Apps I use in my PhD | Life as a PhD student #12
ฝัง
- เผยแพร่เมื่อ 28 ส.ค. 2024
- I talk about the software and apps I use in my PhD to do my research and write my thesis! And a bunch of other stuff besides.
I love Exeter's campus, it's just so green!
For the full discussion of Guardians of the Galaxy Vol. 2: • Simon and Dan talk abo...
LINKS:
- My headphones: bit.ly/runningb...
- My running app: www.strava.com/
- FORTRAN90 intro: www.cs.mtu.edu/...
- Sublime text: www.sublimetex...
- Kile: kile.sourceforg...
- LaTeX: www.latex-proj...
- Mendeley: www.mendeley.com/
- Dropbox: www.dropbox.com/
- Todoist: en.todoist.com/
- Tomato timer: zapier.com/blo...
- Slack: slack.com/
--------- II ---------
You can support the channel by donating at / simonoxfphys
Previous vlog: • The vlog is changing |...
Next vlog: • Framing female scienti...
Vlog playlist: • Life as a PhD student
Music by: David Cutter Music - www.davidcuttermusic.co.uk
Filmed on my Canon G7X: bit.ly/simonvlo...
Editing done in Premiere and After Effects.
Huge thanks to my supporters on Patreon: Samuel Rose, Frederic Ysewijn, Kane Thynne, Eve Dillon, Rowan Gow, Rikke Norgaard Christiansen, Daniel Martin, Matthias Loos, James Bridges, Hanna Scott, James Craig, Angela Cook, Sanaa Al Derei, Mark Anthony Magro, Maddie Sisk, Liam Farrar, Theresa Wang, Hunter Jones, Nathan Smith, Kieran Kelly, Wendover Productions, Kendra Johnson, Caitlin Louise, and Real Engineering.
--------- II ---------
I am Simon, a fourth year PhD candidate at the University of Exeter. I upload videos on bits of science which are relevant to what I do, and sometimes just because they're really cool.
Vlogs from Oxford students - / oxvlog
My twitter - / simonoxfphys
My facebook - / youtubesimon
My insta - / simonoxfphys
My goodreads - / simonoxfphys
Thanks to Vlogbrothers for their sponsorship of this video. Money from the Foundation to Decrease Worldsuck contributed to equipment used in this video.
How do you focus on revising as A Levels are in 15 days :( Helpppp
I refer you to th-cam.com/video/jaS5vouQTfo/w-d-xo.html and the videos after that!
Thank you so much! Keep up the good work love the vids
Just start revising now!! Once you get going it becomes easier. What subjects are you doing?
Frankie Barr Modern History law and politics
Hollo Zirq can't wait until my law exam in 13 days
Our full review of Guardians of the Galaxy Vol 2: th-cam.com/video/47bDBmQ4J08/w-d-xo.html
Getting more than one vlog per week is making me much more happy than I anticipated
I like how you mentioned the times you get in and get out of the office; I bet vlogging is one way to keep loosely "accountable" in the often unstructured world of a researcher. And I love the vignettes you include about time spent with your friends. I really hope I can cultivate a similar friend group when I (fingers crossed) start my PhD journey next year!
Hope it's going well!
@@charonder Hey thanks! You know, it really is going well :) I'm in a lab I like right now as a research assistant and am applying for my PhD this cycle!
The Video starts at 5:43 You're welcome :)
akshay manikandan thnx man
Thank you so much!
God bless u
God bless
Thanks, Simon, I really needed a vlog right now... best way to relax when the A level stress kicks in
Loved the Mark Spitz shout out!! For those who do not know, Mark Spitz used to own the record for the most swim metals in the Olympics prior to Michael Phelps.
Yes! I'm glad somebody got the reference!
What made you choose Atmospheric Physics for a PhD, what made you want to go for a PhD and not just some form of degree and before you started TH-cam, did you have any ideas as to what profession you wanted to do (perhaps to do with physics or something different)? As usual, spectacular video and it's lovely to see a new, shorter video, as to one longer one. Keep up the brilliant work!
The most important thing I have ever, ever, EVER chosen to learn was how to use GDB & Valgrind. DropBox, Git, IDEs etc. all are a matter of preference for solo projects (though 10/10 would recommend the Visual Studio Code + Git stack), but GDB and Valgrind are what have made it possible for me to make any projects of meaningful size.
GDB is a standard debugger, it lets you step through code one line at a time, and with an appropriate IDE you can visually set breakpoints where your program will pause at a given line and you can explore memory at that point in the program (e.g. is a given pointer valid).
Valgrind is on another level though, it detects memory leaks, uninitialised values, illegal memory accesses and so on with an incredible resolution of detail. It has helped me catch bugs that I had no chance of spotting otherwise that would cause programs to only sporadically fail.
