Transcript:

[Reporter] The Russian invasion of Ukraine.
Momentum is building for a war between Ukraine and Russia.
[Reporter] Tensions between Russia and the West
are growing rapidly.
[Reporter] President Biden considering deploying
thousands of troops to Eastern Europe.
There are now 100,000 troops
on the Eastern border of Ukraine.
Russia is setting up field hospitals on this border.
Like this is what preparation for war looks like.
A legitimate war.
Ukrainian troops are watching and waiting,
saying they are preparing for a fight.
The U.S. has ordered the families of embassy staff
to leave Ukraine.
Britain has sent all of their nonessential staff home.
And now the U.S. is sending tons of weapons and munitions
to Ukraine's army.
And we're even considering deploying
our own troops to the region.
I mean, this thing is heating up.
Meanwhile, Russia and the West have been in Geneva
and Brussels trying to talk it out,
and sort of getting nowhere.
The message is very clear.
Should Russia take further aggressive actions
against Ukraine the costs will be severe
and the consequences serious.
It's a scary, grim momentum that is unpredictable.
And the chances of miscalculation
and escalation are growing.

I want to explain what's going on here,
but I want to show you that this isn't just
typical geopolitical behavior.
Stuff that can just be explained on the map.
Instead, to understand why 100,000 troops are camped out
on Ukraine's Eastern border, ready for war,
you have to understand Russia
and how it's been cut down over the ages
from the Slavic empire that dominated this whole region
to then the Soviet Union,
which was defeated in the nineties.
And what you really have to understand here
is how that history is transposed
onto the brain of one man.
This guy, Vladimir Putin.
This is a story about regional domination
and struggles between big powers,
but really it's the story about
what Vladimir Putin really wants.
[Reporter] Russian troops moving swiftly
to take control of military bases in Crimea.
[Reporter] Russia has amassed more than 100,000 troops
and a lot of military hardware
at the border with Ukraine.

Let's dive back in.
Okay. Let's get up to speed on what's happening here.
And I'm just going to quickly give you the highlight version
of like the news that's happening,
because I want to get into the juicy part,
which is like why, the roots of all of this.
So let's go.
A few months ago, Russia started sending
more and more troops to this border.
It's this massive border between Ukraine and Russia.
They said they were doing a military exercise,
but the rest of the world was like,
"Yeah, we totally believe you Russia. Pshaw."
This was right before this big meeting
where North American and European countries
were coming together to talk about a lot
of different things, like these countries often do
in these diplomatic summits.
But soon, because of Russia's aggressive behavior
coming in and setting up 100,000 troops
on the border with Ukraine,
the entire summit turned into a whole, "WTF Russia,
what are you doing on the border of Ukraine," meeting.
Before the meeting Putin comes out and says,
"Listen, I have some demands for the West."
And everyone's like, "Okay, Russia, what are your demands?
You know, we have like, COVID19 right now.
And like, that's like surging.

So like, we don't need your like,
bluster about what your demands are."
And Putin's like, "No, here's my list of demands."
Putin's demands for the summit were this:
number one, that NATO, which is this big military alliance
between U.S., Canada, and Europe stop expanding,
meaning they don't let any new members in, okay.
So, Russia is like, "No more new members to your, like,
cool military club that I don't like.
You can't have any more members."
Number two, that NATO withdraw all of their troops
from anywhere in Eastern Europe.
Basically Putin is saying,
"I can veto any military cooperation
or troops going between countries
that have to do with Eastern Europe,
the place that used to be the Soviet Union."
Okay, and number three, Putin demands that America vow
not to protect its allies in Eastern Europe
with nuclear weapons.
"LOL," said all of the other countries,
"You're literally nuts, Vladimir Putin.
Like these are the most ridiculous demands, ever."
But there he is, Putin, with these demands.
These very, very aggressive demands.
And he sort of is implying that if his demands aren't met,
he's going to invade Ukraine.
I mean, it doesn't work like this.
This is not how international relations work.
You don't just show up and say like,
"I'm not gonna allow other countries to join your alliance
because it makes me feel uncomfortable."
But what I love about this list of demands
from Vladimir Putin for this summit
is that it gives us a clue
on what Vladimir Putin really wants.

