YDOMM) or think geek may have had them at the time. The petridish is just a circle biscuit cutter.

There are a couple products that basically hold your phone in the right place on the eye piece, a few 3D printable designs and things like this https://www.amazon.com/dp/B013D2ULO6/ref=sspa_dk_detail_1 . Unless you have a DSLR and the 1 or 2 lens adapters to hook it up to your microscope, your phone is probably the easiest thing to use.

At the Bench: A Laboratory Navigator by Kathy Barker is really helpful. I bought this book and read it when I started working in the lab. It is very basic!

I've always liked "At the Bench" by Kathy Barker.

I highly recommend you these books: labmaths and at the bench

http://smile.amazon.com/gp/product/B00007LV4B/ref=oh_aui_detailpage_o00_s00?ie=UTF8&psc=1

Big enough that you can glue whole pages in there. Gridded, numbered pages, very professional. And not very pricey.