The best part is whether you're using C++ (another 10/10) or Fortran or many other languages, both GDB and Valgrind work brilliantly!
For compiled code, another thing I've found super useful is running code through every compiler I can get my hands on (GCC and Clang are top of that list for me), each has its own unique way of analysing code, so when one gives a shitty error, one of the others tends to give a good one.
Im a software Developer, currently working in a medium size team and we use Slack as a communication tool for pretty much everything. loved the vid been here since 15k :D
I was totally apprenensive about shorter vlogs...but multiple uploads per week turns out to be pretty awesome!! It spreads out the Simon good influence...
Nice edit once again! Good mix between high quality and not taking itself to serious, if you know what I mean ;) Keep it up
Already loving the smaller vlogs!
Watching your vlogs this week was my reward for finishing my first round of midterms!! haha
I justed began writing my bachelor thesis on IceCube (Neutrino Telescope in the Antarctic) and I also started using Linux Mint and Slack in the IceCube Collaboration. :) And I totally agree with using LaTeX although I prefer Texmaker or even better online on overleaf.com I mainly program in Python or ROOT, I've just heard of FORTRAN to be very archaic.. :D Very nice Vlog, might check out some of the apps!
I wonder if you use "Forest: Stay Focused" as a productivity app. I imagine as a PhD student, or really any kind of student, you are using your phone, responding to texts from friends or browsing social media. Forest: Stay Focused helps you stay focused by a seed being planted and within an amount of time (that you set,) a tree is planted in the app. The catch is if you exit the app, the tree stops growing. It's also offered as an extension on Google Chrome so in case you want to check it out, you can.
EDIT: Your second most recent video shows me that you do use it. So all in all, I wrote this paragraph for no reason :p
Also, great vlogs. I just started watching last night for some reason; I don't even want to get my PhD anymore but I'm always intrigued to see what kind of life a PhD student leads. I say "anymore" because I did at one point but Real Analysis scared me away from pursuing an MS or PhD in pure mathematics (undergrad was in math). Although I do wonder what a PhD in statistics looks like...
God I love these vlogs!! Respect to you mate from New Zealand
My exams are on, and watching these vlogs is a welcome break
Is this a dream??? You posted a vlog other than on weekend??? YEEEEYYY!!!
I am loving this format much more
A good way to start your day: a Simon Clark vlog. Now let's go print out 123 papers and start writing a review #thegoodandthebad
I never manage to hold my camera as straight as you while running and shooting for a vlog xD
He stabilized the video using Premiere Pro to make it less shaking.
Yep, warp stabiliser for the win!
Yeah I work on final cut pro X :-)
Slack is actually a factory standard communication application. It is a graphical shell over IRC. The length of a line in FORTRAN has to be because of the history of programming software
In the early days, punch cards were used to write programs. And the thus there was a limit per line. A FORTRAN compiler often ignores code after the nth character (www.personal.psu.edu/jhm/f90/lectures/5.html). Newer versions of FORTRAN extended the limit.
wow if the vlogs are that recent, I prefer it this way :D
Thanks for sharing this! Slack is pretty good and I used it for my last university team work assignment. I love it.
why don't you use Git?
Danny Burke and why don't you use Atom?
Danny Burke Visual Studio Code, GitHub, Gistbox for notes
Danny Burke I was about to say the same thing! His code might be confidential to his advisor so that might be but who knows.
You can give permissions to people on a private git repository, I don't think this would be the reason why.
Because is garbage.
BIG THUMBS UP for the Nail and Gear T-shirt :D
Slack is good! A lot of startups are using it for collaboration. You can also code custom bots that can automate some stuff for your team. We also use Slack in our research laboratory :)
I love the Hello Internet exercise shirt. Brady would be proud.
you should try numba for python, it speeds up python code to 90% of C/Fortran levels, with only a python function decorator. The only downside is that it limits you to a slightly smaller subset of python, and has poor error messages
I work in an IT support group, and we use also use Slack. It's great to have different channels for different topics
love the new format!
love your vids simon! do you have any tips for those of ua who have to do a lot of practical time consuming lab work, that reaoly takes away from analysis and writing and reading and other PhD-ing tasks. for example, today i worked 9-6.. a short day in the PhD world, I know, but I only sat at my desk for 10 mins!
Thank you enough for highlighting/ suggesting Mendeley. Also, more choral music! Exeter Chapel Choir make a great sound.
You're welcome! And rest assured you'll be hearing more of the choir - next week term is back so we'll be rehearsing again, I'll definitely be recording some pieces to include :)
I second that! Where is the singing? btw, the choir I used to sing in uses Slack for communication. (It's a really big choir though, about 200 people :D )
These make me too productive for my comfort.