What he's after here.
You read them closely and you can grasp his intentions.
But to grasp those intentions
you have to understand what NATO is.
and what Russia and Ukraine used to be.
(dramatic music)
Okay, so a while back I made this video
about why Russia is so damn big,
where I explain how modern day Russia started here in Kiev,
which is actually modern day Ukraine.
In other words, modern day Russia, as we know it,
has its original roots in Ukraine.
These places grew up together
and they eventually became a part
of the same mega empire called the Soviet Union.
They were deeply intertwined,
not just in their history and their culture,
but also in their economy and their politics.
So it's after World War II,
it's like the '50s, '60s, '70s, and NATO was formed,
the North Atlantic Treaty Organization.
This was a military alliance between all of these countries,
that was meant to sort of deter the Soviet Union
from expanding and taking over the world.
But as we all know, the Soviet Union,
which was Russia and all of these other countries,
collapsed in 1991.
And all of these Soviet republics,
including Ukraine, became independent,
meaning they were not now a part
of one big block of countries anymore.
But just because the border's all split up,
it doesn't mean that these cultural ties actually broke.
Like for example, the Soviet leader at the time
of the collapse of the Soviet Union, this guy, Gorbachev,
he was the son of a Ukrainian mother and a Russian father.
Like he grew up with his mother singing him
Ukrainian folk songs.

In his mind, Ukraine and Russia were like one thing.
So there was a major reluctance to accept Ukraine
as a separate thing from Russia.
In so many ways, they are one.
There was another Russian at the time
who did not accept this new division.
This young intelligence officer, Vladimir Putin,
who was starting to rise up in the ranks
of postSoviet Russia.
There's this amazing quote from 2005
where Putin is giving this stateoftheunionlike address,
where Putin declares the collapse of the Soviet Union,
quote, "The greatest catastrophe of the 20th century.
And as for the Russian people, it became a genuine tragedy.
Tens of millions of fellow citizens and countrymen
found themselves beyond the fringes of Russian territory."
Do you see how he frames this?
The Soviet Union were all one people in his mind.
And after it collapsed, all of these people
who are a part of the motherland were now outside
of the fringes or the boundaries of Russian territory.
First off, fact check.
Greatest catastrophe of the 20th century?
Like, do you remember what else happened
in the 20th century, Vladimir?
(ominous music)

Putin's worry about the collapse of this one people
starts to get way worse when the West, his enemy,
starts showing up to his neighborhood
to all these exSoviet countries that are now independent.
The West starts selling their ideology
of democracy and capitalism and inviting them
to join their military alliance called NATO.
And guess what?
These countries are totally buying it.
All these exSoviet countries are now joining NATO.
And some of them, the EU.
And Putin is hating this.
He's like not only did the Soviet Union divide
and all of these people are now outside
of the Russia motherland,
but now they're being persuaded by the West
to join their military alliance.
This is terrible news.
Over the years, this continues to happen,
while Putin himself starts to chip away
at Russian institutions, making them weaker and weaker.
He's silencing his rivals
and he's consolidating power in himself.
(triumphant music)

And in the past few years,
he's effectively silenced anyone who can challenge him;
any institution, any court,
or any political rival have all been silenced.
It's been decades since the Soviet Union fell,
but as Putin gains more power,
he still sees the region through the lens
of the old Cold War, Soviet, Slavic empire view.
He sees this region as one big block
that has been torn apart by outside forces.
"The greatest catastrophe of the 20th century."
And the worst situation of all of these,
according to Putin, is Ukraine,
which was like the gem of the Soviet Union.
There was tons of cultural heritage.
Again, Russia sort of started in Ukraine,
not to mention it was a very populous
and industrious, resourcerich place.
And over the years Ukraine has been drifting west.
It hasn't joined NATO yet, but more and more,
it's been electing proWestern presidents.
It's been flirting with membership in NATO.
It's becoming less and less attached
to the Russian heritage that Putin so adores.
And more than half of Ukrainians say
that they'd be down to join the EU.
64% of them say that it would be cool joining NATO.
But Putin can't handle this. He is in total denial.
Like an exboyfriend who handle his exgirlfriend
starting to date someone else,
Putin can't let Ukraine go.
He won't let go.

