Some Helpful Links

some helpful links

for surviving grad school in the life sciences*

*that I’ve personally used and loved, or have heard good things about. This definitely is not meant to be an all-inclusive masterlist created by an omniscient being though not from lack of trying.

Research/Data Analysis

GraphPad Prism - for all your graphing needs! I use this program exclusively for all my data visualizing, and it can also do some basic statistics. It does cost $$, but your institution or lab may already have a subscription.

NIH ImageJ - free image analysis software (eg. cell counting, quantifying western band intensity, etc), and since it’s open source, there are lots of free plug-ins available to download.

R Studio / R Project - free statistical software. It’ll take some time learning (via tutorials or someone showing you), but it’s a pretty awesome program. I don’t personally use it for stats, but I know many colleagues who do.

Dilution Calculator (C1V1=C2V2) and Molarity Calculator and Outlier test - great for double-checking your math (or doing all the work for you if you’re like me and math is just not your brain’s jam).

IHC World - the motherload of everything IHC or antibody-related, including protocols

BioNumbers - helpful repository of any number you may need for biology-related research (eg. how much DNA or RNA is in a mammalian cell)

Statistics for Biologists - collection of articles about statistical issues that biologists should be aware of

Writing

Mendeley Citation Manager - a (free!) way to save and organize papers using a browser plug-in, along with a Word doc plug-in so you can insert in-text citations and automatically build a reference page when writing. 

Academic Writing Resource - provides the “nuts and bolts” for academic writing, from the University of Manchester

Organizing academic research papers - comprehensive guide on organizing and writing academic research papers from Sacred Heart University

Guide on using Word for writing a Dissertation - such as formatting tips, from University of Michigan

Dissertation templates - from Duke University, available for Word and LaTex (note that every graduate program may have different requirements for formatting, so please only use this resource as an example and/or helpful guide)

PubMed Journal Finder - helps you find the most appropriate journal (from PubMed) to publish your paper in (or find new journals related to your research to check out)

BioRender - If you’re a biologist, this thing is a lifesaver when it comes to creating figures/schematics for papers and presentations. Limited access is free to students for private use (like class presentations).

LaTex - a document preparation program that’s very science-friendly. I’ve never used it, but I wish I did after hearing how much easier it would’ve made things.

Organization

Box Sync or Dropbox - to easily share files between computers (like protocols with everyone in the lab, or editing manuscripts with multiple authors). I personally like Dropbox better and am willing to pay for more space (Box Sync sometimes has delays in syncing).

Google calendars, or some sort of electronic calendar - for scheduling your day, because grad school can get hectic!

Bear - a note-taking app for Macs and other Apple products. I don’t personally use it (I like physical notes), but my old lab mate uses it to keep track of all the notes during his meetings with our previous PI. He’s been using it for years and says it works really well.

Labstep - cloud-based documentation for the entire lab–including notebooks, inventories, data collection and downstream analyses, etc. I personally never used it but it sounds amazing, and would streamline so many aspects in lab. Good to keep in mind for anyone planning on becoming a PI!

Career Development

LinkedIn - if you haven’t already, create an account (even as a student!) This is a great and common way to keep in touch with your network, look for and apply to jobs, and get noticed by companies.

Research Gate - like LinkedIn but for researchers. Their best feature imo is their forum, where users ask research-related questions that the community of scientists help answer.

NIH Office of Intramural Training and Education (OITE) - they regularly host free and open-to-the-public webinars on career development for science and health majors (college and grad school-level)

More Posts from Our-cosy-library and Others

3 years ago

When are Pterotrachea finally going to go viral? How does anyone look at this animal and not flip their shit? I first saw them in a BBC documentary when I was a toddler and I still can’t believe a real thing evolved like this, but somehow as soon as I’m done thinking about them they just quietly retire to the background of my memory. Multiple divers say that they have a tendency to follow you around when they see you. :) :) :)

4 years ago

“When a flower doesn’t bloom, you fix the environment in which it grows, not the flower.”