You inspire me, Simon!! Thank you!
Simon, why did you decide to go for Fortran? Is it because it's a language you're comfortable in? I feel like using C would be just as fast(performance-wise) and would be a little bit easier to integrate any pre-existing Python code.
Very cool Simon!Very cool!
You mentioned todoist doesn't really fit your needs as a note taking app. I had the same problem with any note taking app I tried as I write a huge amount of notes myself (and always reverted to hand written lists). I would recommend you check out trello. It's pretty good once you understand all the features (lists, colors, members, deadlines etc..). I love your videos btw. They really give me the taste of being a phd student :)
Beautiful landscape! One more thing: Keep running!
As a regular user of Slack for my research and revision group in the lead up to my GCSE exams, I'd seriously recommend it for anyone whose apart of a medium to large group and you want a huge collaboration space (especially for when you are on the move).
I do have a question Simon, what is your goal in life? btw keep up the good vids man!!
To make a living doing what I love, educating others and trying to leave the world a better and more just place than I found it
Simon Clark thanks khalessi
@@SimonClark wow
btw you can order a one-side bluetooth earbud from amazon or something. that way you dont feel this cable hiting your back every time you do a movement during your run ;)
Use github / bitbucket for code management. Much easier version control once you get over the basics.
The last time I used Fortran was before you were born. There are times I miss it, usually when I am constipated.
Haha, I love your running path, good on you
Hey Simon,
I wouldn't really recommend re-writing all your code in FORTRAN. Profile it, and optimize performance critical parts with Cython. The performance increases you can get doing so are great and it is FAR less time conusimg than re-doing it in FORTRAN. If you really wanna use FORTRAN, consider only doing performance critical parts also and using the Python-FORTRAN API.
Also, is your code serial or have you considered parallelization?
Why is your office always empty? or you just record it when there's no people around?
This week it was very quiet - but yes I always wait til its empty so I don't disturb people
You can tell how much weight you have lost off your face and you look really well for it! Well done!
You have inspired me to step up my exercise game now!
Also using Slack in my lab. And git for version control, both on personal space and on servers (much more reliable than dropbox!!)
This is good because it makes videos not only more digestible but also more revenue for simon so he can make better vids, win win :D
A great app I use for my PhD is 'EastBib'. Choose the referencing style, scan the barcode of the book and it will give you the full reference for it. Timesaver to the max
Would you mind giving a link to your Strava? I'm always interested to see how people whose videos I watch (or just people I look up to in general) exercise
Also, I recently joined the committee for my university's EE society coming next year and one of the first things the current committee did was invite us all to the Slack they use: I've heard it's used pretty commonly in professional settings
Why do you use dropbox instead of git? :)
Because I was already using dropbox for other things (crash course, notably) and it just keeps things simple to have everything in one place. Plus I've just never used Git!
When you say Dropbox acts as your version control what does that mean? Are you keeping copy of code at different points or? Because Git is a version control system and fulfils it's purpose completely. It's not difficult to learn and I would recommend using it, as would anyone else that writes code.
Ihtasham's comment relates a lot to why I asked the question. I imagine version control with dropbox could potentially be a pain. Although I guess you've almost done your entire PhD using it, so it must work for you! Love the videos Simon, keep up the great work!
I can't believe you never used Git :D ... nevermind... whenever you try to use it in the future go for particularly GitKraken.
You'll love my suggestion. (coming from someone who uses both Dropbox and Git)
Love to see my suggestion on a video
2:26 Why the heck would you have a line that long, anyways?
For to-do list I personally like Nozbe instead of to-doist. They're nearly the same but I like nozbe better
I have an organic chemistry final tomorrow, and I'm watching this instead of studying...
have a try with Overleaf! In case you write collaborative projects/papers
Thanks for sharing this. I was wondering why don't you try google services like Google Drive and Google Keep and Google Calendar. Do you use any other software for reminders?
Dropbox for Version Control???
OUCH!!!
i replaced Sublime Text with Visual Studio Code, no regrets! (although column edit is slightly better in Sublime)
I love your HI T-shirt!
when your meant to be revising for your chemistry GCSE tomorrow but you got to watch the Simon Clark Vlog
Yay, a vlog I actually have time to watch. ;)
I want to try to run a 5k at the end of this month. My only goal is to finish before they open the roads.
I wonder if there would be any value to a Python to Fortran cross-compiler. I know a little about Python and almost nothing about Fortran so that may not be a good fit for automation. Actually a Python to C cross-compiler may also be worth considering. I don't know much about it, but Cython ( cython.org ) may be worth a look.
It was interesting to hear about the software tools you use. My company started using Slack a few months ago. It really shines when people work remotely. Things you would normally pop around the corner to ask when working locally become Slack chats where email would be less optimal. It is imperfect, but I like it. I'd like better threading features.