So for the past decade,
he's been trying to keep the West out
and bring Ukraine back into the motherland of Russia.
This usually takes the form of Putin sending
secret soldiers from Russia into Ukraine
to help the people in Ukraine who want to like separate
from Ukraine and join Russia.
It also takes the form of, oh yeah,
stealing entire parts of Ukraine for Russia.
Russian troops moving swiftly to take control
of military bases in Crimea.
Like in 2014, Putin just did this.
To what America is officially calling
a Russian invasion of Ukraine.
He went down and just snatched this bit of Ukraine
and folded it into Russia.
So you're starting to see what's going on here.
Putin's life's work is to salvage what he calls
the greatest catastrophe of the 20th century,
the division and the separation
of the Soviet republics from Russia.
So let's get to present day. It's 2022.
Putin is at it again.
And honestly, if you really want to understand
the mind of Vladimir Putin and his whole view on this,
you have to read this.
"On the History of Unity of Russians and Ukrainians,"
by Vladimir Putin.
A blog post that kind of sounds
like a ninth grade history essay.
In this essay, Vladimir Putin argues
that Russia and Ukraine are one people.
He calls them essentially the same historical
and spiritual space.

Kind of beautiful writing, honestly.
Anyway, he argues that the division
between the two countries is due to quote,
"a deliberate effort by those forces
that have always sought to undermine our unity."
And that the formula they use, these outside forces,
is a classic one: divide and rule.
And then he launches into this super indepth,
like 10page argument, as to every single historical beat
of Ukraine and Russia's history
to make this argument that like,
this is one people and the division is totally because
of outside powers, i.e. the West.
Okay, but listen, there's this moment
at the end of the post,
that actually kind of hit me in a big way.
He says this, "Just have a look at Austria and Germany,
or the U.S. and Canada, how they live next to each other.
Close in ethnic composition, culture,
and in fact, sharing one language,
they remain sovereign states with their own interests,
with their own foreign policy.
But this does not prevent them
from the closest integration or allied relations.
They have very conditional, transparent borders.
And when crossing them citizens feel at home.
They create families, study, work, do business.
Incidentally, so do millions of those born in Ukraine
who now live in Russia.
We see them as our own close people."
I mean, listen, like,
I'm not in support of what Putin is doing,
but like that, it's like a pretty solid like analogy.
If China suddenly showed up and started like
coaxing Canada into being a part of its alliance,
I would be a little bit like, "What's going on here?"
That's what Putin feels.
And so I kind of get what he means there.
There's a deep heritage and connection between these people.
And he's seen that falter and dissolve
and he doesn't like it.
He clearly genuinely feels a brotherhood
and this deep heritage connection
with the people of Ukraine.
Okay, okay, okay, okay. Putin, I get it.
Your essay is compelling there at the end.
You're clearly very smart and wellread.
But this does not justify what you've been up to. Okay?
It doesn't justify sending 100,000 troops to the border
or sending cyber soldiers to sabotage
the Ukrainian government, or annexing territory,
fueling a conflict that has killed
tens of thousands of people in Eastern Ukraine.
No. Okay.