— Alexander Den Heijer

4 months ago

Just Do It: Advice for Young Friends

By Bud Koenemund

(Written: January 2014)

A few weeks ago, a friend of mine mentioned she was about to begin her last year as a twenty-something; 30 would be upon her before she knew it. She went on to list 50 things she wants to accomplish in the coming year – many of which involve money and her art (she is a wonderful actress). It is an ambitious list. I wished her luck, and gave her a few words of advice. Since then I’ve been thinking about what I said, and realized I needed to add some more – both for her and for my other young friends, many of whom are artists of one type or another.

If I can give you one piece of advice: DO IT! Do everything on your list! Don’t wait around thinking there will be a better time to start. There won’t be. There is only time, and it goes a lot faster than you realize. Before you know it, you’ll be 30. You’ll go from 30 to 40 in about 10 minutes. And, from 40 to 50 even faster. Albert Einstein, Stephen Hawking, or Neil deGrasse Tyson might argue with me, but time really does speed up as you get older.

When I was your age, I thought 30 was old, and that I’d never get there. Hell, there were a few days when I was in the Army, I didn’t think I’d make it to 22. Now, I’m 45 and there’s very little I wouldn’t trade to go back to 25 knowing what I know now.

I wish I could make you understand me. I know you don’t. You can’t. This is not an insult. It’s just the way life works. You don’t know what you don’t know until years down the road. I was young. I had plans, and I didn’t want to listen to “old” people. I had all the answers. I know so much more now.

One of the most important things I’ve learned about life is that it doesn’t mean shit. In a hundred years, you’ll be dead, and very little of this will matter. What people think of you now or then won’t mean a damned thing. Sure, you might change the world; bring about peace in the Middle East; cure cancer; win a dozen awards – but it won’t affect how your private life is judged.

Whether you graduated first in your class at Harvard, or at the bottom of a community college; if you’re buttoned-down and conservative, or you get caught running naked through Times Square; even if your ex- posts your “No, Baby, I swear I’m the only one who’ll ever see it” sex tape on-line; it might rate a line or two in your Wikipedia entry, and that’s it. And, if you’re dead – and if everyone you know, and who judged you, is dead too – what will you care?

Too many people in this world give a shit about things that don’t matter a bit, especially other people’s business. I figure, if you’re not hurting someone else, and what you’re doing works for you, fuck what other people think. It took me a long time to develop that attitude.

You have to do what makes you happy. Do it your way, but do it. Sing your song. If people don’t like it, fuck ‘em. You’re on your journey, not theirs. You have to do what you can with the time you’ve got.

But, remember, it’s also important to stop and look at the world around you once in a while, to sit down and relax; take your bearings, and make sure you’re on the right path. I should say, make sure you’re on the right path for you!

It’s OK to be a waitress, or a tire salesman, or a security guard, as long as you’re also working toward what you love. If you have five minutes, sit down and read the trade papers, or scribble down the words banging around in your head.

Wayne Gretzky says, “You miss 100 percent of the shots you don’t take.” That applies to everything in life. 100 percent of the sonnets you don’t submit get rejected. You’re passed over for 100 percent of the parts you don’t audition for. You don’t get 100 percent of the raises you don’t ask for. The worst anybody can say is no.

Now, I’m not saying you’re automatically entitled to anything. This is life. It’s not fair. The world doesn’t owe you shit; not money, not love, not happiness, not success. You have to work for what you want, and keep at it. And, in the end, it may get you nowhere. But, if you don’t go after what you want, you’ll end up nowhere anyway. You pays your dollar, and you takes your chances!

Oh, and one more thing: Don’t spend too much time sitting around, listening to old men – like me – spout off about what you should be doing. There is no instruction book for life, and most people who claim to have things figured out are faking it, just like the rest of us.