Best wishes on your fitness goals.
are you sure you're not better off trying to improve your python code? Python is slow, but generally not THAT slow
I would suggest zotero because you can't organize search results in Menedely.
use vs code or atom so much better .. + full integration with GitHub which you should be using if you're not .. you get free 2 years subscription since you're a student
Slack is used a lot in the professional world, especially if you're a computer scientist. Also, I wonder why you don't use a git? They're so much better for code version control!
I'm a software developer and I would suggest to you to try Visual Code (not Visual Studio this is a different thing ) :)
Simon don't you know Atom? It's almost the same as Sublimetext and it's totally free!
You should try sharelatex.com. Really cool online editor for compiling Latex into pdf (its a side by side view)!
Fortran has a limit because it was made for punch cards.
Why pay for sublime text when vim is foss? Also using version control like git prevents mistakes that ruin entire projects.
What computer do you use to do all of your coding? I am searching for an appropriate and reliable computer for my Computer Science course at UofT next year. Love the vlogs!
I use a HP-EliteBook-850-G, though I do relatively frequently crash it...
Shorter vlogs = more procrastination (not complaining!)
Great video,
Can you elaborate more on your strategy in managing references using Mendeley, then exporting to BibTeX for paper submissions and thesis writing?
I can help with the Mendeley part since I use it in my scientific writing. You can download their desktop app and their Microsoft Word plugin. Drag a PDF to the desktop app, check that all the information fields are filled out correctly; then, while writing in Microsoft Word, you just go to References>>button for inserting Mendeley Citation>>choose the article you are referencing. Wazam! Instant in-text citation. Whenever you want to, put your cursor where you want bibliography, go back to "References" tab and click (I think) "Insert Bibliography." You can also easily switch between citation formats, depending on the nature of your writing.
Gogo fitotron 5000 lifestyle!
Why wont you try and switch to Gnome desktop environment? Its far more confortable than unity and supposed to replace it with next update...
I wanted so bad to know where you are coding. Thanks a lot, I will try it.
Nice presentation, i have a question with latex. Am writing with it and its not compiling, what could be the issue?
yasss new video!!! :)
Visual studio ftw!
its really interesting facts about PhD.
I'm up at the University of Alaska Anchorage and it is significantly less green. I'm super jealous!
I think I'm going to go out for a run anyway because I saw you doing it and I am very easily influenced :P
P.S. Don't worry, you already look great (no hetero), so if looking hot is your goal then mission accomplished! See you next time, have fun coding!
Ah the joy of doing a code rewrite: unintended different behaviour from the previous version, a new sleuth of problems, the illusion of making progress (whilst actually you're losing time by doing a rewrite instead of fixing or speeding up existing code), thinking about doing it better only to find yourself hacking tidbits after a week because the reality is more complex than you thought it would be, ... Also see th-cam.com/video/XcUUY8ziTuk/w-d-xo.html
Watching back your old PhD vlogs as I started my PhD a week ago and I need to learn FORTRAN90 for the bulk of my coding/modelling (I'm a coding n00b)..... any tips for beginners!?!?
dropbox as version control makes me sad
Hello Internet shirt!
I like your wallpaper on your laptop screen, do you have a link of where i can get it?
Out of curiosity, which packages do you use on Sublime Text? Been considering using it for a while now
A tree zoo. Forever my favorite line
444k subs is a great number hoping for 555k ....and so on
Haha. This is like Mr Steel's drone vids but about a load of _really_ dull stuff. "This morning I've been coding since 8:59, but I normally start around 8:52 (except on Wednesdays when I start at 8:54 or 5)."
Visual Studio Code. Best text editor by far(very very extensible, powerful, beautiful), and free, crossplatform. No need to pay for sublime.
Berserker Well, Sublime is free and is also really fast.
Zyphicx true; its a matter of taste really, however i think one is wasting money by buying sublime full version or sth like he said in video when one has vs code or even sth as crazy as emacs or vim. features wise sublime isnt much better than above(imo even worse), so to me it seems useless to pay for it.
You don't get any extra features if you buy it. It's basically a donation.
A ok. If one wants to donate, then that's sth. else. In video he said it in a sense that you get so much more by buying it. So i thought that if you wanna get many features VS Code would be a better choice, since it's free. I didn't know Sublime was totally free.
Hey Simon , quick question... how do you keep your schedule organised ?
Your movie is nice!
Well done:-)
Hi Simon, what model is your laptop? I would like to buy a HP very soon!
Who are the other people in your office? What do they do?
I love Mendeley but their font is just too small sometimes.
good to see that I'm not the only watching these after 3 years
What an awesome life