No matter how much affection you feel for Ukrainian heritage
and its connection to Russia, this is not okay.
Again, it's like the boyfriend
who genuinely loves his girlfriend.
They had a great relationship,
but they broke up and she's free to see whomever she wants.
But Putin is not ready to let go.
[Man In Blue Shirt] What the hell's wrong with you?
I love you, Jessica.
What the hell is wrong with you?
Dude, don't fucking touch me.
I love you. Worldstar!
What is wrong with you? Just stop!
Putin has constructed his own reality here.
One in which Ukraine is actually being controlled
by shadowy Western forces
who are holding the people of Ukraine hostage.
And if that he invades, it will be a swift victory
because Ukrainians will accept him with open arms.
The great liberator.
(triumphant music)

Like, this guy's a total romantic.
He's a history buff and a romantic.
And he has a hill to die on here.
And it is liberating the people
who have been taken from the Russian motherland.
Kind of like the abusive boyfriend, who's like,
"She actually really loves me,
but it's her annoying friends
who were planting all these ideas in her head.
That's why she broke up with me."
And it's like, "No, dude, she's over you."
[Man In Blue Shirt] What the hell is wrong with you?
I love you, Jessica.
I mean, maybe this video should be called
Putin is just like your abusive exboyfriend.
[Man In Blue Shirt] What the hell is wrong with you?
I love you, Jessica!
Worldstar! What's wrong with you?
Okay. So where does this leave us?
It's 2022, Putin is showing up to these meetings in Europe
to tell them where he stands.
He says, "NATO, you cannot expand anymore. No new members.
And you need to withdraw all your troops
from Eastern Europe, my neighborhood."
He knows these demands will never be accepted
because they're ludicrous.
But what he's doing is showing a false effort to say,
"Well, we tried to negotiate with the West,
but they didn't want to."
Hence giving a little bit more justification
to a Russian invasion.
So will Russia invade? Is there war coming?
Maybe; it's impossible to know
because it's all inside of the head of this guy.
But, if I were to make the best argument
that war is not coming tomorrow,
I would look at a few things.
Number one, war in Ukraine would be incredibly costly
for Vladimir Putin.
Russia has a far superior army to Ukraine's,
but still, Ukraine has a very good army
that is supported by the West
and would give Putin a pretty bad bloody nose
in any invasion.

Controlling territory in Ukraine would be very hard.
Ukraine is a giant country.
They would fight back and it would be very hard
to actually conquer and take over territory.
Another major point here is that if Russia invades Ukraine,
this gives NATO new purpose.
If you remember, NATO was created because of the Cold War,
because the Soviet Union was big and nuclear powered.
Once the Soviet Union fell,
NATO sort of has been looking for a new purpose
over the past couple of decades.
If Russia invades Ukraine,
NATO suddenly has a brand new purpose to unite
and to invest in becoming more powerful than ever.
Putin knows that.
And it would be very bad news for him if that happened.
But most importantly, perhaps the easiest clue
for me to believe that war isn't coming tomorrow
is the Russian propaganda machine
is not preparing the Russian people for an invasion.
In 2014, when Russia was about to invade
and take over Crimea, this part of Ukraine,
there was a barrage of state propaganda
that prepared the Russian people
that this was a justified attack.
So when it happened, it wasn't a surprise
and it felt very normal.

That isn't happening right now in Russia.
At least for now. It may start happening tomorrow.
But for now, I think Putin is showing up to the border,
flexing his muscles and showing the West that he is earnest.
I'm not sure that he's going to invade tomorrow,
but he very well could.
I mean, read the guy's blog post
and you'll realize that he is a romantic about this.
He is incredibly idealistic about the glory days
of the Slavic empires, and he wants to get it back.
So there is dangerous momentum towards war.
And the way war works is even a small little, like, fight,
can turn into the other guy
doing something bigger and crazier.
And then the other person has to respond
with something a little bit bigger.
That's called escalation.
And there's not really a ceiling
to how much that momentum can spin out of control.
That is why it's so scary when two nuclear countries
go to war with each other,
because there's kind of no ceiling.
So yeah, it's dangerous. This is scary.
I'm not sure what happens next here,
but the best we can do is keep an eye on this.
At least for now, we better understand
what Putin really wants out of all of this.

Thanks for watching.