4 years ago

mental health tips i wish i’d been given before starting university

trying is much more important than succeeding

10 minutes of studying > not studying at all

being a college student is more than academics. it’s also learning how to enjoy your own company, learning and occasionally screwing up meals, wandering outside campus like a tourist, questioning your ideals and presuppositions, discovering new talents and skills for the hell of it, and SO much more. if you feel burnt out in one dimension of college life, that’s a sign to spend some time relishing in another dimension.

if you need more time, take a deep breath and shoot that email to your professor/TA asking for an extension. at worst, they say no. and don’t stress over properly explaining yourself/your situation. hell, just email them: “Hi, Professor. I need your help. Sincerely, y/n.” all it takes is that one initial reach out and the rest will follow.

failure does not reflect character. read that again. remind yourself as often as you see fit because at one point or another, you will feel like you’ve failed. it’s growing pains. once you’ve accepted that, learn to view any setbacks as a hint that you need to try a new method/approach. didn’t do well on that math quiz? don’t beat yourself up over it–instead, regroup with yourself and see which metaphorical gear got stuck in your personal learning process machine. for instance, maybe you used flash cards and that wasn’t really your style. act like a detective, not a bully.

THERE IS NO NORMAL TIMELINE FOR YOUR COLLEGE CAREER(!!!!!!). a lot of people need more than 4 years, a lot of people need 4 years, and a lot of people need less than 4 years. and every single one of those timelines are valid. the worst thing you could do is squeeze the living hell out of yourself into some rigid schedule that is incompatible with who you are and how you learn. trust me when i say u will find yourself doing the best work when u do it at YOUR pace.

2 years ago

there are FERNS?? that grow like TREES???? no fucking way

There Are FERNS?? That Grow Like TREES???? No Fucking Way
There Are FERNS?? That Grow Like TREES???? No Fucking Way
There Are FERNS?? That Grow Like TREES???? No Fucking Way
There Are FERNS?? That Grow Like TREES???? No Fucking Way
There Are FERNS?? That Grow Like TREES???? No Fucking Way
There Are FERNS?? That Grow Like TREES???? No Fucking Way

so what sent me down this rabbit hole is earlier on a walk with my husband we saw some glorious "palms" in a garden that were about 6 feet high, once i inspected the fern-like leaf pattern and saw the new leaves were curled i was blown away because it was so similar to a fern but had a trunk and i didnt know ferns could grow like that. (see the last two images, i took them so i could identify it later using an app + research, it might be sphaeropteris brunoniana) look how hairy that frond is! i love plants 🤎ferns my beloved🤎

1 year ago

I got to hold a 500,000 year old hand axe at the museum today.

It's right-handed

I am right-handed

There are grooves for the thumb and knuckle to grip that fit my hand perfectly

I have calluses there from holding my stylus and pencils and the gardening tools.

There are sharper and blunter parts of the edge, for different types of cutting, as well as a point for piercing.

I know exactly how to use this to butcher a carcass.

A homo erectus made it

Some ancestor of mine, three species ago, made a tool that fits my hand perfectly, and that I still know how to use.

Who were you

A man? A woman? Did you even use those words?

Did you craft alone or were you with friends? Did you sing while you worked?

Did you find this stone yourself, or did you trade for it? Was it a gift?

Did you make it for yourself, or someone else, or does the distinction of personal property not really apply here?

Who were you?

What would you think today, seeing your descendant hold your tool and sob because it fits her hands as well?

What about your other descendant, the docent and caretaker of your tool, holding her hands under it the way you hold your hands under your baby's head when a stranger holds them.

Is it bizarre to you, that your most utilitarian object is now revered as holy?

Or has it always been divine?

Or is the divine in how I am watching videos on how to knap stone made by your other descendants, learning by example the way you did?

Tomorrow morning I am going to the local riverbed in search of the appropriate stones, and I will follow your example.

The first blood spilled on it will almost certainly be my own, as I learn the textures and rhythm of how it's done.

Did you have cuss words back then? Gods to blaspheme when the rock slips and you almost take your thumbnail off instead? Or did you just scream?

I'm not religious.

But if spilling my own blood to connect with a stranger who shared it isn't partaking in the divine

I don't know what is.

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our-cosy-library - Struggling Academic
Struggling Academic

Here I share some scientific, artistic, literary and more material that I find interesting and important. I'm 30, studied biology in the University of Damascus. هنا اترجم بعض المقالات و المواد العلمية و الادبية و المواضيع التي اجدها مهمة و مثيرة للاهتمام.عمري 30 سنة,  ادرس علم احياء بجامعة دمشق

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