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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!

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

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

​

Science fiction:

Asimmov:

I robot

The foundation trilogy

Dune | Hibbert

Flatworld

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Self help:

​

​

Online resources:

bitesizebio.com

​

​

Great articles:

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

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

the song of the dodo by david quammen. one of my favorite science books. i wish there was an audiobook available, i’d love to experience it again on my commute to work.

Everyone needs to read 'The Immortal Life of Henrietta Lacks' - hands down the best science book I've ever read. The audiobook is good too.

I think this book is super handy to have around:
https://www.amazon.com/Lab-Math-Measurements-Calculations-Quantitative/dp/0879696346

It covers the math for all sorts of lab techniques and has one of the best versions of the dilution formula I've found;

[(Concentration you want) / (Concentration you have)] * Total reaction volume = volume of stock to add to reaction.

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.

http://kirschner.med.harvard.edu/files/protocols/Novagen_petsystem.pdf
pet plasmids manual from novagen. Some protein work scattered about, a lot of cloning. Mostly just generic stuff but can bring up ideas to consider.
https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma-Aldrich/General_Information/1/ge-strategies-for-protein-purification.pdf No protocols but general information on purifications in general.
https://www.amazon.com/Principles-Techniques-Biochemistry-Molecular-Biology/dp/0521731674 Same. Some useful tips and explains care of equipment and uses.

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.

https://www.amazon.com/gp/aw/d/0815344325/ref=dp_ob_neva_mobile

Best book ever on the subject.

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!

https://www.amazon.com/Writing-Science-Papers-Proposals-Funded/dp/0199760241

I enjoyed this one.

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

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

Bad Science by Ben Goldacre is the only science book I've convinced my non-scientist family to read. It drastically cut down on the number of phone calls I get about whether or not some Facebook-promoted scam is going to cure whatever ails them.

Exactly what I was going to recommend. Fantastic book.

https://www.amazon.com/Lab-Math-Measurements-Calculations-Quantitative/dp/0879696346

For a light-hearted survival guide, check out http://www.amazon.com/Surviving-Your-Stupid-Decision-School/dp/0307589447 .

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

Something of an origin story of a lot of common-day drug discovery.

As always: Molecular Cloning
https://www.amazon.co.uk/Molecular-Cloning-Laboratory-Manual-Fourth/dp/1936113422

https://www.amazon.com/Molecular-Cloning-Laboratory-Manual-Three/dp/1936113422

Green and Sambrook's Molecular Cloning is usually my go-to reference for techniques.

https://www.amazon.com/Channels-Excitable-Membranes-Bertil-Hille/dp/0878933212

https://www.amazon.com/Patch-Clamping-Introductory-Guide-Electrophysiology/dp/047148685X/ref=sr_1_1?s=books&ie=UTF8&qid=1518292111&sr=1-1&keywords=patch+clamp+physiology

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.

We use these tackle boxes and haven't had any issues. We use 3-4mL of liquid to cover a membrane.