Many believe Putin is simply sabre rattling and intimidating us. They see no threat of nuclear war. We can send NATO troops into Ukraine without risking a nuclear war.

I keep reading that Putin is just using nuclear blackmail and that a strong leader will call the bluff. That, in my opinion, misunderstands the danger of sending NATO into Ukraine.
It assumes that once NATO moves in, Putin can either push the red nuclear button or not.
Sure, Putin won't go nuclear if NATO invades Ukraine. So we're safe? Can't we just move NATO?

No, because history has taught us that wars often escalate far beyond our initial expectations. One domino falls, knocking down another. That's why having clear boundaries is vital. Crossing a seemingly harmless line can set off a chain of events that are unstoppable once started.
One example is WWI. The assassin of Archduke Franz Ferdinand could not have known that his actions would kill millions. They couldn't have known that invading Serbia to punish them for not handing over the accomplices would start a world war. Every action triggered a counter-action, plunging Europe into a brutal and bloody war. Each leader saw their actions as limited, not realizing how they kept the dominos falling.

Nobody can predict the future, but it's easy to imagine how NATO intervention could trigger a chain of events leading to a total war. Let me suggest some outcomes.
NATO creates a no-fly-zone. In retaliation, Russia bombs NATO airfields. Russia may see this as a limited counter-move that shouldn't cause further NATO escalation. They think it's a reasonable response to force NATO out of Ukraine. Nobody has yet thought to use the nuke.
Will NATO act? Polish airfields bombed, will they be stuck? Is this an article 5 event? If so, what should be done?

It could happen. Maybe NATO sends troops into Ukraine to punish Russia. Maybe NATO will bomb Russian airfields.

Putin's response Is bombing Russian airfields an invasion or an attack? Remember that Russia has always used nuclear weapons for defense, not offense. But let's not panic, let's assume Russia doesn't go nuclear.

Maybe Russia retaliates by attacking NATO military bases with planes. Maybe they use ships to attack military targets. How does NATO respond? Will they fight Russia in Ukraine or escalate? Will they invade Russia or attack more military installations there?
Seen the pattern? As each nation responds, smaller limited military operations can grow in scope.

So far, the Russian military has shown that they begin with less brutal methods. As losses and failures increase, brutal means are used. Syria had the same. Assad used chemical weapons and attacked hospitals, schools, residential areas, etc.
A NATO invasion of Ukraine would cost Russia dearly. “Oh, this isn't looking so good, better pull out and finish this war,” do you think? No way. Desperate, they will resort to more brutal tactics. If desperate, Russia has a huge arsenal of ugly weapons. They have nerve agents, chemical weapons, and other nasty stuff.

What happens if Russia uses chemical weapons? What if Russian nerve agents kill NATO soldiers horribly? West calls for retaliation will grow. Will we invade Russia? Will we bomb them?

We are angry and determined to punish war criminal Putin, so NATO tanks may be heading to Moscow. We want vengeance for his chemical attacks and bombing of our cities.
Do you think the distance between that red nuclear button and Putin's finger will be that far once NATO tanks are on their way to Moscow?

We might avoid a nuclear apocalypse. A NATO invasion force or even Western cities may be used by Putin. Not as destructive as ICBMs. Putin may think we won't respond to tactical nukes with a full nuclear counterattack. Why would we risk a nuclear Holocaust by launching ICBMs on Russia?

Maybe. My point is that at every stage of the escalation, one party may underestimate the other's response. This war is spiraling out of control and the chances of a nuclear exchange are increasing. Nobody really wants it.

Fear, anger, and resentment cause it. If Putin and his inner circle decide their time is up, they may no longer care about the rest of the world. We saw it with Hitler. Hitler, seeing the end of his empire, ordered the destruction of Germany. Nobody should win if he couldn't. He wanted to destroy everything, including Paris.

In other words, the danger isn't what happens after NATO intervenes The danger is the potential chain reaction. Gambling has a psychological equivalent. It's best to exit when you've lost less. We humans are willing to take small risks for big rewards. To avoid losses, we are willing to take high risks. Daniel Kahneman describes this behavior in his book Thinking, Fast and Slow.

And so bettors who have lost a lot begin taking bigger risks to make up for it. We get a snowball effect. NATO involvement in the Ukraine conflict is akin to entering a casino and placing a bet. We'll start taking bigger risks as we start losing to Russian retaliation. That's the game's psychology.

It's impossible to stop. So will politicians and citizens from both Russia and the West, until we risk the end of human civilization.

You can avoid spiraling into ever larger bets in the Casino by drawing a hard line and declaring “I will not enter that Casino.” We're doing it now. We supply Ukraine. We send money and intelligence but don't cross that crucial line.

It's difficult to watch what happened in Bucha without demanding NATO involvement. What should we do? Of course, I'm not in charge. I'm a writer. My hope is that people will think about the consequences of the actions we demand. My hope is that you think ahead not just one step but multiple dominos.

More and more, we are driven by our emotions. We cannot act solely on emotion in matters of life and death. If we make the wrong choice, more people will die.

Read the original post here.

Tools for managing your PhD projects, reading lists, notes, and inspiration.

As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.

The article has three parts:

1. What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
2. Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
3. Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.

This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.

1. Philosophy: Taking and organizing notes

Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/

Notes

We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:

• Deep Learning
• Recurrent Neural Networks
  - Convolutional Neural Networks

Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:

The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:

- /Proteins/ 
     - Protein Folding
- /Deep Learning/
     - /Proteins/ 

Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).

You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.

My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.

My Knowledge Graph and the note “Backrpropagation” and its links.

Backpropagation note and all its links

Why use Folders?

Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:

My Zettelkasten's 5 folders

They usually gather data from various sources:

MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.

Keeping images separate from other files can help keep your main folders clean.

I will elaborate on these in the Workflow Section.

My general recommendation is to use tags and links instead of folders.

Maps of Content (MOC) 

Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:

An example of a Machine Learning MOC generated with Dataview.

As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.

2. Tools: Knowing Obsidian

Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/

Obsidian interface. 

Obsidian is highly customizable, so here is my preferred interface:

The theme is customized from https://github.com/colineckert/obsidian-things

Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).

My interface is organized as follows:

How my Obsidian Interface is organized.

Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.

Tags:
I use nested tags and look into each one to find specific notes to link.

cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)

Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.

Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.

Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.

Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.

Plugins

An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.

Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)

Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.

Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.

Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.

3. Workflows: Cool stuff

Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary

3.1 Using Templates to Structure Notes

Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:

An example of a note using a template.

### [[YOUR MOC]]
# Note Title of your note
**Tags**:: 
**Links**::

The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:

### [[Books MOC]]
# Title
**Author**:: 
**Date::
**Tags:: 
**Links::

A book template example.

Using a simple query, I can hook Dataview to it.

dataview  
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”  
from “4. Books”  
SORT grade DESCENDING

using Dataview to query templates.

3.2 Free Note Syncing (Laptop, Phone, Tablet)

No plugins used.

One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).

Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).

For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).

3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers

My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.

My Zotero library is tagged as follows:

My reference manager's tags

For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:

An example of my citations template.

Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.

Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144

You can then convert your notes to digital. I found that transcribing helped me retain information better.

3.4 Projects and Lab Books

Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.

Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:

• One folder for all my projects
• One file for each project
  I use a template to create each project

### [[Projects MOC]]  
# <% tp.file.title %>  
**Tags**::  
**Links**::  
**URL**::  
**Project Description**::## Notes:  
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>  
#### Done:  
#### TODO:  
#### Notes

You can insert a template into a new note with CMD + P and looking for the Templater option.

I then keep adding new days with another template:

### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>  
#### Done:  
#### TODO:  
#### Notes:

This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:

Example of project note with timestamped notes.

3.5 Private Encrypted Diary

This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:

1. It had to be private, and nobody had to be able to read the entries.
2. Cloud syncing was required for editing on multiple devices.

Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:

Conclusion

So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)

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